US20150218640A1 - Biomarker signature method, and apparatus and kits therefor - Google Patents

Biomarker signature method, and apparatus and kits therefor Download PDF

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Publication number
US20150218640A1
US20150218640A1 US14/616,565 US201514616565A US2015218640A1 US 20150218640 A1 US20150218640 A1 US 20150218640A1 US 201514616565 A US201514616565 A US 201514616565A US 2015218640 A1 US2015218640 A1 US 2015218640A1
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biomarker
indicator
immune system
determining
irs
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Richard Bruce Brandon
Leo Charles MCHUGH
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Immunexpress Pty Ltd
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Immunexpress Pty Ltd
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Priority claimed from AU2014900363A external-priority patent/AU2014900363A0/en
Application filed by Immunexpress Pty Ltd filed Critical Immunexpress Pty Ltd
Priority to US14/714,188 priority Critical patent/US10865447B2/en
Publication of US20150218640A1 publication Critical patent/US20150218640A1/en
Assigned to IMMUNEXPRESS PTY LTD reassignment IMMUNEXPRESS PTY LTD ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: BRANDON, RICHARD BRUCE, MCHUGH, LEO CHARLES
Priority to US17/678,658 priority patent/US20220325348A1/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • G06F19/22—
    • G06F19/345—
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Definitions

  • the present invention relates to method, kit and apparatus and to reagents and compositions associated therewith for deriving an indicator for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject, to a biomarker signature for use in diagnosing the presence, absence or degree of at least one condition in a biological subject or in prognosing at least one condition in a biological subject, and to a method, kit and apparatus, as well as reagents and compositions associated therewith, for identifying biomarkers for use in a biomarker signature.
  • WO2004/044236 describes a method of determining the status of a subject. In particular, this is achieved by obtaining subject data including respective values for each of a number of parameters, the parameter values being indicative of the current biological status of the subject. The subject data are compared to predetermined data that includes values for at least some of the parameters and an indication of the condition. The status of the subject, and in particular, the presence and/or absence of the one or more conditions, can then be determined in accordance with the results of the comparison.
  • US2010/0028876 describes methods for diagnosing biological states or conditions based on ratios of gene expression data from cell or tissue samples, such as cancer cell or tissue samples, by differentiating between cell types, including cancer cell types.
  • the invention provides sets of genes that are expressed differentially in normal and cancer lung cells and tissues to be able to differentiate these cells and tissues. Such cellular differentiation is important in diagnosing cancer and cancer types.
  • the sets of genes are identified by the degree (fold change) of up or down regulation. These sets of genes can be used to discriminate between normal and malignant cells or tissues, and between classes of malignant cells or tissues. Accordingly, diagnostic assays for classification of tumors, prediction of tumor outcome, selecting and monitoring treatment regimens and monitoring tumor progression/regression also are provided.
  • the present invention seeks to provide a method for determining an indicator used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition, the method including:
  • the method includes:
  • the method includes combining the derived biomarker values using a combining function, the combining function being at least one of:
  • the method is performed at least in part using an electronic processing device.
  • the method includes, in at least one electronic processing device:
  • the method includes, in at least one processing device, generating a representation of the indicator.
  • the representation includes:
  • the method includes:
  • the indicator reference is based on at least one of:
  • the indicator reference is derived from indicators determined for a number of individuals in a reference population.
  • the indicator reference is based on a distribution of indicators determined for a group of a reference population, the group consisting of individuals diagnosed as having the medical condition or lacking the medical condition.
  • the reference population includes:
  • the indicator is for use in determining the likelihood that a biological subject has at least one medical condition, and wherein the reference population includes:
  • the indicator reference is retrieved from a database.
  • the likelihood is based on a probability generated using the results of the comparison.
  • the indicator is for determining a likelihood of the subject having a first or second condition, and wherein the method includes:
  • the method includes:
  • the first and second indicator references are distributions of indicators determined for first and second groups of a reference population, the first and second group consisting of individuals diagnosed with the first or second condition respectively.
  • the method includes:
  • the method includes, determining the indicator at least in part using a ratio of concentrations of the polynucleotide expression products.
  • the method includes:
  • the amplification amount is at least one of:
  • the method includes determining:
  • the immune system biomarker is a biomarker of an immune system of the biological subject that is altered, or whose level of expression is altered, as part of an inflammatory response to damage or pathogenic insult.
  • the mutual correlation range is at least one of:
  • each immune system biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • condition correlation range is at least one of:
  • the performance threshold is indicative of an explained variance of at least one of:
  • the immune system biomarker value is indicative of a level or abundance of a molecule selected from one or more of a nucleic acid molecule and a proteinaceous molecule.
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein the method includes:
  • the indicator is for determining a likelihood of the subject having inSIRS or a healthy condition, and wherein biomarker values are determined from at least one inflammatory response syndrome (IRS) immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • IRS inflammatory response syndrome
  • the indicator is for determining a likelihood of the subject having ipSIRS or a healthy condition, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first, second, third and fourth IRS immune system biomarker groups, wherein:
  • the first IRS immune system biomarker is a PLA2G7 expression product
  • the second IRS immune system biomarker is a PLAC8 expression product
  • the third IRS immune system biomarker is a CEACAM4 expression product
  • the fourth IRS immune system biomarker is a LAMP1 expression product.
  • the indicator is for determining a likelihood of the subject having mild sepsis or severe sepsis, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having mild sepsis or septic shock, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having severe sepsis or septic shock, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the present invention seeks to provide apparatus for determining an indicator used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition, the apparatus including at least one electronic processing device that:
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a first pair and a second pair of reverse transcribed mRNAs, wherein the first pair comprises a PLAC8 reverse transcribed mRNA and a PLA2G7 reverse transcribed mRNA and wherein the second pair comprises a CEACAM4 reverse transcribed mRNA and a LAMP1 reverse transcribed mRNA.
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group A IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group B IRS immune system biomarker genes.
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group C IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group D IRS immune system biomarker genes.
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group E IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group F IRS immune system biomarker genes.
  • the present invention seeks to provide a composition comprising at least two pairs of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least two pairs of reverse transcribed mRNAs comprising a first pair and a second pair of reverse transcribed mRNAs, wherein the first pair comprises a reverse transcribed mRNA from a first IRS immune system biomarker gene and a reverse transcribed mRNA from a second IRS immune system biomarker gene, and wherein the second pair comprises a reverse transcribed mRNA from a third IRS immune system biomarker gene and a reverse transcribed mRNA from a fourth IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group G IRS immune system biomarker genes, wherein the second IRS immune system biomarker gene is selected from group H IRS immune system biomarker genes, wherein the third IRS immune system biomarker gene is
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group K IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group L IRS immune system biomarker genes.
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group M IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group N IRS immune system biomarker genes.
  • the present invention seeks to provide a composition
  • a composition comprising at least one pair of reverse transcribed mRNAs and at least one oligonucleotide primer or probe that hybridizes to an individual one of the reverse transcribed mRNAs, the at least one pair of reverse transcribed mRNAs comprising a reverse transcribed mRNA from a first IRS immune system biomarker gene selected from group O IRS immune system biomarker genes and a reverse transcribed mRNA from a second IRS immune system biomarker gene selected from group P IRS immune system biomarker genes.
  • the at least one oligonucleotide primer or probe can be hybridized to an individual one of the reverse transcribed mRNAs.
  • the reverse transcribed mRNAs can be derived from components of the immune system.
  • the reverse transcribed mRNAs can be derived from leukocytes.
  • the reverse transcribed mRNAs can be derived from blood cells.
  • the reverse transcribed mRNAs can be derived from peripheral blood cells.
  • composition can further comprise a labeled reagent for detecting the reverse transcribed mRNAs.
  • the labeled reagent can be a labeled said at least one oligonucleotide primer or probe.
  • the labeled reagent can be a labeled said reverse transcribed mRNA.
  • the labeled reagent can be a labeled oligonucleotide linker or tag for labeling a said reverse transcribed mRNA.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of inSIRS and ipSIRS, the kit comprising at least one pair of reagents comprising a first pair of reagents and a second pair of reagents, wherein the first pair of reagents comprises (i) a reagent that allows quantification of a polynucleotide expression product of the PLA2G7 gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of the PLAC8 gene, wherein the second pair of reagents comprises: (iii) a reagent that allows quantification of a polynucleotide expression product of the CEACAM4 gene; and (iv) a reagent that allows quantification of a polynucleotide expression product of the LAMP1 gene.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of inSIRS and a healthy condition, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group A IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group B IRS immune system biomarker genes.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of ipSIRS and a healthy condition, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group C IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group D IRS immune system biomarker genes.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of inSIRS and ipSIRS, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group E IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group F IRS immune system biomarker genes.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of inSIRS and ipSIRS, the kit comprising at least two pairs of reagents comprising a first pair of reagents and a second pair of reagents, wherein the first pair of reagents comprises (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, and wherein the second pair of reagents comprises (i) a reagent that allows quantification of a polynucleotide expression product of a third IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a fourth IRS immune system biomark
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of mild sepsis and severe sepsis, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group K IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group L IRS immune system biomarker genes.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of mild sepsis and septic shock, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group M IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group N IRS immune system biomarker genes.
  • the present invention seeks to provide a kit for determining an indicator indicative of the likelihood of the presence or absence of at least one condition selected from the group consisting of severe sepsis and septic shock, the kit comprising at least one pair of reagents comprising (i) a reagent that allows quantification of a polynucleotide expression product of a first IRS immune system biomarker gene; and (ii) a reagent that allows quantification of a polynucleotide expression product of a second IRS immune system biomarker gene, wherein the first IRS immune system biomarker gene is selected from group O IRS immune system biomarker genes and wherein the second IRS immune system biomarker gene is selected from group P IRS immune system biomarker genes.
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of inSIRS and ipSIRS, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value
  • the indicator-determining method comprises: determining the first pair and second pair of biomarker values and determining a first derived biomarker value calculated using the first pair of biomarker values and a second derived biomarker value calculated using the second pair of biomarker values; and determining the indicator based on a combination of the first and second derived biomarker values.
  • the present invention seeks to provide a method for inhibiting the development or progression of inSIRS in a subject, the method comprising: exposing the subject to a treatment regimen for treating inSIRS based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of inSIRS in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value, wherein the at least one pair of biomarker values comprises first and second biomarker values corresponding
  • the present invention seeks to provide a method for inhibiting the development or progression of ipSIRS in a subject, the method comprising: exposing the subject to a treatment regimen for treating ipSIRS based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of ipSIRS in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value, wherein the at least one pair of biomarker values comprises
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of inSIRS and ipSIRS, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of inSIRS and ipSIRS, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least two pairs of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least two derived biomarker values using the at least two pairs of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of each pair of immune system biomarkers; and (c) determining the indicator based on the at least two derived biomarker values, wherein
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of mild sepsis and severe sepsis, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of mild sepsis and septic shock, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value,
  • the present invention seeks to provide a method for inhibiting the development or progression in a subject of at least one condition selected from the group consisting of severe sepsis and septic shock, the method comprising: exposing the subject to a treatment regimen for treating the at least one condition based on an indicator obtained from an indicator-determining method, wherein the indicator is indicative of the presence of the at least one condition in the subject, the indicator-determining method comprising: (a) determining at least one pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject, (b) determining at least one derived biomarker value using the at least one pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the at least one pair of immune system biomarkers; and (c) determining the indicator based on the at least one derived biomarker value,
  • the method comprises taking the sample from the subject and obtaining the indicator according to the indicator-determining method.
  • the method comprises: sending the sample taken from the subject to a laboratory at which the indicator is determined.
  • the sample comprises cells obtained from the subject or a nucleic acid sample thereof.
  • the present invention seeks to provide a method for differentiating between inSIRS and ipSIRS in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between inSIRS and a healthy condition in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between ipSIRS and a healthy condition in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between inSIRS and ipSIRS in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between inSIRS and ipSIRS in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between mild sepsis and severe sepsis in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between mild sepsis and septic shock in a biological subject, the method including:
  • the present invention seeks to provide a method for differentiating between severe sepsis and septic shock in a biological subject, the method including:
  • the method includes determining:
  • the first and second indicator references are distributions of indicators determined for first and second groups of a reference population, the first and second group consisting of individuals diagnosed with inSIRS and ipSIRS respectively.
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing the likelihood of a biological subject having at least one medical condition, the method including:
  • the method includes determining:
  • the method includes determining:
  • the amplification amount is at least one of:
  • the present invention seeks to provide a method for use in assessing the likelihood of a biological subject having a medical condition, the method including, in one or more processing devices:
  • the method includes determining:
  • the present invention seeks to provide apparatus for determining an indicator used in determining the likelihood of a biological subject having at least one medical condition, the apparatus including:
  • the present invention seeks to provide a method for differentiating between inSIRS and ipSIRS in a biological subject, the method including:
  • the present invention seeks to provide a method for determining an indicator used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition, the method including:
  • the method includes:
  • the function includes at least one of:
  • the method includes determining at least one derived biomarker value corresponding to a ratio of two measured biomarker values.
  • the method includes combining at least two biomarker values to determine an indicator value representing the indicator.
  • the method includes combining at least two biomarker values using a combining function, the combining function being at least one of:
  • At least one of the at least two biomarkers is a derived biomarker.
  • the method includes:
  • the method is performed at least in part using an electronic processing device.
  • the method includes, in the electronic processing device:
  • the mutual correlation range is at least one of:
  • each biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • condition correlation range is at least one of:
  • the performance threshold is indicative of an explained variance of at least one of:
  • the biomarker value is indicative of a level or abundance of a molecule selected from one or more of a nucleic acid molecule and a proteinaceous molecule.
  • the method includes generating a representation of the indicator.
  • the representation includes:
  • the method includes:
  • the indicator reference is based on at least one of:
  • the indicator reference is derived from indicators determined for a number of individuals in a reference population.
  • the indicator reference is based on a distribution of indicators determined for a group of a reference population, the group consisting of individuals diagnosed with the medical condition.
  • the reference population includes:
  • the indicator is for use in determining the likelihood that a biological subject has at least one medical condition, and wherein the reference population includes:
  • the indicator reference is retrieved from a database.
  • the likelihood is based on a probability generated using the results of the comparison.
  • the indicator is for determining a likelihood of the subject having a first or second condition, and wherein the method includes:
  • the method includes:
  • the first and second indicator references are distributions of indicators determined for first and second groups of a reference population, the first and second group consisting of individuals diagnosed with the first or second condition respectively.
  • the method includes:
  • the method includes, determining the indicator at least in part using a ratio of concentrations of the polynucleotide expression products.
  • the method includes:
  • the amplification amount is at least one of:
  • the method includes determining:
  • the immune system biomarker is an IRS biomarker of an immune system of the biological subject that is altered, or whose level of expression is altered, as part of an inflammatory response to damage or pathogenic insult.
  • the indicator is for determining a likelihood of the subject having at least one of inSIRS and ipSIRS, and wherein the method includes:
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein the method includes:
  • the indicator is for determining a likelihood of the subject having inSIRS or a healthy condition, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having ipSIRS or a healthy condition, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having inSIRS or ipSIRS, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first, second, third and fourth IRS immune system biomarker groups, wherein:
  • the first IRS immune system biomarker is a PLA2G7 expression product
  • the second IRS immune system biomarker is a PLAC8 expression product
  • the third IRS immune system biomarker is a CEACAM4 expression product
  • the fourth IRS immune system biomarker is a LAMP1 expression product.
  • the indicator is for determining a likelihood of the subject having mild sepsis or severe sepsis, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having mild sepsis or septic shock, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the indicator is for determining a likelihood of the subject having severe sepsis or septic shock, and wherein biomarker values are determined from at least one IRS immune system biomarker in each of first and second IRS immune system biomarker groups, wherein:
  • the present invention seeks to provide apparatus for determining an indicator used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition, the apparatus including a processing device that:
  • the present invention seeks to provide a method for determining an indicator for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, the method including:
  • the method includes:
  • the function includes at least one of:
  • the method includes determining at least one derived biomarker value corresponding to a ratio of two measured biomarker values.
  • the method includes combining at least two biomarker values to determine an indicator value representing the indicator.
  • the method includes combining at least two biomarker values using a combining function, the combining function being at least one of:
  • At least one of the at least two biomarkers is a derived biomarker.
  • the method includes:
  • the method includes:
  • the method is performed at least in part using an electronic processing device.
  • the method includes, in the electronic processing device:
  • the method includes generating a representation in accordance with the at least one indicator value.
  • the method includes:
  • the mutual correlation range is at least one of:
  • each biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • condition correlation range is at least one of:
  • the performance threshold is indicative of an explained variance of at least one of:
  • the biomarker value is indicative of a level or abundance of a molecule or entity selected from one or more of:
  • the present invention seeks to provide apparatus for determining an indicator for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, the apparatus including an electronic processing device that:
  • the present invention seeks to provide a diagnostic signature for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, the diagnostic signature defining a combination of at least two biomarker values corresponding to values of biomarkers that can be measured for or derived from the biological subject, wherein:
  • the diagnostic signature defines a function to be applied to at least one measured biomarker value to determine at least one derived biomarker value, the at least one derived biomarker value being indicative of a value of a corresponding derived biomarker.
  • the function includes at least one of:
  • the at least one derived biomarker value corresponds to a ratio of two measured biomarker values.
  • the diagnostic signature defines a combination of at least two biomarker values for determining an indicator value representing the indicator.
  • the diagnostic signature defines a combining function for combining at least two biomarker values, the combining function being at least one of:
  • At least one of the at least two biomarkers is a derived biomarker.
  • diagnostic signature defines:
  • the diagnostic signature defines at least one indicator value range and wherein comparison of at least one indicator value to the at least one indicator value range is used in diagnosing the presence, absence, degree or prognosis of at least one condition.
  • the mutual correlation range is at least one of:
  • each biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • condition correlation range is at least one of:
  • the performance threshold is indicative of an explained variance of at least one of:
  • the biomarker value is indicative of a level or abundance of a molecule or entity selected from one or more of:
  • the present invention seeks to provide a method of identifying biomarkers for use in a diagnostic signature, the diagnostic signature being for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, the method including:
  • the method includes determining a combination of at least two candidate biomarkers using a combining function, the combining function being at least one of:
  • the method includes:
  • the method includes:
  • the method includes combining a number of candidate biomarkers up to a limit.
  • the method includes:
  • the method includes:
  • the method includes:
  • the method includes using reference values measured for reference biomarkers for the at least one individual to identify the candidate biomarkers.
  • the method includes using reference values to filter reference biomarkers to determine candidate biomarkers.
  • At least one of the candidate biomarkers is a derived biomarker derived from at least one of the reference biomarkers using a function.
  • the derived biomarkers are derived from filtered biomarkers.
  • the method includes:
  • the method includes:
  • the mutual correlation range is at least one of:
  • each biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • condition correlation range is at least one of:
  • the performance threshold is indicative of an explained variance of at least one of:
  • the present invention seeks to provide apparatus for identifying markers for use in a diagnostic signature, the diagnostic signature being for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, the apparatus including an electronic process device that:
  • the present invention seeks to provide a method for diagnosing the presence or absence of inSIRS or a healthy condition in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and a healthy condition, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the performance
  • the present invention seeks to provide a method for diagnosing the presence or absence of ipSIRS or a healthy condition in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from ipSIRS and a healthy condition, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one
  • the present invention seeks to provide a method for diagnosing the presence or absence of inSIRS or ipSIRS in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and ipSIRS, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one
  • the present invention seeks to provide a method for diagnosing the presence or absence of inSIRS or ipSIRS in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and ipSIRS, wherein: (i) at least four IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one
  • the first IRS biomarker is a PLA2G7 expression product
  • the second IRS biomarker is a PLAC8 expression product
  • the third IRS biomarker is a CEACAM4 expression product
  • the fourth IRS biomarker is a LAMP1 expression product.
  • the present invention seeks to provide a method for diagnosing the presence or absence of mild sepsis or severe sepsis in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from mild sepsis and severe sepsis, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one
  • the present invention seeks to provide a method for diagnosing the presence or absence of mild sepsis or septic shock in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from mild sepsis and septic shock, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the
  • the present invention seeks to provide a method for diagnosing the presence or absence of severe sepsis or septic shock in a biological subject, the method comprising: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from severe sepsis and septic shock, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the
  • the present invention seeks to provide a kit comprising: (i) a reagent that allows quantification of a first IRS biomarker; and (ii) a reagent that allows quantification of a second IRS biomarker, wherein the first and second IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a stage of ipSIRS selected from mild sepsis, severe sepsis and septic shock, which at least one condition lies within a mutual correlation range of between ⁇ 0.9, and wherein a combination of respective biomarker values for the first and second IRS biomarkers that are measured for or derived from a biological subject has a performance value greater than or equal to a performance threshold representing the ability of the combination of the first and second IRS biomarkers to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the performance threshold being a variance explained of at least 0.3
  • the kit further comprises: (iii) a reagent that allows quantification of a third IRS biomarker; and (iv) a reagent that allows quantification of a fourth IRS biomarker, wherein the third and fourth IRS biomarkers have a mutual correlation in respect of at the least one condition that lies within a mutual correlation range of between ⁇ 0.9, and wherein a combination of respective biomarker values for the third and fourth IRS biomarkers that are measured for or derived from a biological subject has a performance value greater than or equal to a performance threshold representing the ability of the combination of the third and fourth IRS biomarkers to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the performance threshold being a variance explained of at least 0.3.
  • the kit is for diagnosing the presence or absence of inSIRS or a healthy condition, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group A IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group B IRS biomarker genes.
  • the kit is for diagnosing the presence or absence of ipSIRS or a healthy condition, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group C IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group D IRS biomarker genes.
  • the kit is for diagnosing the presence or absence of inSIRS or ipSIRS, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group E IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group F IRS biomarker genes.
  • the kit is for diagnosing the presence or absence of inSIRS or ipSIRS, wherein the first IRS biomarker is selected from a first IRS biomarker group, wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the third IRS biomarker is selected from a third IRS biomarker group and wherein the fourth IRS biomarker is selected from a fourth IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group G IRS biomarker genes, wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group H IRS biomarker genes, wherein the third IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group I IRS biomarker genes and wherein the fourth IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group J IRS biomarker genes.
  • the first IRS biomarker is a PLA2G7 expression product
  • the second IRS biomarker is a PLAC8 expression product
  • the third IRS biomarker is a CEACAM4 expression product
  • the fourth IRS biomarker is a LAMP1 expression product.
  • the kit is for diagnosing the presence or absence of mild sepsis or severe sepsis, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group K IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group L IRS biomarker genes.
  • the kit is for diagnosing the presence or absence of mild sepsis or septic shock, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group M IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group N IRS biomarker genes.
  • the kit is for diagnosing the presence or absence of severe sepsis or septic shock, wherein the first IRS biomarker is selected from a first IRS biomarker group and wherein the second IRS biomarker is selected from a second IRS biomarker group, wherein the first IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group O IRS biomarker genes and wherein the second IRS biomarker group consists of polynucleotide and/or polypeptide expression products from group P IRS biomarker genes.
  • the present invention seeks to provide a method for treating, preventing or inhibiting the development of at least one condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis or septic shock) in a subject, the method comprising (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining an indicator using a combination of the plurality of IRS biomarker values, the indicator being at least partially indicative of the presence, absence or degree of the at least one condition, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree
  • the method further comprises: (1) determining a plurality of measured IRS biomarker values, each measured IRS biomarker value being a measured value of an IRS biomarker of the biological subject; and (2) applying a function to at least one of the measured IRS biomarker values to determine at least one derived IRS biomarker value, the at least one derived IRS biomarker value being indicative of a value of a corresponding derived IRS biomarker.
  • the function includes at least one of: (a) multiplying two IRS biomarker values; (b) dividing two IRS biomarker values; (c) adding two IRS biomarker values; (d) subtracting two IRS biomarker values; (e) a weighted sum of at least two IRS biomarker values; (f) a log sum of at least two IRS biomarker values; and (g) a sigmoidal function of at least two IRS biomarker values.
  • the present invention seeks to provide a method of monitoring the efficacy of a particular treatment regimen in a subject towards a desired health state, the method comprising: a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject after treatment with a treatment regimen; (b) determining an indicator using a combination of the plurality of IRS biomarker values, the indicator being at least partially indicative of the presence, absence or degree of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or
  • the present invention seeks to provide a method of correlating a biomarker signature with an effective treatment regimen for a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), the method comprising: (a) determining a biomarker signature defining a combination of at least two IRS biomarker values corresponding to values of at least two IRS biomarkers that can be measured for or derived from a biological subject having the condition and for whom an effective treatment has been identified, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of the condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence, absence or degree of the condition, or to provide a prognosis
  • the present invention seeks to provide a method of determining whether a treatment regimen is effective for treating a subject with a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), the method comprising: (a) determining a plurality of post-treatment IRS biomarker values, each post-treatment IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject after treatment with the treatment regimen; (b) determining a post-treatment indicator using a combination of the plurality of post-treatment IRS biomarker values, the post-treatment indicator being at least partially indicative of the presence, absence or degree of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, wherein: (i) at the least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies
  • the present invention seeks to provide a method of correlating a biomarker signature with a positive or negative response or a side effect to a treatment regimen, the method comprising: (a) determining a biomarker signature defining a combination of at least two IRS biomarker values corresponding to values of at least two IRS biomarkers that can be measured for or derived from a biological subject following commencement of the treatment regimen, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), which lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence, absence or degree of the
  • the present invention seeks to provide a method of determining a positive or negative response to a treatment regimen and/or a side effect of a treatment regimen by a subject with a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), the method: (a) correlating a reference biomarker signature with a positive or negative response or a side effect to the treatment regimen, wherein the biomarker signature defines a combination of at least two IRS biomarker values corresponding to values of at least two IRS biomarkers that are measured for or derived from a control biological subject or control group, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock
  • the present invention seeks to provide a method of determining a positive or negative response to a treatment regimen and/or a side effect to a treatment regimen by a biological subject, the method comprising: (a) determining a sample biomarker signature defining a combination of at least two IRS biomarker values corresponding to values of at least two IRS biomarkers that are measured for or derived from a biological subject following commencement of the treatment regimen, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), which lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence,
  • FIG. 1A is a flowchart of an example of a method for deriving an indicator for use in diagnosing the presence, absence or degree of at least one condition or in providing a prognosis of at least one condition in a biological subject;
  • FIG. 1B is a flowchart of an example of a method for identifying biomarkers for use in a biomarker signature
  • FIG. 2 is a schematic diagram of an example of a distributed computer architecture
  • FIG. 3 is a schematic diagram of an example of a processing system of FIG. 2 ;
  • FIG. 4 is a schematic diagram of an example of a computer system of FIG. 2 ;
  • FIG. 5 is a flowchart of a specific example of a method for identifying biomarkers for use in a biomarker signature
  • FIG. 6A is a flowchart of a first example of a method for selecting candidate biomarkers
  • FIG. 6B is a flowchart of a second example of a method for selecting candidate biomarkers
  • FIG. 7 is a flowchart of a second example of a method for use in diagnosing the presence, absence or degree of at least one condition or in providing a prognosis of at least one condition in a biological subject;
  • FIG. 8A is a plot of 941 mRNA biomarkers against the AUC for differentiating between healthy condition and post-surgical inflammation (PS) (also referred to herein as “infection-negative SIRS” (inSIRS)), for individual biomarkers having an AUC greater than 0.7;
  • PS healthy condition and post-surgical inflammation
  • inSIRS infection-negative SIRS
  • FIG. 8B is a box and whisker plot showing the best mRNA biomarker for separating healthy condition and PS;
  • FIG. 8C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating healthy condition and PS with all derived biomarkers having an AUC of 1.0;
  • FIG. 8D is a box and whisker plot of the best performing derived biomarker, based on AUC, for separating healthy condition and PS;
  • FIGS. 8E and 8F are two plots showing the correlation to each other of the biomarkers in each group.
  • FIGS. 8G and 8H are two plots demonstrating the AUC of the biomarkers in each group (groups 1 and 2);
  • FIG. 8I is a box and whisker plot showing that when biomarkers are derived from group 1 and group 2 that a greater overall AUC is obtained;
  • FIG. 9A is a plot of the 941 mRNA biomarkers against the AUC for differentiating between healthy condition and sepsis (also referred to herein as “infection-positive SIRS” (ipSIRS)) with all individual biomarkers having an AUC greater than 0.7;
  • ipSIRS infection-positive SIRS
  • FIG. 9B is a box and whisker plot showing the best mRNA biomarker for separating healthy condition and sepsis
  • FIG. 9C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating healthy condition and sepsis with all derived biomarkers having an AUC of 1.0;
  • FIG. 9D is a box and whisker plot of the best performing derived biomarker, based on AUC, for separating healthy condition and sepsis;
  • FIGS. 9E and 9F show the correlation to each other of the biomarkers groups correlated to each group
  • FIGS. 9G and 9H are two plots demonstrating the AUC of the biomarkers in each group (bucketgroups 1 and 2);
  • FIG. 9I is a box and whisker plot showing that when biomarkers are derived from bucketgroup 1 and bucketgroup 2 that a greater overall AUC is obtained;
  • FIG. 10A is a plot of the 359 mRNA biomarkers against the AUC for differentiating between PS and sepsis with all individual biomarkers having had an AUC greater than 0.7;
  • FIG. 10B is a box and whisker plot showing the best mRNA biomarker for separating PS and sepsis
  • FIG. 10C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating PS and sepsis with all derived biomarkers having an AUC of 0.9;
  • FIG. 10D is a box and whisker plot of the best derived biomarker for separating PS and sepsis
  • FIG. 10E is a plot showing the correlation of the biomarkers in each bucketgroup to the condition.
  • FIG. 10F is a box and whisker plot showing that when biomarkers are derived from bucketgroup 1 and bucketgroup 2 that a greater overall AUC is obtained;
  • FIG. 10G is a plot demonstrating the AUC of the biomarkers in each of four bucketgroups.
  • FIG. 10H is a box and whisker plot showing that when biomarkers are derived from each of the four bucketgroups a greater overall AUC is obtained;
  • FIG. 11A is a plot of the 66 mRNA biomarkers against the AUC for differentiating between mild sepsis and severe sepsis with all individual biomarkers selected having an AUC greater than 0.7;
  • FIG. 11B is a box and whisker plot showing the best mRNA biomarker for separating mild sepsis and severe sepsis;
  • FIG. 11C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating mild sepsis and severe sepsis with all derived biomarkers have an AUC of at least 0.87;
  • FIG. 11D is a box and whisker plot of the best performing derived biomarker, based on AUC, for separating mild sepsis and severe sepsis;
  • FIGS. 11E and 11F are plots showing the correlation to each other of the biomarkers in each group.
  • FIGS. 11G and 11H are plots demonstrating the AUC of the biomarkers in each group.
  • FIG. 11I is a box and whisker plot showing that when biomarkers are derived from group 1 and group 2 that a greater overall AUC is obtained;
  • FIG. 12A is a plot of the 48 mRNA biomarkers against the AUC for differentiating between mild sepsis and septic shock (also referred to herein as “infection-positive SIRS-shock” (ipSIRS-shock)) with all individual biomarkers having an AUC greater than 0.7;
  • FIG. 12B is a box and whisker plot showing the best mRNA biomarker for separating mild sepsis and septic shock;
  • FIG. 12C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating mild sepsis and septic shock with all derived biomarkers having an AUC of at least 0.793;
  • FIG. 12D is a box and whisker plot of the best performing derived biomarker, based on AUC, for separating mild sepsis and septic shock;
  • FIGS. 12E and 12F are plots showing the correlation to each other of the biomarkers in each group.
  • FIGS. 12G and 12H are plots demonstrating the AUC of the biomarkers in each group.
  • FIG. 12I is a box and whisker plot showing that when biomarkers are derived from group 1 and group 2 that a greater overall AUC is obtained;
  • FIG. 13A is a plot of the 61 mRNA biomarkers against the AUC for differentiating between severe sepsis and septic shock with all individual biomarkers selected having an AUC greater than 0.7;
  • FIG. 13B is a box and whisker plot showing the best mRNA biomarker for separating severe sepsis and septic shock
  • FIG. 13C is a plot of the AUC for the diagnostic ability of 1000 derived biomarkers in separating severe sepsis and septic shock with all derived biomarkers have an AUC of at least 0.821;
  • FIG. 13D is a box and whisker plot of the best performing derived biomarker, based on AUC, for separating severe sepsis and septic shock;
  • FIGS. 13E and 13F are plots showing the correlation to each other of the biomarkers in each group.
  • FIGS. 13G and 13H are plots demonstrating the AUC of the biomarkers in each group.
  • FIG. 13I is a box and whisker plot showing that when biomarkers are derived from group 1 and group 2 that a greater overall AUC is obtained;
  • FIG. 14 is a user interface illustrating an example of a thermal cycler protocol
  • FIG. 15 is a diagram of an example of a report.
  • FIGS. 16A to 16L are box and whisker plots for the top twelve biomarker combinations for distinguishing between healthy condition and PS;
  • FIGS. 17A to 17L are box and whisker plots for the top twelve biomarker combinations for distinguishing between healthy condition and sepsis;
  • FIGS. 18A to 18L are box and whisker plots for the top twelve biomarker combinations for distinguishing between PS and sepsis;
  • FIGS. 19A to 19L are box and whisker plots for the top twelve biomarker combinations for distinguishing between sepsis and severe sepsis;
  • FIGS. 20A to 20L are box and whisker plots for the top twelve biomarker combinations for distinguishing between severe sepsis and septic shock;
  • FIGS. 21A to 21L are box and whisker plots for the top twelve biomarker combinations for distinguishing between sepsis and septic shock;
  • FIG. 22 is a graph of the effect on AUC of adding biomarkers to a biomarker signature
  • FIG. 23 is a graph showing an example of the ability of the biomarker signature to distinguish between PS and sepsis for two patient populations
  • FIG. 24 is a flowchart of an example of a method for determining indicator references
  • FIGS. 25A and 25B are a flowchart of an example of a method for validating an indicator derived from biomarker measurements
  • FIG. 26 is an example showing the comparison of an indicator value to an indicator reference.
  • FIGS. 27A and 27B are example representation of indicator values.
  • FIG. 1A An example of a method for determining an indicator for use in diagnosing the presence, absence or degree of at least one condition in or of a biological subject, or in monitoring the progression of at least one condition in or of the subject, or in prognosing at least one condition in or of the subject, will now be described with reference to FIG. 1A .
  • biomarker refers to a measurable parameter, or combination of parameters, that can be used as an indicator of a biological state and includes, without limitation, proteins, nucleic acids, carbohydrates, lipids, metabolites, gases, steroids, ions, nutrients, toxins, cells, pathogenic organisms, non-pathogenic organisms, organic compounds and inorganic compounds.
  • Biomarkers also encompass non-blood-borne factors, non-analyte physiological markers of health status, or other factors or biomarkers not measured from samples (e.g., biological samples such as bodily fluids), such as “clinical” or “phenotypic” parameters, including, without limitation, age, ethnicity, gender, species, breed, genetic information, white blood cell count, diastolic blood pressure and systolic blood pressure, bone density, height, weight, waist and hip circumference, body-mass index, as well as others such as Type I or Type II diabetes mellitus or gestational diabetes mellitus (collectively referred to here as diabetes), resting heart rate, homeostatic model assessment (HOMA), HOMA insulin resistance (HOMA-IR), intravenous glucose tolerance (SI(IVGT)), resting heart rate, ⁇ cell function, macrovascular function, microvascular function, atherogenic index, low-density lipoprotein/high-density lipoprotein ratio, intima-media thickness, body temperature, sequential organ failure
  • biomarker value refers to a value measured or derived for at least one corresponding biomarker of the biological subject and which is typically at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject.
  • biomarker values could be measured biomarker values, which are values of biomarkers measured for the subject, or alternatively could be derived biomarker values, which are values that have been derived from one or more measured biomarker values, for example by applying a function to the one or more measured biomarker values.
  • Biomarker values can be of any appropriate form depending on the manner in which the values are determined.
  • the biomarker values could be determined using high-throughput technologies such as mass spectrometry, sequencing platforms, array and hybridization platforms, immunoassays, flow cytometry, or any combination of such technologies and in one preferred example, the biomarker values relate to a level of activity or abundance of an expression product or other measurable molecule, quantified using a technique such as PCR, sequencing or the like.
  • the biomarker values can be in the form of amplification amounts, or cycle times, which are a logarithmic representation of the concentration of the biomarker within a sample, as will be appreciated by persons skilled in the art and as will be described in more detail below.
  • reference biomarkers is used to refer to biomarkers whose activity has been quantified for a sample population of one or more individuals having one or more conditions, stages of one or more conditions, subtypes of one or more conditions or different prognoses.
  • reference data refers to data measured for one or more individuals in a sample population, and may include quantification of the level or activity of the biomarkers measured for each individual, information regarding any conditions of the individuals, and optionally any other information of interest.
  • candidate biomarkers refers to a subset of the reference biomarkers that have been identified as being potentially useful in distinguishing between different groups of individuals, such as individuals suffering from different conditions, or having different stages or prognoses.
  • the number of candidate biomarkers will vary, but is typically about 200.
  • signature biomarkers is used to refer to a subset of the candidate biomarkers that have been identified for use in a biomarker signature that can be used in performing a clinical assessment, such as to rule in or rule out a specific condition, different stages or severity of conditions, subtypes of different conditions or different prognoses.
  • the number of signature biomarkers will vary, but is typically of the order of 10 or less.
  • biomarker signature means a combination of at least two biomarker values corresponding to values of biomarkers that can be measured for or derived from one or more biological subjects, which combination is characteristic for a discrete condition, stage of condition, subtype of condition or a prognosis for a discrete condition, stage of condition, subtype of condition.
  • biological subject refers to an animal subject, particularly a vertebrate subject, and even more particularly a mammalian subject.
  • Suitable vertebrate animals include, but are not restricted to, any member of the phylum Chordata, subphylum vertebrata including primates, rodents (e.g., mice rats, guinea pigs), lagomorphs (e.g., rabbits, hares), bovines (e.g., cattle), ovines (e.g., sheep), caprines (e.g., goats), porcines (e.g., pigs), equines (e.g., horses), canines (e.g., dogs), felines (e.g., cats), avians (e.g., chickens, turkeys, ducks, geese, companion birds such as canaries, budgerigars etc.), marine mammals (e.
  • rodents e.g., mice rats, guinea pigs
  • lagomorphs
  • SIRS systemic inflammatory response syndrome
  • a body temperature greater than 38° C. or less than 36° C.
  • a heart rate greater than 90 beats per minute
  • a respiratory rate greater than 20 per minute
  • a white blood cell count total leukocytes
  • a band neutrophil percentage greater than 10%. From an immunological perspective, it may be seen as representing a systemic response to insult (e.g., major surgery) or systemic inflammation.
  • inSIRS (which includes within its scope “post-surgical” (PS) inflammation) includes the clinical response noted above but in the absence of a systemic infectious process.
  • ipSIRS also referred to herein as “sepsis” includes the clinical response noted above but in the presence of a presumed or confirmed infection. Confirmation of infection can be determined using microbiological culture or isolation of the infectious agent. From an immunological perspective, ipSIRS may be seen as a systemic response to microorganisms, whether it is a local, peripheral or systemic infection.
  • the term “degree” of a condition refers to the seriousness, severity, stage or state of a condition.
  • a condition may be characterized as mild, moderate or severe.
  • a person of skill in the art would be able to determine or assess the degree of a particular condition.
  • the degree of a condition may be determined by comparing the likelihood or length of survival of a subject having a condition with the likelihood or length of survival in other subjects having the same condition.
  • the degree of a condition may be determined by comparing the clinical signs of a subject having a condition with the degree of the clinical signs in other subjects having the same condition.
  • the method includes determining a plurality of biomarker values at step 100 , each biomarker value being indicative of a value measured or derived for at least one biomarker of the biological subject.
  • biomarker values and biomarkers corresponding to the biomarker values can be of any appropriate form and in particular can relate to any attribute of a subject for which a value can be quantified. This technique is particularly suited to high-throughput technologies such as mass spectrometry, sequencing platforms, array and hybridization platforms, or any combination of such technologies and in one preferred example, the biomarker values relate to a level of activity or abundance of an expression product or other measurable molecule.
  • biomarker values could be measured biomarker values, which are values of biomarkers measured for the subject, or alternatively could be derived biomarker values, which are values that have been derived from one or more measured biomarker values, for example by applying a function to the one or more measured biomarker values.
  • biomarkers to which a function has been applied are referred to as “derived markers”.
  • the biomarker values may be determined in any one of a number of ways.
  • the process of determining the biomarker values can include measuring the biomarker values, for example by performing tests on the biological subject. More typically however, the step of determining the biomarker values includes having an electronic processing device receive or otherwise obtain biomarker values that have been previously measured or derived. This could include for example, retrieving the biomarker values from a data store such as a remote database, obtaining biomarker values that have been manually input, using an input device, or the like.
  • the indicator is determined using a combination of the plurality of biomarker values, the indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition.
  • the biomarker values can be combined in any one of a number of ways and this can include for example adding, multiplying, subtracting, or dividing biomarker values to determine an indicator value. This step is performed so that multiple biomarker values can be combined into a single indicator value, providing a more useful and straightforward mechanism for allowing the indicator to be interpreted and hence used in diagnosing the presence, absence or degree of the at least one condition in the subject, or prognosing the at least one condition in the subject.
  • an indication of the indicator is optionally displayed or otherwise provided to the user.
  • the indication could be a graphical or alphanumeric representation of an indicator value.
  • the indication could be the result of a comparison of the indicator value to predefined thresholds or ranges, or alternatively could be an indication of the presence, absence, degree or prognosis for at least one condition, derived using the indicator.
  • At least two of the biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9.
  • This requirement means that the two biomarkers are not entirely correlated in respect of each other when considered in the context of the condition(s) being diagnosed or prognosed.
  • at least two of the biomarkers in the combination respond differently as the condition changes, which adds significantly to their ability when combined to discriminate between at least two conditions, to diagnose the presence, absence or degree of at least one condition, and/or to provide a prognosis of at least condition in or of the biological subject.
  • “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (or).
  • biomarkers may relate to different biological attributes or domains such as but not limited to different molecular functions, different biological processes and different cellular components.
  • molecular function include addition of or removal of one of more of the following moieties to or from a protein, polypeptide, peptide, nucleic acid (e.g., DNA, RNA): linear, branched, saturated or unsaturated alkyl (e.g., C 1 -C 24 alkyl); phosphate; ubiquitin; acyl; fatty acid, lipid, phospholipid; nucleotide base; hydroxyl and the like.
  • Molecular functions also include signaling pathways, including without limitation, receptor signaling pathways and nuclear signaling pathways.
  • Non-limiting examples of molecular functions also include cleavage of a nucleic acid, peptide, polypeptide or protein at one or more sites; polymerization of a nucleic acid, peptide, polypeptide or protein; translocation through a cell membrane (e.g., outer cell membrane; nuclear membrane); translocation into or out of a cell organelle (e.g., Golgi apparatus, lysosome, endoplasmic reticulum, nucleus, mitochondria); receptor binding, receptor signaling, membrane channel binding, membrane channel influx or efflux; and the like.
  • a cell membrane e.g., outer cell membrane; nuclear membrane
  • a cell organelle e.g., Golgi apparatus, lysosome, endoplasmic reticulum, nucleus, mitochondria
  • receptor binding, receptor signaling membrane channel binding, membrane channel influx or efflux; and the like.
  • stages of the cell cycle such as meiosis, mitosis, cell division, prophase, metaphase, anaphase, telophase and interphase, stages of cell differentiation; apoptosis; necrosis; chemotaxis; immune responses including adaptive and innate immune responses, pro-inflammatory immune responses, autoimmune responses, tolerogenic responses and the like.
  • RNA processes include generating or breaking down adenosine triphosphate (ATP), saccharides, polysaccharides, fatty acids, lipids, phospholipids, sphingolipids, glycolipids, cholesterol, nucleotides, nucleic acids, membranes (e.g., cell plasma membrane, nuclear membrane), amino acids, peptides, polypeptides, proteins and the like.
  • ATP adenosine triphosphate
  • saccharides e.g., fatty acids, lipids, phospholipids, sphingolipids, glycolipids, cholesterol
  • nucleotides e.g., cell plasma membrane, nuclear membrane
  • amino acids peptides, polypeptides, proteins and the like.
  • cellular components include organelles, membranes, as for example noted above, and others.
  • biomarkers that have different biological attributes or domains provides further information than if the biomarkers were related to the same or common biological attributes or domains.
  • the method uses biomarkers that are not well correlated with each other, thereby ensuring that the inclusion of each biomarker in the method adds significantly to the discriminative ability of the indicator.
  • the indicator has a performance value that is greater than or equal to a performance threshold.
  • the performance threshold may be of any suitable form but is to be typically indicative of an explained variance of at least 0.3, or an equivalent value of another performance measure.
  • the biomarkers used within the above-described method can define a biomarker signature for the at least one condition, which includes a minimal number of biomarkers, whilst maintaining sufficient performance to allow the biomarker signature to be used in making a clinically relevant diagnosis, prognosis, or differentiation.
  • Minimizing the number of biomarkers used minimizes the costs associated with performing diagnostic or prognostic tests and in the case of nucleic acid expression products, allows the test to be performed utilizing relatively straightforward techniques such as nucleic acid array, and polymerase chain reaction (PCR) processes, or the like, allowing the test to be performed rapidly in a clinical environment.
  • PCR polymerase chain reaction
  • biomarker signature by analyzing a large number of biomarkers and then selecting a combination of biomarkers that meet the above described criteria.
  • the process includes ranking a number of candidate biomarkers in accordance with the ability of each biomarker to distinguish between the presence, absence, degree or prognosis of at least one condition in a biological subject.
  • the candidate biomarkers can be obtained in any appropriate matter, but typically this would involve acquiring reference data including reference biomarker values relating to a number of reference biomarkers that have been measured or derived for one or more reference individuals having different presences, absences, degrees or prognoses of the one or more conditions of interest.
  • the candidate biomarkers can include measured and/or derived biomarkers, as will be described in more detail below.
  • the reference data typically includes measurements of a plurality of reference biomarkers, the measurements including information regarding the activity, such as the level, abundance or functional activity, of any expression product or measurable molecule, as will be described in more detail below.
  • the reference data may also include information such as clinical data regarding one or more conditions suffered by each individual.
  • SOFA Simple Organic Failure Assessment
  • the candidate biomarkers can include some or all of the reference biomarkers, depending on the preferred implementation.
  • reference biomarker values could be analyzed to determine correlations between the reference biomarkers and the at least one condition, with the reference biomarkers being coarsely filtered to remove those with a low correlation, for example with a correlation with the condition that is below 0.3.
  • At step 160 at least two candidate biomarkers are selected based on the ranking and a mutual correlation.
  • at least two candidate biomarkers are selected which have a mutual correlation within a mutual correlation range of ⁇ 0.9.
  • this process excludes any biomarkers which are highly mutually correlated, when considered in the context of the one or more conditions, and which would not therefore add significantly to the ability to discriminate between the presence, absence, degree or prognosis of at least one condition.
  • a performance value of a combination of the selected candidate biomarkers is determined.
  • the combination may be any combination of the candidate biomarker values, such as addition, subtraction, multiplication, or division of the candidate biomarker values, and this will not therefore be described in any further detail.
  • step 180 it is determined if the performance value of the combination exceeds a performance threshold, the performance threshold being equivalent to an explained variance of at least 0.3. If so, the combination of the candidate biomarkers can be used to define a biomarker signature. Otherwise, the previous steps can be repeated, for example by determining alternative combinations of the candidate biomarkers, selecting different candidate biomarkers, or adding additional candidate biomarkers as will be described in more detail below. In this regard, it will be appreciated that other measures could be used, and reference to an explained variance of at least 0.3 is intended to be a particular example for illustrative purposes.
  • the above described method can be utilized to select a combination of candidate biomarkers that are suitable for use as signature biomarkers in a biomarker signature for diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject, for example using the method of FIG. 1A above.
  • this is achieved by ensuring that at least two of the biomarkers used are not highly mutually correlated, thereby ensuring that each of these biomarkers contributes to the performance of the resulting signature.
  • the method includes determining a plurality of measured biomarker values, each measured biomarker value being a measured value of a corresponding biomarker of the biological subject and applying a function to at least one of the measured biomarker values to determine at least one derived biomarker value, the at least one derived biomarker value being indicative of a value of a corresponding derived biomarker.
  • the function includes at least one of multiplying two biomarker values; dividing two biomarker values; adding two biomarker values; subtracting two biomarker values; a weighted sum of at least two biomarker values; a log sum of at least two biomarker values; and, a sigmoidal function of at least two biomarker values.
  • the function is division of two biomarker values, so that the derived biomarker value corresponds to a ratio of two measured biomarker values.
  • the ratio might be preferred. For example, use of a ratio is self-normalizing, meaning variations in measuring techniques will automatically be accommodated. For example, if the input concentration of a sample is doubled, the relative proportions of biomarkers will remain the same. As a result, the type of function therefore has a stable profile over a range of input concentrations, which is important because input concentration is a known variable for expression data.
  • many biomarkers are nodes on biochemical pathways, so the ratio of biomarkers gives information about the relative activation of one biological pathway to another, which is a natural representation of biological change within a system. Finally, ratios are typically easily interpreted.
  • the method typically includes combining at least two biomarker values to determine an indicator value representing the indicator. This is usually achieved by combining at least two biomarker values using a combining function, such as: an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; and a weighted sum.
  • a combining function such as: an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; and a weighted sum.
  • At least one of the at least two biomarkers is a derived biomarker and in a preferred example, the combining function is addition of derived biomarker values that are ratios, in which case the method includes determining first and second derived biomarker values from ratios of first and second and third and fourth measured biomarker values, and then adding the first and second derived biomarker values to generate an indicator value.
  • the method includes determining an indicator value, comparing the indicator value to at least one indicator value range, and using a result of the comparison in diagnosing the presence, absence, degree or prognosis of at least one condition.
  • the above-described process is typically performed using an electronic processing device, forming part of a processing system such as a computer system or the like.
  • the method typically involves having the electronic processing device receive a plurality of measured biomarker values, apply a function to at least one of the measured biomarker values to determine the at least one derived biomarker value and combining at least one derived biomarker value and at least one other biomarker value to determine an indicator value.
  • the electronic processing device can then generate a representation in accordance with the at least one indicator value, for example by displaying a numerical indication of the indicator value. More typically however the electronic processing device compares the indicator value to at least one indicator value range and displays a result of the comparison. This can be used to compare the indicator to defined ranges representing specific stages, progressions or prognoses of one or more conditions, allowing an indication of the respective stage, progression or prognosis to be displayed.
  • the mutual correlation range is typically at least one of: ⁇ 0.8; ⁇ 0.7; ⁇ 0.6; ⁇ 0.5; ⁇ 0.4; ⁇ 0.3; ⁇ 0.2; and ⁇ 0.1.
  • the smaller the mutual correlation range used the less correlated the biomarkers will be and hence the more useful these will be in discriminating between the specific stages, progressions or prognoses of one or more conditions.
  • each biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3.
  • the condition correlation is more typically one of: ⁇ 0.9; ⁇ 0.8; ⁇ 0.7; ⁇ 0.6; ⁇ 0.5; and ⁇ 0.4.
  • the performance threshold is typically indicative of an explained variance of at least one of: 0.4; 0.5; 0.6; 0.7; 0.8; and 0.9.
  • the biomarker value can be of any suitable form.
  • the technique is particularly suited to biomarker values indicative of a level or abundance of a molecule selected from one or more of: a nucleic acid molecule; a proteinaceous molecule; an amino acid; a carbohydrate; a lipid; a steroid; an inorganic molecule; an ion; a drug; a chemical; a metabolite; a toxin; a nutrient; a gas; a cell; a pathogenic organism; and a non-pathogenic organism.
  • the method When determining biomarkers for use in a biomarker signature, the method typically includes selecting a combining function, determining if a performance value of a combination of the at least two candidate biomarkers determined by the combining function is greater than or equal to a performance threshold and if the performance value is not greater than or equal to a performance threshold, repeating these steps for successive different combining functions.
  • a combining function determines if a performance value of a combination of the at least two candidate biomarkers determined by the combining function is greater than or equal to a performance threshold and if the performance value is not greater than or equal to a performance threshold, repeating these steps for successive different combining functions.
  • the method typically further includes selecting two candidate biomarkers, determining if a performance value of a combination of the two candidate biomarkers is greater than or equal to a performance threshold and if not, combining the selected candidate biomarkers with at least one additional candidate biomarker before repeating the steps with at least one additional candidate biomarker.
  • the method typically includes selecting a highest and a next highest ranked candidate biomarker, for the selected candidate biomarkers, determining if the mutual correlation for the candidate biomarkers within the mutual correlation range and if not repeating these steps until two candidate biomarkers are selected having a mutual correlation within the mutual correlation range.
  • this can be achieved by defining at least two groups of candidate biomarkers, candidate biomarkers in different groups having a mutual correlation within the mutual correlation range, ranking the candidate biomarkers in each group and selecting candidate biomarkers from the different groups.
  • the candidate biomarkers are determined by using reference data for at least one individual to define a number of groups indicative of the presence, absence, degree or prognosis of the at least one condition and then using at least one analysis technique to identify a number of candidate biomarkers that are potentially useful for distinguishing the groups.
  • the groups can also be used to establish a range of at least two reference biomarker values to determine an indicator value range for the group.
  • reference values measured for reference biomarkers for the at least one individual can then be used to identify the candidate biomarkers, for example by filtering reference biomarkers to determine candidate biomarkers based on a correlation of each biomarker with the condition.
  • the process is performed by one or more processing systems operating as part of a distributed architecture, an example of which will now be described with reference to FIG. 2 .
  • the arrangement includes a number of processing systems 201 and computer systems 203 interconnected via one or more communications networks, such as the Internet 202 , and/or a number of local area networks (LANs) 204 .
  • networks 202 , 204 are for the purpose of example only, and in practice the processing and computer systems 201 , 203 can communicate via any appropriate mechanism, such as via wired or wireless connections, including, but not limited to mobile networks, private networks, such as an 802.11 networks, the Internet, LANs, WANs, or the like, as well as via direct or point-to-point connections, such as Bluetooth, or the like.
  • processing system and “computer system” is for illustrative purposes and to enable distinction between different devices, optionally having different functionality.
  • the processing and computer systems 201 , 203 could represent servers and clients respectively, as will become apparent from the following description. However, this is not intended to be limiting and in practice any suitable computer network architecture can be used.
  • the processing system 201 includes an electronic processing device, such as at least one microprocessor 300 , a memory 301 , an optional input/output device 302 , such as a keyboard and/or display, and an external interface 303 , interconnected via a bus 304 as shown.
  • the external interface 303 can be utilized for connecting the processing system 201 to peripheral devices, such as the communications networks 202 , 204 , databases 211 , other storage devices, or the like.
  • peripheral devices such as the communications networks 202 , 204 , databases 211 , other storage devices, or the like.
  • the microprocessor 300 executes instructions in the form of applications software stored in the memory 301 to perform required processes, such as communicating with other processing or computer systems 201 , 203 .
  • actions performed by a processing system 201 are performed by the processor 300 in accordance with instructions stored as applications software in the memory 301 and/or input commands received via the I/O device 302 , or commands received from other processing or computer systems 201 , 203 .
  • the applications software may include one or more software modules, and may be executed in a suitable execution environment, such as an operating system environment, or the like.
  • the processing systems 201 may be formed from any suitable processing system, such as a suitably programmed computer system, PC, web server, network server, or the like.
  • the processing systems 201 are standard processing system such as a 32-bit or 64-bit Intel Architecture based processing system, which executes software applications stored on non-volatile (e.g., hard disk) storage, although this is not essential.
  • the processing system could be or could include any electronic processing device such as a microprocessor, microchip processor, logic gate configuration, firmware optionally associated with implementing logic such as an FPGA (Field Programmable Gate Array), or any other electronic device, system or arrangement.
  • FPGA Field Programmable Gate Array
  • the computer systems 203 include an electronic processing device, such as at least one microprocessor 400 , a memory 401 , an input/output device 402 , such as a keyboard and/or display, and an external interface 403 , interconnected via a bus 404 as shown.
  • the external interface 403 can be utilized for connecting the computer system 203 to peripheral devices, such as the communications networks 202 , 204 , databases, other storage devices, or the like.
  • peripheral devices such as the communications networks 202 , 204 , databases, other storage devices, or the like.
  • a single external interface 403 is shown, this is for the purpose of example only, and in practice multiple interfaces using various methods (e.g., Ethernet, serial, USB, wireless or the like) may be provided.
  • the microprocessor 400 executes instructions in the form of applications software stored in the memory 401 to perform required processes, for example to allow communication with other processing or computer systems 201 , 203 .
  • actions performed by a processing system 203 are performed by the processor 400 in accordance with instructions stored as applications software in the memory 401 and/or input commands received from a user via the I/O device 402 .
  • the applications software may include one or more software modules, and may be executed in a suitable execution environment, such as an operating system environment, or the like.
  • the computer systems 203 may be formed from any suitable processing system, such as a suitably programmed PC, Internet terminal, lap-top, hand-held PC, smart phone, PDA, tablet, or the like.
  • the processing system 300 is a standard processing system such as a 32-bit or 64-bit Intel Architecture based processing system, which executes software applications stored on non-volatile (e.g., hard disk) storage, although this is not essential.
  • the processing systems 203 can be any electronic processing device such as a microprocessor, microchip processor, logic gate configuration, firmware optionally associated with implementing logic such as an FPGA (Field Programmable Gate Array), or any other electronic device, system or arrangement.
  • FPGA Field Programmable Gate Array
  • processing and computer systems 201 , 203 are shown as single entities, it will be appreciated that this is not essential, and instead one or more of the processing and/or computer systems 201 , 203 can be distributed over geographically separate locations, for example by using processing systems provided as part of a cloud based environment.
  • the process is performed by one or more of the processing systems 201 , acting as diagnostic servers.
  • Interaction by a user is via a user computer system 203 , which is used to allow a user to submit raw data, for example obtained from measurements on a subject, with the processing system 201 generating the indicator, allowing this to be displayed on the computer system 203 .
  • reference data is obtained from at least one individual.
  • the reference data is typically in the form of measured biomarker values obtained for at least one individual for different stages of the at least one condition.
  • the reference data may be acquired in any appropriate manner but typically this involves obtaining gene expression product data from a plurality of individuals, selected to include individuals diagnosed with one or more conditions of interest, as well as healthy individuals. Detection of either types of gene expression in use of any of the methods described herein is encompassed by the present invention.
  • expression or “gene expression” refer to production of RNA only or production of RNA and translation of RNA into proteins or polypeptides.
  • expression products encompass (i) polynucleotides including RNA transcripts and corresponding nucleic acids including complementary cDNA copies of RNA transcripts, and (ii) polypeptides encoded by RNA transcripts.
  • the conditions are typically medical, veterinary or other health status conditions and may include any illness, disease, stages of disease, disease subtypes, severities of disease, diseases of varying prognoses or the like.
  • the terms “healthy individual”, “healthy subject” and the like are used herein to refer to a subject, in particular a mammal, having no diagnosed disease, disorder, infirmity, or ailment.
  • the condition of such an individual or subject is referred to herein as a “healthy condition” such that in one example a condition can include healthy.
  • a healthy subject lacks SIRS (e.g., inSIRS or ipSIRS).
  • gene expression product data are collected, for example by obtaining a biological sample, such as a peripheral blood sample, and then performing a quantification process, such as a nucleic acid amplification process, including PCR (Polymerase Chain Reaction) or the like, in order to assess the activity, and in particular, level or abundance of a number of reference biomarkers. Quantified values indicative of the relative activity are then stored as part of the reference data.
  • a biological sample such as a peripheral blood sample
  • a quantification process such as a nucleic acid amplification process, including PCR (Polymerase Chain Reaction) or the like
  • Example reference biomarkers could include expression products such as nucleic acid or proteinaceous molecules, as well as other molecules relevant in making a clinical assessment.
  • the number of biomarkers measured for use as reference biomarkers will vary depending upon the preferred implementation, but typically include a large number such as, 1000, 5000, 10000 or above, although this is not intended to be limiting.
  • SIRS Systemic Inflammatory Response Syndrome
  • D Pittet M Costigan
  • T Hwang T Hwang
  • C S Davis C S Davis
  • R P Wenzel “The Natural History of the Systemic Inflammatory Response Syndrome (SIRS). a Prospective Study.”, JAMA: the Journal of the American Medical Association 273, no. 2 (Jan. 11, 1995): 117-123.).
  • SIRS is an overwhelming whole body reaction that may have an infectious or non-infectious etiology
  • sepsis is SIRS that occurs during infection. Both are defined by a number of non-specific host response parameters including changes in heart and respiratory rate, body temperature and white cell counts (Mitchell M Levy et al., “2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference”, Critical Care Medicine 31, no. 4 (April 2003): 1250-1256.; K Reinhart, M Bauer, N C Riedemann, and C S Hartog, “New Approaches to Sepsis: Molecular Diagnostics and Biomarkers”, Clinical Microbiology Reviews 25, no. 4 (Oct.
  • SIRS both conditions
  • IMS infection-negative SIRS
  • ipSIRS infection-positive SIRS
  • SIRS infection-positive SIRS
  • the causes of SIRS are multiple and varied and can include, but are not limited to, trauma, burns, pancreatitis, endotoxemia, surgery, adverse drug reactions, and infections (local and systemic). It will be appreciated from the following, however, that this can be applied to a range of different conditions, and reference to SIRS or sepsis is not intended to be limiting.
  • the reference data may include additional biomarkers such as one or more phenotypic or clinical parameters of the individuals and/or their relatives.
  • Phenotypic parameters can include information such as the gender, ethnicity, age, hair color, eye color, height, weight, waist and hip circumference, or the like. Also, in the case of the technology being applied to individuals other than humans, this can also include information such as designation of a species, breed or the like.
  • Clinical traits may include genetic information, white blood cell count, diastolic blood pressure and systolic blood pressure, bone density, body-mass index, diabetes, resting heart rate, HOMA, HOMA-IR, IVGT, resting heart rate, ⁇ cell function, macrovascular function, microvascular function, atherogenic index, low-density lipoprotein/high-density lipoprotein ratio, intima-media thickness, body temperature, SOFA and the like.
  • the reference data can include for each of the reference individuals information relating to at least one and desirably to a plurality of reference biomarkers and a presence, absence, degree or progression of a condition.
  • the reference data may be collected from individuals presenting at a medical center with clinical signs relating to relevant any conditions of interest, and may involve follow-on consultations in order to confirm clinical assessments, as well as to identify changes in biomarkers, and/or clinical signs, and/or severity of clinical signs, over a period of time.
  • the reference data can include time series data indicative of the progression of a condition, and/or the activity of the reference biomarkers, so that the reference data for an individual can be used to determine if the condition of the individual is improving, worsening or static.
  • the reference biomarkers are preferably substantially similar for the individuals within the sample population, so that comparisons of measured activities between individuals can be made.
  • This reference data could also be collected from a single individual over time, for example as a condition within the individual progresses, although more typically it would be obtained from multiple individuals each of which has a different stage of the one or more conditions of interest.
  • the reference data can be stored in the database 211 allowing this to be subsequently retrieved by the processing system 201 for subsequent analysis.
  • the processing system 201 also typically stores an indication of an identity of each of the reference biomarkers.
  • the measurements are received as raw data, which then undergoes preliminary processing.
  • raw data corresponds to information that has come from a source without modification, such as outputs from instruments such as PCR machines, array (e.g., microarray) scanners, sequencing machines, clinical notes or any other biochemical, biological, observational data, or the like.
  • This step can be used to convert the raw data into a format that is better suited to analysis. In one example this is performed in order to normalize the raw data and thereby assist in ensuring the biomarker values demonstrate consistency even when measured using different techniques, different equipment, or the like.
  • the goal of normalization is to remove the variation within the samples that is not directly attributable to the specific analysis under consideration. For example, to remove variances caused by differences in sample processing at different sites.
  • Classic examples of normalization include z-score transformation for generic data, or popular domain specific normalizations, such as RMA normalization for microarrays.
  • this step may not strictly be necessary, in which case the function can be a Null function producing an output identical to the input.
  • the preferred approach is a paired function approach over log normalized data.
  • Log normalization is a standard data transformation on microarray data, because the data follow a log-normal distribution when coming off the machine. Applying a log transform turns the data into process-friendly normal data.
  • the processing system 201 Prior to this occurring, the processing system 201 optionally removes a validation subgroup of individuals from the reference data to allow the processing system 201 to determine the candidate biomarkers using the reference data without the validation subgroup so that the validation subgroup can be subsequently used to validate the candidate biomarkers or signatures including a number of the candidate biomarkers.
  • data from the validation subgroup is used to validate the efficacy of the candidate or signature biomarkers in identifying the presence, absence, degree, stage, severity, prognosis or progression of any one or more of the conditions to ensure the potential or signature biomarkers are effective.
  • this is achieved by having the processing system 201 flag individuals within the validation subgroup or alternatively store these in either an alternative location within the database 211 or an alternative database to the reference data.
  • the validation subgroup of individuals is typically selected randomly and may optionally be selected to include individuals having different phenotypic traits. When a validation subgroup of individuals is removed, the remaining individuals will simply be referred to as reference data for ease throughout the remaining description.
  • the reference data (i.e., excluding the validation subgroup) are classified into groups.
  • the groups may be defined in any appropriate manner and may be defined based on any one or more of an indication of a presence, absence, degree, stage, severity, prognosis or progression of a condition, other tests or assays, or measured biomarkers associated with the individuals.
  • a first selection of groups may be to identify one or more groups of individuals suffering from SIRS, one or more groups of individuals suffering ipSIRS, one or more groups of individuals suffering inSIRS, and one or more groups of healthy individuals. Further groups may also be defined for individuals suffering from other conditions.
  • the groups may include overlapping groups, so for example it may be desirable to define groups of healthy individuals and individuals having SIRS, with further being defined to distinguish inSIRS patients from ipSIRS patients, as well as different degree of inSIRS or ipSIRS, with these groups having SIRS in common, but each group of patients differing in whether a clinician has determined the presence of an infection or not.
  • further subdivision may be performed based on phenotypic traits, so groups could be defined based on gender, ethnicity or the like so that a plurality of groups of individuals suffering from a condition are defined, with each group relating to a different phenotypic trait.
  • identification of different groups can be performed in other manners, for example on the basis of particular activities of biomarkers within the biological samples of the reference individuals, and accordingly, reference to conditions is not intended to be limiting and other information may be used as required.
  • classification into groups may vary depending on the preferred implementation. In one example, this can be performed automatically by the processing system 201 , for example, using unsupervised methods such as Principal Components Analysis (PCA), or supervised methods such as k-means or Self Organizing Map (SOM). Alternatively, this may be performed manually by an operator by allowing the operator to review reference data presented on a Graphical User Interface (GUI), and define respective groups using appropriate input commands.
  • PCA Principal Components Analysis
  • SOM Self Organizing Map
  • GUI Graphical User Interface
  • biomarkers are filtered based on their ability to distinguish between the groups.
  • This process typically examines the activity of the reference biomarkers for individuals within and across the groups, to identify reference biomarkers whose activities differ between and hence can distinguish groups.
  • a range of different analysis techniques can be utilized including, for example, regression or correlation analysis techniques. Examples of the techniques used can include established methods for parameterized model building such as Partial Least Squares, Random Forest or Support Vector Machines, usually coupled to a feature reduction technique for the selection of the specific subset of the biomarkers to be used in a signature.
  • Partial Least Squares a versatile tool for the analysis of high-dimensional genomic data” by Boulesteix, Anne-Laure and Strimmer, Korbinian, from Briefings in Bioinformatics 2007 vol 8. no. 1, pg 32-44.
  • Support Vector machines are described in “LIBSVM: a library for support vector machines” by Chang, C. C. and Lin, C. J. from ACM Transactions on Intelligent Systems and Technology (TIST), 2011 vol 2, no. 3, pg 27.
  • Standard Random Forest in R language is described in “Classification and Regression by random Forest” by Liaw, A. and Wiener, M., in R news 2002, vol 2, no. 3, pg 18-22.
  • the analysis techniques are implemented by the processing system 201 , using applications software, which allows the processing system 201 to perform multiple ones of the analysis techniques in sequence. This is advantageous as the different analysis techniques typically have different biases and can therefore be used to identify different potential biomarkers that can distinguish the groups, thereby reducing the risk of clinically relevant biomarkers being overlooked.
  • the process involves filtering out any biomarkers that demonstrate a correlation with the groups, and hence with the condition, that is below a certain correlation threshold, such as 0.3.
  • derived biomarkers are generated from the filtered reference biomarkers using one or more functions.
  • functions can include division, subtraction, multiplication, addition of two markers, sigmoidal functions applied to the product of two biomarkers, negative logs of the division of two biomarkers, least-squares regression applied to two vectors of markers to produce a function (equation) output, concordance correlation coefficient of two vectors of categorical biomarkers, or the like.
  • the function is selected based on a number of rules.
  • rules can include: utility, functions that provide the best results; interpretability, functions that can be understood in terms of biological function; output, functions that produce informative outputs; simplicity; performance assessment; least number of biomarkers for best performance; number of biomarkers at a statistical overfitting threshold or the like.
  • the preferred function is division, with the resulting biomarkers being different ratios. It will be appreciated that the division can be performed in multiple different ways, so that for three biomarkers, nine different derived biomarkers can be determined.
  • a performance measure is determined for each of the candidate biomarkers, including the filtered reference biomarkers and any derived markers.
  • the performance measure may be of any suitable form and typically includes a correlation or performance explained measure that is indicative of a correlation of the corresponding biomarker and its ability to distinguish between groups.
  • the performance function used to determine the performance measure is a standard univariate statistical test over all candidate biomarkers. Other examples however include a t-test, a non-parametric equivalent or area under receiver operator curve, chi squared or regression analyses or their equivalents, extensions or derivatives may be used.
  • the outcome of the applying the performance function to each in the candidate selection step is a ranked list of biomarkers, with the top N ranked biomarkers proceeding to the next stage.
  • the biomarkers falling below this threshold are no longer considered.
  • the threshold applied may be an absolute number or proportion of all biomarkers, or determined by performance, such as a p value ⁇ 0.05.
  • the threshold should be chosen to contain a sufficiently large number of biomarkers to bias towards including sufficiently independent biomarkers (i.e., low mutual correlation).
  • the processing system 201 selects a next two candidate biomarkers based on the performance measure and on a mutual correlation.
  • two markers that are highly correlated with each other in terms of the context of the condition will not necessarily improve the ability to distinguish a particular presence, absence, degree or prognosis of the condition any more than a single one of the markers.
  • the mutual correlation threshold used will vary depending upon the preferred implementation, and is typically selected to be as low as possible, as described above. Examples of the manner in which the biomarkers are selected will be described in more detail below with respect to FIGS. 6A and 6B .
  • the processing system 201 determines a performance of a next candidate biomarker combination.
  • the processing system 201 will use a combining function such as addition, to combine the biomarker values of the selected candidate biomarkers and use this to determine and indicator value based on the combination of biomarker values.
  • the performance can be determined in any suitable manner, such as using statistical measurements, correlation measurements, concordance measurements or aggregate performance measurements such as averages.
  • the performance measure is a ‘variance explained’ (VE).
  • a VE of “1” means that using the biomarkers, you can perfectly classify/predict the disease.
  • a VE of “0.8” means that your markers account for 80% of the result in practice.
  • the processing system 201 compares the performance of the indicator to a performance threshold and determines if this is exceeded at step 540 . In the event that the threshold is exceeded, this indicates that the selected combination of markers provides the required degree of discrimination allowing the presence, absence, degree or prognosis of the condition to be determined.
  • the processing system 201 returns to step 530 to determine the performance of a next candidate biomarker combination.
  • the combinations used will typically be ordered in terms of preference, so that preferred combinations are tried first, with less preferred combinations being tried only in the event that preferred combinations prove unsuccessful.
  • step 550 the process moves onto step 550 to compare the current number of candidate biomarkers being considered to a limit.
  • the limit is used to control the overall number of biomarkers in the biomarker signature, thereby minimizing signature size and hence the cost of performing the associated measurements and diagnosis.
  • an additional biomarker is added based on the correlation and performance at step 560 , with the process moving onto step 530 to determine a performance of the next candidate biomarker combination. Otherwise if a limit has been reached, then an alternative next two candidate biomarkers are selected at step 525 .
  • this process allows additional candidate biomarkers to be progressively included, with a combination of the multiple candidate biomarkers being compared to the performance threshold, to determine if the required performance is met. If this is not achieved before the number of candidate biomarkers reaches the limit, the process is recommenced using two different candidate biomarkers.
  • the selected candidate biomarkers can be defined as signature biomarkers for inclusion in a biomarker signature for the one or more conditions at step 565 .
  • biomarker signature is finalized at step 565 , additional checks might be performed, to ensure that the candidate biomarkers included in the signature should not be excluded for any reason.
  • candidate biomarkers might be excluded for cost considerations as some combinations of candidate biomarkers may cost more than others.
  • a larger number of biomarkers may cost more than a smaller number, and the additional cost may not be justified by a small improvement in performance.
  • the cost might be increased if multiple different tests are required in order to measure required biomarker values.
  • Biomarkers might also be excluded from use for legal reasons, for example if their use is restricted for approval or intellectual property reasons. Some biomarkers may be difficult to measure from a technical perspective, for example very low expression in vivo, which increases variability and therefore reduces robustness.
  • each biomarker combination panel may also include some variability, typically expressed as confidence intervals around the reported performance. Although a point estimate for one panel may be higher than for another, if the difference given the variability is not significant, the combinations may be considered equivalent.
  • the processing system 201 can determine an indicator value range associated with each group.
  • the range of reference biomarker values for the signature biomarkers within each group are used to calculate indicator value ranges for each group. These can then be compared to an indicator value calculated for a biological subject having an unknown presence absence, degree or progression of the at least one condition and used to identify a group to which the subject would belong and hence the presence, absence, degree or progression of the condition.
  • the above-described process iteratively assesses the biomarkers, initially selecting two biomarkers, with various combinations of these being considered to determine if these have the required performance for use in diagnosing the presence, absence, degree or progression of a condition.
  • additional biomarkers can be added and further combinations tried.
  • the process can consider three biomarkers, four biomarkers, five biomarkers, six biomarkers, seven biomarkers, eight biomarkers, nine biomarkers or more. Typically this is performed to a limit which may be defined based for example on the number of biomarkers that can practically be measured within given cost or process parameters.
  • the process moves onto to select alternative candidate biomarkers with this being repeated.
  • biomarkers which have the suitable performance and which are not highly correlated on the basis that these provide the maximum performance.
  • the ability of these biomarkers to distinguish is then tested and in the event that this is insufficient, further biomarkers can be added to a limit. If this still does not provide the required discriminatory performance alternative biomarkers can be selected.
  • the process of selecting two candidate biomarkers at step 525 can be achieved in any number of ways depending upon the preferred implementation and examples of this will now be described with reference to FIGS. 6A and 6B .
  • biomarkers are grouped according to their mutual similarity. Thus, highly correlated biomarkers are put together in common groups. Biomarkers within the group are ranked at step 610 based on their performance measure in terms of their correlation with the condition, with the highest ranked biomarkers from two of the groups being selected at step 620 to define the next two candidate biomarkers. It will be appreciated if additional candidate biomarkers are required, these can be selected from different groups to the first two candidate biomarkers.
  • biomarkers are ranked based on their performance at discriminating the condition(s).
  • a next highest biomarker is selected, with the remaining biomarkers being re-ranked on the combination of their similarity with the selected biomarker, for example using mutual information, as well as their performance.
  • the next highest biomarker is then selected at step 680 with this process being repeated as required.
  • the above-described processes provide mechanisms for selecting a combination of biomarkers, and more typically derived biomarkers, that can be used to form a biomarker signature, which in turn can be used in diagnosing the presence, absence or degree of at least one condition or in providing a prognosis of at least one condition.
  • the biomarker signature defines the biomarkers that should be measured (i.e., the signature biomarkers), how derived biomarker values should be determined for measured biomarker values, and then how biomarker values should be subsequently combined to generate an indicator value.
  • the biomarker signature can also specify defined indicator value ranges that indicate a particular presence, absence, degree or prognosis of one or more conditions.
  • a plurality of measured biomarker values are measured for a biological subject whose condition is unknown, with these typically being provided to the processing system 201 , for example by download from measuring equipment or the like.
  • the processing system 201 applies one or more functions to the measured biomarker values to determine any required derived biomarker values.
  • a derived biomarker value and another biomarker value i.e., another derived biomarker value or a measured biomarker value
  • an indicator value which can then be displayed or otherwise used in determining the presence, absence, degree or prognosis of one or more conditions.
  • this can involve simply displaying the indicator value, allowing an assessment to be made by a medical practitioner or alternatively may involve further processing, such as comparing the indicator to defined indicator value ranges that indicate a particular presence, absence, degree or prognosis of one or more conditions, with the results of the comparison being displayed.
  • the biomarker signature defines the biomarker values that need to be measured and/or derived, allowing the processing system 201 to automatically generate an indicator value based on received measured biomarker values.
  • the processing system 201 can compare the indicator value to the indicator value ranges, and either display results of the comparison, or alternative interpret the results of the comparison, allowing an indicator to be displayed that is indicative of the presence, absence, degree or prognosis of a condition. This can then be used by a medical practitioner as required in performing a medical diagnosis of the biological subject.
  • ratios of “immune system biomarkers” is particularly beneficial when assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition.
  • immune system biomarker refers to a biomarker of the host's immune system that is altered, or whose level of expression is altered, as part of an inflammatory response to damage or pathogenic insult, including metabolic, toxic, neurotoxic, iatrogenic, thermal or chemical insults, illustrative examples of which include trauma, surgery, drugs including chemotherapeutic drugs, radiation, disease including pathogenic infection, metabolic disease and ischemia, as well as foreign or implanted substances.
  • immune system refers to cells, molecular components and mechanisms, including antigen-specific and non-specific categories of the adaptive and innate immune systems, respectively, that provide a defense against damage and insults and matter, the latter comprised of antigenic molecules, including but not limited to tumors, pathogens, and self-reactive cells.
  • innate immune system refers to a host's non-specific reaction to insult to include antigen-nonspecific defense cells, molecular components and mechanisms that come into action immediately or within several hours after exposure to almost any insult or antigen.
  • Elements of the innate immunity include for example phagocytic cells (monocytes, macrophages, dendritic cells, polymorphonuclear leukocytes such as neutrophils, reticuloendothelial cells such as kupffer cells, and microglia), cells that release inflammatory mediators (basophils, mast cells and eosinophils), natural killer cells (NK cells) and physical barriers and molecules such as keratin, mucous, secretions, complement proteins, immunoglobulin M (IgM), acute phase proteins, fibrinogen and molecules of the clotting cascade, and cytokines.
  • Effector compounds of the innate immune system include chemicals such as lysozymes, IgM, mucous and chemoattractants (e.g
  • adaptive immune system refers to antigen-specific cells, molecular components and mechanisms that emerge over several days, and react with and remove a specific antigen.
  • the adaptive immune system develops throughout a host's lifetime.
  • the adaptive immune system is based on leukocytes, and is divided into two major sections: the humoral immune system, which acts mainly via immunoglobulins produced by B cells, and the cell-mediated immune system, which functions mainly via T cells.
  • an indicator is determined that correlates to a ratio of immune system biomarkers, which can be used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition.
  • the method includes determining a pair of biomarker values, each biomarker value being a value measured or derived for at least one corresponding immune system biomarker of the biological subject and being at least partially indicative of a concentration of the immune system biomarker in a sample taken from the subject.
  • the biomarker values are used to determine a derived biomarker value using the pair of biomarker values, the derived biomarker value being indicative of a ratio of concentrations of the pair of immune system biomarkers.
  • the biomarker values are the concentrations of the biomarkers, then the derived biomarker value will be based on a ratio of the biomarker values.
  • the biomarker values are related to the concentrations of the biomarkers, for example if they are logarithmically related by virtue of the biomarker values being based on PCR cycle times, or the like, then the biomarker values may be combined in some other manner, such as by subtracting the cycle times to determine a derived biomarker value indicative of a ratio of the concentrations.
  • the derived biomarker is then used to determine the indicator, either by using the derived biomarker value as an indicator value, or by performing additional processing, such as comparing the derived biomarker value to a reference or the like, as will be described in more detail below.
  • biomarker values to determine a ratio of concentrations of immune system biomarkers, and then using this to determine an indicator allows indicators to be determined for use in determining a likelihood of a subject suffering from a range of different conditions, depending on the immune system biomarkers selected, which as it will be appreciated can be performed using the above described process.
  • the process involves determining a first derived biomarker value using a first pair of biomarker values, the first derived biomarker value being indicative of a ratio of concentrations of first and second immune system biomarkers, determining a second derived biomarker value using a second pair of biomarker values, the second derived biomarker value being indicative of a ratio of concentrations of third and fourth immune system biomarkers and determining the indicator by combining the first and second derived biomarker values.
  • two pairs of derived biomarker values can be used, which can assist in increasing the ability of the indicator to reliably determine the likelihood of a subject having a condition.
  • the derived biomarker values could be combined using a combining function such as an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; a weighted sum; a nearest neighbor model; and a probabilistic model.
  • a combining function such as an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; a weighted sum; a nearest neighbor model; and a probabilistic model.
  • the indicator is compared to an indicator reference, with a likelihood being determined in accordance with results of the comparison.
  • the indicator reference is typically derived from indicators determined for a number of individuals in a reference population.
  • the reference population typically includes individuals having different characteristics, such as a plurality of individuals of different sexes; and/or ethnicities, with different groups being defined based on different characteristics, with the subject's indicator being compared to indicator references derived from individuals with similar characteristics.
  • the reference population can also include a plurality of healthy individuals, a plurality of individuals suffering from at least one diagnosed medical condition, a plurality of individuals showing clinical signs of at least one medical condition and/or first and second groups of individuals, each group of individuals suffering from a respective diagnosed medical condition.
  • the individuals selected will depend on the intended use of the indicator.
  • the sample population includes individuals presenting with clinical signs of the specific medical condition, individuals diagnosed with the specific medical condition and healthy individuals. This ensures that the assessment of indicator validity applies regardless of not or whether the individual has the specific condition or not.
  • sample population could also include a plurality of individuals of different sexes, ethnicities, ages, or the like, allowing the control value ranges to be common across populations.
  • this is not essential, and alternatively control value thresholds could be established that are specific to a particular sub-set of the population. In this case, it would be necessary to ensure that the control value threshold ranges used are appropriate for the subject under consideration.
  • the indicator can also be used for determining a likelihood of the subject having a first or second condition, in other words to distinguish between the conditions. In this case, this would typically be achieved by comparing the indicator to first and second indicator references, the first and second indicator references being indicative of first and second conditions and determining the likelihood in accordance with the results of the comparison. In particular, this can include determining first and second indicator probabilities using the results of the comparisons and combining the first and second indicator probabilities, for example using a Bayes method, to determine a condition probability corresponding to the likelihood of the subject having one of the conditions. In this situation the first and second conditions could include two medical conditions, or a single medical condition and a healthy condition.
  • the first and second indicator references are distributions of indicators determined for first and second groups of a reference population, the first and second group consisting of individuals diagnosed with the first or second condition respectively.
  • this can be achieved by determining first and second groups of individuals, each group of individuals having a presence or absence of a diagnosed medical condition and determining first and second indicator references for the first and second groups respectively.
  • This allows the indicator to be used to distinguish between first and second conditions, which could include different medical conditions, as well as healthy conditions. It will also be appreciated that whilst two groups are described, this is not essential and three or more groups could also be defined.
  • the process is usually performed using at least one electronic processing device, such as a suitably programmed computer system or the like.
  • the electronic processing device typically obtains at least two pairs of measured biomarker values, either by receiving these from a measuring or other quantifying device, or by retrieving these from a database or the like.
  • the processing device determines a first derived biomarker value indicative of a ratio of concentrations of first and second immune system biomarkers and a second derived biomarker value indicative of a ratio of third and fourth immune system biomarkers.
  • the processing device determines the indicator by combining the first and second derived biomarker values.
  • the processing device can then generate a representation of the indicator, for example by generating an alphanumeric indication of the indicator, a graphical indication of a comparison of the indicator to one or more indicator references or an alphanumeric indication of a likelihood of the subject having at least one medical condition.
  • the method would also typically include obtaining a sample taken from the biological subject, the sample including polynucleotide expression products and quantifying at least some of the polynucleotide expression products within the sample to determine the pair of biomarker values. This can be achieved using any suitable technique, and will depend on the nature of the immune system biomarkers.
  • this process would typically include quantifying polynucleotide expression products by amplifying at least some polynucleotide expression products in the sample, determining an amplification amount representing a degree of amplification required to obtain a defined level of each of a pair of polynucleotide expression products and determining the indicator by determining a difference between the amplification amounts.
  • the amplification amount is generally a cycle time, a number of cycles, a cycle threshold and an amplification time.
  • the method includes determining a first derived biomarker value by determining a difference between the amplification amounts of a first pair of polynucleotide expression products, determining a second derived biomarker value by determining a difference between the amplification amounts of a second pair of polynucleotide expression products and determining the indicator by adding the first and second derived biomarker values.
  • the at least two immune system biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9 and the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence, degree or prognosis of the at least one condition, the performance threshold being indicative of an explained variance of at least 0.3.
  • the mutual correlation range is one of ⁇ 0.8; ⁇ 0.7; ⁇ 0.6; ⁇ 0.5; ⁇ 0.4; ⁇ 0.3; ⁇ 0.2; and, ⁇ 0.1.
  • each immune system biomarker has a condition correlation with the presence, absence, degree or prognosis of the at least one condition that lies outside a condition correlation range, the condition correlation range being between ⁇ 0.3 and more typically ⁇ 0.9; ⁇ 0.8; ⁇ 0.7; ⁇ 0.6; ⁇ 0.5; and, ⁇ 0.4.
  • the performance threshold is indicative of an explained variance of at least one of 0.4; 0.5; 0.6; 0.7; 0.8; and, 0.9.
  • biomarkers of inflammatory response syndromes also referred to interchangeably herein as “IRS biomarkers” or “IRS immune system biomarkers”
  • IRS biomarkers also referred to interchangeably herein as “IRS biomarkers” or “IRS immune system biomarkers”
  • SIRS affected subjects i.e., subjects having inSIRS or ipSIRS
  • healthy subjects or subjects not affected by SIRS i.e., subjects having inSIRS or ipSIRS
  • ipSIRS i.e., subjects having inSIRS or ipSIRS
  • ipSIRS e.g., sepsis, severe sepsis and septic shock.
  • the present inventors have developed various methods, compositions, apparatus and kits, which take advantage of these biomarkers to provide an indicator for use in diagnosing the presence, absence or degree of at least one condition, or for prognosing at least one condition, wherein the at least one condition is selected from a healthy condition (e.g., a normal condition or one in which inSIRS and inSIRS are absent), inSIRS, ipSIRS, or a stage of ipSIRS (e.g., a stage of ipSIRS with a particular severity, illustrative examples of which include mild sepsis, severe sepsis and septic shock).
  • a healthy condition e.g., a normal condition or one in which inSIRS and inSIRS are absent
  • inSIRS ipSIRS
  • ipSIRS e.g., a stage of ipSIRS with a particular severity, illustrative examples of which include mild sepsis
  • the methods and kits involve monitoring the expression of IRS biomarker genes in cells of the immune systems, including blood cells (e g., immune cells such as leukocytes), which may be reflected in changing patterns of RNA levels or protein production that correlate for example with the presence of active disease or response to disease.
  • blood cells e g., immune cells such as leukocytes
  • the IRS biomarkers are expression products of genes (also referred to interchangeably herein as “IRS biomarker genes” or IRS immune system biomarker genes”), including polynucleotide and polypeptide expression products.
  • polynucleotide expression products of IRS biomarker genes are referred to herein as “IRS biomarker polynucleotides.”
  • Polypeptide expression products of the IRS biomarker genes are referred to herein as “IRS biomarker polypeptides.”
  • the IRS biomarker genes are selected from the group consisting of: PRKCZ, SKI, RER1, TAS1R1, VAMP3, AGTRAP, VPS13D, KLHDC7A, NBLH/Clorf151, MDS2, RCAN3, LDLRAP1, MAN1C1, SH3BGRL3, DHDDS, HCRTR1, CCDC28B, LCK, ZNF362, THRAP3, PPIE//CCDC25, CAP1, CTPS, Clorf84, FAAH, DMBX1, CYP4B1, BTF3L4, LRRC42, Clorf175//TTC4, TMEM61, FPGT//TNNI3K, ACADM, SPATA1, EPHX4, RPAP2, RPL5//SNORA66//SNORD21//FAM69A, RTCD1, SLC30A7, RNPC3//AMY2B, CELSR2, AHCYL1, CEPT1//DRAM2, CHIA, LIX1L
  • the methods, compositions, apparatus and kits of the present invention take advantage of the IRS biomarkers broadly described above and elsewhere herein to provide an indicator for use in diagnosing the presence, absence or degree of the at least one condition selected from a healthy condition (e.g., a normal condition or one in which inSIRS and inSIRS are absent), inSIRS, ipSIRS or a stage of ipSIRS (e.g., a stage of ipSIRS with a particular severity such as mild sepsis, severe sepsis and septic shock), or in providing a prognosis of the at least one condition, which may involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values (also referred to
  • the diagnostic or prognostic methods, compositions, apparatus and kits of the present invention involve: (1) determining a plurality of measured IRS biomarker values, each measured IRS biomarker value being a measured value of an IRS biomarker of the biological subject; and (2) applying a function to at least one of the measured IRS biomarker values to determine at least one derived IRS biomarker value, the at least one derived IRS biomarker value being indicative of a value of a corresponding derived IRS biomarker.
  • the function suitably includes at least one of: (a) multiplying two IRS biomarker values; (b) dividing two IRS biomarker values; (c) adding two IRS biomarker values; (d) subtracting two IRS biomarker values; (e) a weighted sum of at least two IRS biomarker values; (f) a log sum of at least two IRS biomarker values; and (g) a sigmoidal function of at least two IRS biomarker values.
  • the diagnostic or prognostic methods, compositions, apparatus and kits involve: determining at least one derived IRS biomarker value corresponding to a ratio of two measured IRS biomarker values.
  • the diagnostic or prognostic methods, apparatus and kits suitably include combining at least two IRS biomarker values to determine an indicator value representing the indicator and in illustrative examples of this type, the at least two IRS biomarker values are combined using a combining function (e.g., any one or more of: an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; weighted sum; a nearest neighbor model; and a probabilistic model).
  • a combining function e.g., any one or more of: an additive model; a linear model; a support vector machine; a neural network model; a random forest model; a regression model; a genetic algorithm; an annealing algorithm; weighted sum; a nearest neighbor
  • the diagnostic or prognostic methods, apparatus and kits include: (a) determining a first derived IRS biomarker value, the first derived IRS biomarker value being a ratio of first and second measured IRS biomarker values; (b) determining a second derived IRS biomarker value, the second derived IRS biomarker value being a ratio of third and fourth measured IRS biomarker values; and (c) adding the first and second derived IRS biomarker values to generate an indicator value.
  • the methods, compositions, kits and apparatus of the present invention are useful for diagnosing that inSIRS or a healthy condition is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and a healthy condition, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least
  • the methods, apparatus and kits are useful for diagnosing that ipSIRS or a healthy condition is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from ipSIRS and a healthy condition, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition,
  • the methods, apparatus and kits are useful for diagnosing that inSIRS or ipSIRS is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and ipSIRS, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition
  • the methods, apparatus and kits are useful for diagnosing that inSIRS or ipSIRS is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from inSIRS and ipSIRS, wherein: (i) at least four IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition,
  • the methods, apparatus and kits are useful for diagnosing that mild sepsis or severe sepsis is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from mild sepsis and severe sepsis, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition
  • the methods, apparatus and kits are useful for diagnosing that mild sepsis or septic shock is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from mild sepsis and septic shock, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the
  • the methods, apparatus and kits are useful for diagnosing that severe sepsis or septic shock is present or absent in the biological subject, which suitably involve: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one IRS biomarker of a biological subject; (b) determining the indicator using a combination of the plurality of IRS biomarker values, the at least one indicator being at least partially indicative of the presence, absence, degree or prognosis of the at least one condition selected from severe sepsis and septic shock, wherein: (i) at least two IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the
  • diagnosis As used herein, the terms “diagnosis”, “diagnosing” and the like are used interchangeable herein to encompass determining the likelihood that a subject will develop a condition, or the existence or nature of a condition in a subject. These terms also encompass determining the severity of disease or episode of disease, as well as in the context of rational therapy, in which the diagnosis guides therapy, including initial selection of therapy, modification of therapy (e.g., adjustment of dose or dosage regimen), and the like.
  • likelihood is meant a measure of whether a biological subject with particular measured or derived biomarker values actually has a condition (or not) based on a given mathematical model. An increased likelihood for example may be relative or absolute and may be expressed qualitatively or quantitatively.
  • an increased likelihood may be determined simply by determining the subject's measured or derived biomarker values for at least two IRS biomarkers and placing the subject in an “increased likelihood” category, based upon previous population studies.
  • the term “likelihood” is also used interchangeably herein with the term “probability”.
  • the biomarkers are obtained from a biological sample.
  • biological sample refers to a sample that may be extracted, untreated, treated, diluted or concentrated from an animal.
  • the biological sample is suitably a biological fluid such as whole blood, serum, plasma, saliva, urine, sweat, ascitic fluid, peritoneal fluid, synovial fluid, amniotic fluid, cerebrospinal fluid, tissue biopsy, and the like.
  • the biological sample contains blood, especially peripheral blood, or a fraction or extract thereof.
  • the biological sample comprises blood cells such as mature, immature or developing leukocytes, including lymphocytes, polymorphonuclear leukocytes, neutrophils, monocytes, reticulocytes, basophils, coelomocytes, hemocytes, eosinophils, megakaryocytes, macrophages, dendritic cells natural killer cells, or fraction of such cells (e.g., a nucleic acid or protein fraction).
  • the biological sample comprises leukocytes including peripheral blood mononuclear cells (PBMC).
  • PBMC peripheral blood mononuclear cells
  • nucleic acid or “polynucleotide” as used herein includes RNA, mRNA, miRNA, cRNA, cDNA mtDNA, or DNA.
  • the term typically refers to a polymeric form of nucleotides of at least 10 bases in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
  • the term includes single and double stranded forms of DNA or RNA.
  • Protein “Protein”, “polypeptide” and “peptide” are used interchangeably herein to refer to a polymer of amino acid residues and to variants and synthetic analogues of the same.
  • biomarker signatures are determined through analysis of measured or derived IRS biomarker values for IRS biomarkers of one or more control subjects that have or do not have a condition. These biomarkers are referred to herein as “reference IRS biomarkers”.
  • individual control subjects are selected from “healthy control subjects”, “non-healthy control subjects”, “SIRS control subjects”, “inSIRS control subjects”, “ipSIRS control subjects”, “control subjects with a particular stage of ipSIRS”, illustrative examples of which include “mild sepsis control subjects”, “severe sepsis control subjects” and “septic shock control subjects”, etc.), which are also referred to herein as control groups (e.g., “healthy control group”, “non-healthy control group”, “SIRS control group”, “inSIRS control group”, “ipSIRS control group”, “ipSIRS stage group”, illustrative examples of which include “mild sepsis control group”, “severe sepsis control group”, and “septic shock control group”, etc.).
  • control groups e.g., “healthy control group”, “non-healthy control group”, “SIRS control group”, “inSIRS control group”, “ipS
  • an individual measured or derived IRS biomarker value corresponds to the level or amount of a respective IRS biomarker or to a function that is applied to that level or amount.
  • level and “amount” are used interchangeably herein to refer to a quantitative amount (e.g., weight or moles), a semi-quantitative amount, a relative amount (e.g., weight % or mole % within class), a concentration, and the like. Thus, these terms encompass absolute or relative amounts or concentrations of IRS biomarkers in a sample.
  • the presence, absence, degree or prognosis of at least one condition in a biological subject is established by determining a plurality of IRS biomarker values, wherein each IRS biomarker value is indicative of a value measured or derived for at least one IRS biomarker in a biological sample obtained from the biological subject.
  • sample IRS biomarkers are referred to herein as “sample IRS biomarkers”.
  • a sample IRS biomarker corresponds to a reference IRS biomarker (also referred to herein as a “corresponding IRS biomarker”).
  • corresponding IRS biomarker is meant an IRS biomarker that is structurally and/or functionally similar to a reference IRS biomarker.
  • Representative corresponding IRS biomarkers include expression products of allelic variants (same locus), homologues (different locus), and orthologues (different organism) of reference IRS biomarker genes.
  • Nucleic acid variants of reference IRS biomarker genes and encoded IRS biomarker polynucleotide expression products can contain nucleotide substitutions, deletions, inversions and/or insertions. Variation can occur in either or both the coding and non-coding regions. The variations can produce both conservative and non-conservative amino acid substitutions (as compared in the encoded product).
  • conservative variants include those sequences that, because of the degeneracy of the genetic code, encode the amino acid sequence of a reference IRS polypeptide.
  • variants of a particular IRS biomarker gene or polynucleotide will have at least about 40%, 45%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59% 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69% 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to that particular nucleotide sequence as determined by sequence alignment programs known in the art using default parameters.
  • the IRS biomarker gene or polynucleotide displays at least about 40%, 45%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59% 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69% 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to a nucleotide sequence selected from any one of SEQ ID NO: 1-1650, as summarized in Table 1.
  • Corresponding IRS biomarkers also include amino acid sequences that display substantial sequence similarity or identity to the amino acid sequence of a reference IRS biomarker polypeptide.
  • an amino acid sequence that corresponds to a reference amino acid sequence will display at least about 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 97, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% or even up to 100% sequence similarity or identity to a reference amino acid sequence selected from any one of SEQ ID NO: 1651-3284, as summarized in Table 2.
  • calculations of sequence similarity or sequence identity between sequences are performed as follows:
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 30%, usually at least 40%, more usually at least 50%, 60%, and even more usually at least 70%, 80%, 90%, 100% of the length of the reference sequence.
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • the percentage identity between the two sequences is a function of the number of identical amino acid residues shared by the sequences at individual positions, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the percentage similarity between the two sequences is a function of the number of identical and similar amino acid residues shared by the sequences at individual positions, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percentage identity or percentage similarity between sequences can be accomplished using a mathematical algorithm.
  • the percentage identity or similarity between amino acid sequences is determined using the Needleman and Wunsch, (1970 , J. Mol. Biol. 48: 444-453) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • An non-limiting set of parameters includes a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.
  • the percentage identity or similarity between amino acid or nucleotide sequences can be determined using the algorithm of E. Meyers and W. Miller (1989 , Cabios, 4: 11-17) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • nucleic acid and protein sequences described herein can be used as a “query sequence” to perform a search against public databases to, for example, identify other family members or related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al., (1990 , J Mol Biol., 215: 403-10).
  • Gapped BLAST can be utilized as described in Altschul et al., (1997 , Nucleic Acids Res, 25: 3389-3402).
  • the default parameters of the respective programs e.g., XBLAST and NBLAST.
  • Corresponding IRS biomarker polynucleotides also include nucleic acid sequences that hybridize to reference IRS biomarker polynucleotides, or to their complements, under stringency conditions described below.
  • the term “hybridizes under low stringency, medium stringency, high stringency, or very high stringency conditions” describes conditions for hybridization and washing.
  • “Hybridization” is used herein to denote the pairing of complementary nucleotide sequences to produce a DNA-DNA hybrid or a DNA-RNA hybrid.
  • Complementary base sequences are those sequences that are related by the base-pairing rules. In DNA, A pairs with T and C pairs with G. In RNA, U pairs with A and C pairs with G.
  • match and “mismatch” as used herein refer to the hybridization potential of paired nucleotides in complementary nucleic acid strands. Matched nucleotides hybridize efficiently, such as the classical A-T and G-C base pair mentioned above. Mismatches are other combinations of nucleotides that do not hybridize efficiently.
  • Reference herein to low stringency conditions include and encompass from at least about 1% v/v to at least about 15% v/v formamide and from at least about 1 M to at least about 2 M salt for hybridization at 42° C., and at least about 1 M to at least about 2 M salt for washing at 42° C.
  • Low stringency conditions also may include 1% Bovine Serum Albumin (BSA), 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65° C., and (i) 2 ⁇ SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO 4 (pH 7.2), 5% SDS for washing at room temperature.
  • BSA Bovine Serum Albumin
  • 1 mM EDTA 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65° C.
  • 2 ⁇ SSC 0.1% SDS
  • BSA Bovine Serum Albumin
  • BSA Bovine Serum Albumin
  • SSC sodium chloride/sodium citrate
  • Medium stringency conditions include and encompass from at least about 16% v/v to at least about 30% v/v formamide and from at least about 0.5 M to at least about 0.9 M salt for hybridization at 42° C., and at least about 0.1 M to at least about 0.2 M salt for washing at 55° C.
  • Medium stringency conditions also may include 1% Bovine Serum Albumin (BSA), 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65° C., and (i) 2 ⁇ SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO 4 (pH 7.2), 5% SDS for washing at 60-65° C.
  • BSA Bovine Serum Albumin
  • 1 mM EDTA 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65° C.
  • 2 ⁇ SSC 0.1% SDS
  • medium stringency conditions includes hybridizing in 6 ⁇ SSC at about 45° C., followed by one or more washes in 0.2 ⁇ SSC, 0.1% SDS at 60° C.
  • High stringency conditions include and encompass from at least about 31% v/v to at least about 50% v/v formamide and from about 0.01 M to about 0.15 M salt for hybridization at 42° C., and about 0.01 M to about 0.02 M salt for washing at 55° C.
  • High stringency conditions also may include 1% BSA, 1 mM EDTA, 0.5 M NaHPO 4 (pH 7.2), 7% SDS for hybridization at 65° C., and (i) 0.2 ⁇ SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO 4 (pH 7.2), 1% SDS for washing at a temperature in excess of 65° C.
  • One embodiment of high stringency conditions includes hybridizing in 6 ⁇ SSC at about 45° C., followed by one or more washes in 0.2 ⁇ SSC, 0.1% SDS at 65° C.
  • a corresponding IRS biomarker polynucleotide is one that hybridizes to a disclosed nucleotide sequence under very high stringency conditions.
  • very high stringency conditions includes hybridizing 0.5 M sodium phosphate, 7% SDS at 65° C., followed by one or more washes at 0.2 ⁇ SSC, 1% SDS at 65° C.
  • the IRS biomarkers disclosed herein each have significant sensitivity and specificity for diagnosing the presence, absence or degree of at least condition selected from a healthy condition (e.g., a normal condition or one in which inSIRS and inSIRS are absent), inSIRS, ipSIRS or a stage of ipSIRS (e.g., a stage of ipSIRS with a particular severity such as mild sepsis, severe sepsis and septic shock). Accordingly, it is feasible to use individual IRS biomarkers in methods, apparatus and kits that do not rely on the use of low mutual correlation between biomarkers to diagnose the presence, absence or degree of the at least condition.
  • a healthy condition e.g., a normal condition or one in which inSIRS and inSIRS are absent
  • inSIRS e.g., a normal condition or one in which inSIRS and inSIRS are absent
  • ipSIRS or a stage of ipSIRS
  • the invention contemplates methods, kits and apparatus that are useful for diagnosing that inSIRS or a healthy condition is present or absent in a biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from inSIRS and a healthy condition, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group A and group B IRS biomarker genes as defined herein.
  • the methods, apparatus and kits are useful for diagnosing that ipSIRS or a healthy condition is present or absent in the biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from ipSIRS and a healthy condition, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group C and group D IRS biomarker genes as defined herein.
  • the methods, apparatus and kits are useful for diagnosing that inSIRS or ipSIRS is present or absent in the biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from inSIRS and ipSIRS, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group E and group F IRS biomarker genes as defined herein.
  • the methods, apparatus and kits are useful for diagnosing that mild sepsis or severe sepsis is present or absent in the biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from mild sepsis and severe sepsis, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group K and group L IRS biomarker genes as defined herein.
  • the methods, apparatus and kits are useful for diagnosing that mild sepsis or septic shock is present or absent in the biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from mild sepsis and septic shock, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group M and group N IRS biomarker genes as defined herein.
  • the methods, apparatus and kits are useful for diagnosing that severe sepsis or septic shock is present or absent in the biological subject, which suitably involve: (1) correlating a reference biomarker signature with the presence or absence of a condition selected from severe sepsis and septic shock, wherein the reference biomarker signature evaluates at least one IRS biomarker; (2) obtaining a biomarker signature of a sample from a subject, wherein the sample biomarker signature evaluates for an individual IRS biomarker in the reference biomarker signature a corresponding IRS biomarker; and (3) diagnosing the presence or absence of the condition in the subject based on the sample biomarker signature and the reference biomarker signature, wherein an individual IRS biomarker is an expression product of an IRS biomarker gene selected from the group O and group P IRS biomarker genes as defined herein.
  • the biomarkers may be quantified or detected using any suitable technique.
  • the biomarkers including the IRS biomarkers, are quantified using reagents that determine the level or abundance of individual biomarkers.
  • Non-limiting reagents of this type include reagents for use in nucleic acid- and protein-based assays.
  • nucleic acid is isolated from cells contained in the biological sample according to standard methodologies (Sambrook, et al., 1989, supra; and Ausubel et al., 1994, supra).
  • the nucleic acid is typically fractionated (e.g., poly A + RNA) or whole cell RNA. Where RNA is used as the subject of detection, it may be desired to convert the RNA to a complementary DNA.
  • the nucleic acid is amplified by a template-dependent nucleic acid amplification technique. A number of template dependent processes are available to amplify the IRS biomarker sequences present in a given template sample.
  • PCR polymerase chain reaction
  • the primers will bind to the biomarker and the polymerase will cause the primers to be extended along the biomarker sequence by adding on nucleotides. By raising and lowering the temperature of the reaction mixture, the extended primers will dissociate from the biomarker to form reaction products, excess primers will bind to the biomarker and to the reaction products and the process is repeated.
  • a reverse transcriptase PCR amplification procedure may be performed in order to quantify the amount of mRNA amplified. Methods of reverse transcribing RNA into cDNA are well known and described in Sambrook et al., 1989, supra. Alternative methods for reverse transcription utilize thermostable, RNA-dependent DNA polymerases. These methods are described in WO 90/07641. Polymerase chain reaction methodologies are well known in the art.
  • the template-dependent amplification involves quantification of transcripts in real-time.
  • RNA or DNA may be quantified using the Real-Time PCR technique (Higuchi, 1992, et al., Biotechnology 10: 413-417).
  • the concentration of the amplified products of the target DNA in PCR reactions that have completed the same number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA mixture. If the DNA mixtures are cDNAs synthesized from RNAs isolated from different tissues or cells, the relative abundance of the specific mRNA from which the target sequence was derived can be determined for the respective tissues or cells.
  • MT-PCR multiplexed, tandem PCR
  • RNA is converted into cDNA and amplified using multiplexed gene specific primers.
  • each individual gene is quantitated by real time PCR.
  • target nucleic acids are quantified using blotting techniques, which are well known to those of skill in the art.
  • Southern blotting involves the use of DNA as a target
  • Northern blotting involves the use of RNA as a target.
  • a probe is used to target a DNA or RNA species that has been immobilized on a suitable matrix, often a filter of nitrocellulose.
  • the different species should be spatially separated to facilitate analysis. This often is accomplished by gel electrophoresis of nucleic acid species followed by “blotting” on to the filter.
  • the blotted target is incubated with a probe (usually labeled) under conditions that promote denaturation and rehybridization. Because the probe is designed to base pair with the target, the probe will bind a portion of the target sequence under renaturing conditions. Unbound probe is then removed, and detection is accomplished as described above. Following detection/quantification, one may compare the results seen in a given subject with a control reaction or a statistically significant reference group or population of control subjects as defined herein. In this way, it is possible to correlate the amount of an IRS biomarker nucleic acid detected with the progression or severity of the disease.
  • probe refers to a molecule that binds to a specific sequence or sub-sequence or other moiety of another molecule. Unless otherwise indicated, the term “probe” typically refers to a nucleic acid probe that binds to another nucleic acid, also referred to herein as a “target polynucleotide”, through complementary base pairing. Probes can bind target polynucleotides lacking complete sequence complementarity with the probe, depending on the stringency of the hybridization conditions. Probes can be labeled directly or indirectly and include primers within their scope.
  • primer an oligonucleotide which, when paired with a strand of DNA, is capable of initiating the synthesis of a primer extension product in the presence of a suitable polymerizing agent.
  • the primer is preferably single-stranded for maximum efficiency in amplification but can alternatively be double-stranded.
  • a primer must be sufficiently long to prime the synthesis of extension products in the presence of the polymerization agent. The length of the primer depends on many factors, including application, temperature to be employed, template reaction conditions, other reagents, and source of primers.
  • the primer may be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, 500, to one base shorter in length than the template sequence at the 3′ end of the primer to allow extension of a nucleic acid chain, though the 5′ end of the primer may extend in length beyond the 3′ end of the template sequence.
  • primers can be large polynucleotides, such as from about 35 nucleotides to several kilobases or more.
  • Primers can be selected to be “substantially complementary” to the sequence on the template to which it is designed to hybridize and serve as a site for the initiation of synthesis.
  • substantially complementary it is meant that the primer is sufficiently complementary to hybridize with a target polynucleotide.
  • the primer contains no mismatches with the template to which it is designed to hybridize but this is not essential.
  • non-complementary nucleotide residues can be attached to the 5′ end of the primer, with the remainder of the primer sequence being complementary to the template.
  • non-complementary nucleotide residues or a stretch of non-complementary nucleotide residues can be interspersed into a primer, provided that the primer sequence has sufficient complementarity with the sequence of the template to hybridize therewith and thereby form a template for synthesis of the extension product of the primer.
  • biochip-based technologies such as those described by Hacia et al. (1996 , Nature Genetics 14: 441-447) and Shoemaker et al. (1996 , Nature Genetics 14: 450-456). Briefly, these techniques involve quantitative methods for analyzing large numbers of genes rapidly and accurately. By tagging genes with oligonucleotides or using fixed nucleic acid probe arrays, one can employ biochip technology to segregate target molecules as high-density arrays and screen these molecules on the basis of hybridization. See also Pease et al. (1994 , Proc. Natl. Acad. Sci. U.S.A. 91: 5022-5026); Fodor et al. (1991 , Science 251: 767-773).
  • nucleic acid probes to IRS biomarker polynucleotides are made and attached to biochips to be used in screening and diagnostic methods, as outlined herein.
  • the nucleic acid probes attached to the biochip are designed to be substantially complementary to specific expressed IRS biomarker nucleic acids, i.e., the target sequence (either the target sequence of the sample or to other probe sequences, for example in sandwich assays), such that hybridization of the target sequence and the probes of the present invention occur.
  • This complementarity need not be perfect; there may be any number of base pair mismatches, which will interfere with hybridization between the target sequence and the nucleic acid probes of the present invention.
  • the sequence is not a complementary target sequence.
  • more than one probe per sequence is used, with either overlapping probes or probes to different sections of the target being used. That is, two, three, four or more probes, with three being desirable, are used to build in a redundancy for a particular target.
  • the probes can be overlapping (i.e. have some sequence in common), or separate.
  • oligonucleotide probes on the biochip are exposed to or contacted with a nucleic acid sample suspected of containing one or more IRS biomarker polynucleotides under conditions favoring specific hybridization.
  • Sample extracts of DNA or RNA may be prepared from fluid suspensions of biological materials, or by grinding biological materials, or following a cell lysis step which includes, but is not limited to, lysis effected by treatment with SDS (or other detergents), osmotic shock, guanidinium isothiocyanate and lysozyme.
  • Suitable DNA which may be used in the method of the invention, includes cDNA. Such DNA may be prepared by any one of a number of commonly used protocols as for example described in Ausubel, et al., 1994, supra, and Sambrook, et al., 1989, supra.
  • RNA which may be used in the method of the invention, includes messenger RNA, complementary RNA transcribed from DNA (cRNA) or genomic or subgenomic RNA.
  • cRNA complementary RNA transcribed from DNA
  • genomic or subgenomic RNA Such RNA may be prepared using standard protocols as for example described in the relevant sections of Ausubel, et al. 1994, supra and Sambrook, et al. 1989, supra).
  • cDNA may be fragmented, for example, by sonication or by treatment with restriction endonucleases.
  • cDNA is fragmented such that resultant DNA fragments are of a length greater than the length of the immobilized oligonucleotide probe(s) but small enough to allow rapid access thereto under suitable hybridization conditions.
  • fragments of cDNA may be selected and amplified using a suitable nucleotide amplification technique, as described for example above, involving appropriate random or specific primers.
  • target IRS biomarker polynucleotides are detectably labeled so that their hybridization to individual probes can be determined.
  • the target polynucleotides are typically detectably labeled with a reporter molecule illustrative examples of which include chromogens, catalysts, enzymes, fluorochromes, chemiluminescent molecules, bioluminescent molecules, lanthanide ions (e.g., Eu 34 ), a radioisotope and a direct visual label.
  • a reporter molecule illustrative examples of which include chromogens, catalysts, enzymes, fluorochromes, chemiluminescent molecules, bioluminescent molecules, lanthanide ions (e.g., Eu 34 ), a radioisotope and a direct visual label.
  • a direct visual label use may be made of a colloidal metallic or non-metallic particle, a dye particle, an enzyme or a substrate, an organic polymer, a latex particle, a liposome, or other vesicle containing a signal producing substance and the like.
  • Illustrative labels of this type include large colloids, for example, metal colloids such as those from gold, selenium, silver, tin and titanium oxide.
  • an enzyme is used as a direct visual label
  • biotinylated bases are incorporated into a target polynucleotide.
  • the hybrid-forming step can be performed under suitable conditions for hybridizing oligonucleotide probes to test nucleic acid including DNA or RNA.
  • suitable conditions for hybridizing oligonucleotide probes to test nucleic acid including DNA or RNA.
  • whether hybridization takes place is influenced by the length of the oligonucleotide probe and the polynucleotide sequence under test, the pH, the temperature, the concentration of mono- and divalent cations, the proportion of G and C nucleotides in the hybrid-forming region, the viscosity of the medium and the possible presence of denaturants.
  • Such variables also influence the time required for hybridization.
  • the preferred conditions will therefore depend upon the particular application. Such empirical conditions, however, can be routinely determined without undue experiment
  • the probes are washed to remove any unbound nucleic acid with a hybridization buffer. This washing step leaves only bound target polynucleotides. The probes are then examined to identify which probes have hybridized to a target polynucleotide.
  • a signal may be instrumentally detected by irradiating a fluorescent label with light and detecting fluorescence in a fluorimeter; by providing for an enzyme system to produce a dye which could be detected using a spectrophotometer; or detection of a dye particle or a colored colloidal metallic or non-metallic particle using a reflectometer; in the case of using a radioactive label or chemiluminescent molecule employing a radiation counter or autoradiography.
  • a detection means may be adapted to detect or scan light associated with the label which light may include fluorescent, luminescent, focused beam or laser light.
  • a charge couple device (CCD) or a photocell can be used to scan for emission of light from a probe:target polynucleotide hybrid from each location in the micro-array and record the data directly in a digital computer.
  • electronic detection of the signal may not be necessary.
  • the detection means is suitably interfaced with pattern recognition software to convert the pattern of signals from the array into a plain language genetic profile.
  • oligonucleotide probes specific for different IRS biomarker polynucleotides are in the form of a nucleic acid array and detection of a signal generated from a reporter molecule on the array is performed using a ‘chip reader’.
  • a detection system that can be used by a ‘chip reader’ is described for example by Pirrung et al. (U.S. Pat. No. 5,143,854).
  • the chip reader will typically also incorporate some signal processing to determine whether the signal at a particular array position or feature is a true positive or maybe a spurious signal.
  • Exemplary chip readers are described for example by Fodor et al. (U.S. Pat. No. 5,925,525).
  • the reaction may be detected using flow cytometry.
  • the IRS biomarker is a target RNA (e.g., mRNA) or a DNA copy of the target RNA whose level is measured using at least one nucleic acid probe that hybridizes under at least low, medium, or high stringency conditions to the target RNA or to the DNA copy, wherein the nucleic acid probe comprises at least 15 (e.g., 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more) contiguous nucleotides of an IRS biomarker polynucleotide.
  • the measured level or abundance of the target RNA or its DNA copy is normalized to the level or abundance of a reference RNA or a DNA copy of the reference RNA.
  • the nucleic acid probe is immobilized on a solid or semi-solid support.
  • the nucleic acid probe forms part of a spatial array of nucleic acid probes.
  • the level of nucleic acid probe that is bound to the target RNA or to the DNA copy is measured by hybridization (e.g., using a nucleic acid array).
  • the level of nucleic acid probe that is bound to the target RNA or to the DNA copy is measured by nucleic acid amplification (e.g., using a polymerase chain reaction (PCR)).
  • the level of nucleic acid probe that is bound to the target RNA or to the DNA copy is measured by nuclease protection assay.
  • IRS biomarker protein levels are assayed using protein-based assays known in the art.
  • an IRS biomarker protein is an enzyme
  • the protein can be quantified based upon its catalytic activity or based upon the number of molecules of the protein contained in a sample.
  • Antibody-based techniques may be employed including, for example, immunoassays, such as the enzyme-linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA).
  • protein-capture arrays that permit simultaneous detection and/or quantification of a large number of proteins are employed.
  • low-density protein arrays on filter membranes such as the universal protein array system (Ge, 2000 Nucleic Acids Res. 28(2):e3) allow imaging of arrayed antigens using standard ELISA techniques and a scanning charge-coupled device (CCD) detector
  • CCD scanning charge-coupled device
  • Immuno-sensor arrays have also been developed that enable the simultaneous detection of clinical analytes. It is now possible using protein arrays, to profile protein expression in bodily fluids, such as in sera of healthy or diseased subjects, as well as in subjects pre- and post-drug treatment.
  • Exemplary protein capture arrays include arrays comprising spatially addressed antigen-binding molecules, commonly referred to as antibody arrays, which can facilitate extensive parallel analysis of numerous proteins defining a proteome or subproteome.
  • Antibody arrays have been shown to have the required properties of specificity and acceptable background, and some are available commercially (e.g., BD Biosciences, Clontech, Bio-Rad and Sigma).
  • Various methods for the preparation of antibody arrays have been reported (see, e.g., Lopez et al., 2003 J. Chromatogram. B 787:19-27; Cahill, 2000 Trends in Biotechnology 7:47-51; U.S. Pat. App. Pub. 2002/0055186; U.S. Pat. App. Pub.
  • the antigen-binding molecules of such arrays may recognize at least a subset of proteins expressed by a cell or population of cells, illustrative examples of which include growth factor receptors, hormone receptors, neurotransmitter receptors, catecholamine receptors, amino acid derivative receptors, cytokine receptors, extracellular matrix receptors, antibodies, lectins, cytokines, serpins, proteases, kinases, phosphatases, ras-like GTPases, hydrolases, steroid hormone receptors, transcription factors, heat-shock transcription factors, DNA-binding proteins, zinc-finger proteins, leucine-zipper proteins, homeodomain proteins, intracellular signal transduction modulators and effectors, apoptosis-related factors, DNA synthesis factors, DNA repair factors, DNA recombination factors and cell-surface antigens.
  • growth factor receptors include growth factor receptors, hormone receptors, neurotransmitter receptors, catecholamine receptors, amino acid derivative receptors, cytokine receptor
  • a support surface which is generally planar or contoured.
  • Common physical supports include glass slides, silicon, microwells, nitrocellulose or PVDF membranes, and magnetic and other microbeads.
  • Particles in suspension can also be used as the basis of arrays, providing they are coded for identification; systems include color coding for microbeads (e.g., available from Luminex, Bio-Rad and Nanomics Biosystems) and semiconductor nanocrystals (e.g., QDotsTM, available from Quantum Dots), and barcoding for beads (UltraPlexTM, available from Smartbeads) and multimetal microrods (NanobarcodesTM particles, available from Surromed). Beads can also be assembled into planar arrays on semiconductor chips (e.g., available from LEAPS technology and BioArray Solutions). Where particles are used, individual protein-capture agents are typically attached to an individual particle to provide the spatial definition or separation of the array. The particles may then be assayed separately, but in parallel, in a compartmentalized way, for example in the wells of a microtiter plate or in separate test tubes.
  • color coding for microbeads e.g., available from
  • a protein sample which is optionally fragmented to form peptide fragments (see, e.g., U.S. Pat. App. Pub. 2002/0055186), is delivered to a protein-capture array under conditions suitable for protein or peptide binding, and the array is washed to remove unbound or non-specifically bound components of the sample from the array.
  • the presence or amount of protein or peptide bound to each feature of the array is detected using a suitable detection system.
  • the amount of protein bound to a feature of the array may be determined relative to the amount of a second protein bound to a second feature of the array. In certain embodiments, the amount of the second protein in the sample is already known or known to be invariant.
  • the IRS biomarker is a target polypeptide whose level is measured using at least one antigen-binding molecule that is immuno-interactive with the target polypeptide.
  • the measured level of the target polypeptide is normalized to the level of a reference polypeptide.
  • the antigen-binding molecule is immobilized on a solid or semi-solid support.
  • the antigen-binding molecule forms part of a spatial array of antigen-binding molecule.
  • the level of antigen-binding molecule that is bound to the target polypeptide is measured by immunoassay (e.g., using an ELISA).
  • immunoassay e.g., using an ELISA.
  • Reference herein to “immuno-interactive” includes reference to any interaction, reaction, or other form of association between molecules and in particular where one of the molecules is, or mimics, a component of the immune system.
  • kits comprises: (i) a reagent that allows quantification (e.g., determining the level or abundance) of a first biomarker; and (ii) a reagent that allows quantification (e.g., determining the level or abundance) of a second biomarker, wherein the first and second biomarkers have a mutual correlation in respect of at least one condition (e.g., at least one of a healthy condition and one or more diseases such as but not limited to inSIRS, ipSIRS or a stage of ipSIRS (e.g., a stage of ipSIRS with a particular severity such as mild sepsis, severe sepsis and septic shock)) that lies within a mutual correlation range of between ⁇ 0.9, and wherein a combination of respective biomarker values for the first and second bio
  • the kit further comprises (iii) a reagent that allows quantification (e.g., determining the level or abundance) of a third biomarker; and (iv) a reagent that allows quantification (e.g., determining the level or abundance) of a fourth biomarker, wherein the third and fourth biomarkers have a mutual correlation in respect of at the least one condition that lies within a mutual correlation range of between ⁇ 0.9, and wherein a combination of respective biomarker values for the third and fourth biomarkers that are measured for or derived from a biological subject has a performance value greater than or equal to a performance threshold representing the ability of the combination of the third and fourth biomarkers to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the performance threshold being a variance explained of at least 0.3.
  • kits of the present invention are useful for diagnosing the presence, absence or degree of at least one condition, or for providing a prognosis for at least one condition, wherein the at least one condition is selected from a healthy condition, inSIRS, ipSIRS or a stage of ipSIRS.
  • IRS biomarkers are suitably selected from a group as broadly described above and elsewhere herein.
  • kits are understood to mean a product containing the different reagents necessary for carrying out the methods of the invention packed so as to allow their transport and storage.
  • Materials suitable for packing the components of the kit include crystal, plastic (polyethylene, polypropylene, polycarbonate and the like), bottles, vials, paper, envelopes and the like.
  • the kits of the invention can contain instructions for the simultaneous, sequential or separate use of the different components contained in the kit.
  • the instructions can be in the form of printed material or in the form of an electronic support capable of storing instructions such that they can be read by a subject, such as electronic storage media (magnetic disks, tapes and the like), optical media (CD-ROM, DVD) and the like.
  • the media can contain Internet addresses that provide the instructions.
  • a “reagent that allows quantification of a biomarker” means a compound or material, or set of compounds or materials, which allow quantification of the biomarker.
  • the compound, material or set of compounds or materials permit determining the expression level of a gene (e.g., an IRS biomarker gene), including without limitation the extraction of RNA material, the determination of the level of a corresponding RNA, etc., primers for the synthesis of a corresponding cDNA, primers for amplification of DNA, and/or probes capable of specifically hybridizing with the RNAs (or the corresponding cDNAs) encoded by the genes, TaqMan probes, etc.
  • a gene e.g., an IRS biomarker gene
  • kits may also optionally include appropriate reagents for detection of labels, positive and negative controls, washing solutions, blotting membranes, microtiter plates, dilution buffers and the like.
  • a nucleic acid-based detection kit may include (i) a biomarker polynucleotide (e.g., an IRS biomarker polynucleotide) (which may be used as a positive control), (ii) a primer or probe that specifically hybridizes to a biomarker polynucleotide (e.g., an IRS biomarker polynucleotide).
  • kits may comprise, in suitable means, distinct containers for each individual reagent and enzyme as well as for each primer or probe.
  • enzymes suitable for amplifying nucleic acids including various polymerases (reverse transcriptase, Taq, SequenaseTM, DNA ligase etc. depending on the nucleic acid amplification technique employed), deoxynucleotides and buffers to provide the necessary reaction mixture for amplification.
  • Such kits also generally will comprise, in suitable means, distinct containers for each individual reagent and enzyme as well as for each primer or probe.
  • a protein-based detection kit may include (i) a biomarker polypeptide (e.g., an IRS biomarker polypeptide) (which may be used as a positive control), (ii) an antibody that binds specifically to a biomarker polypeptide (e.g., an IRS biomarker polypeptide).
  • the kit can also feature various devices (e.g., one or more) and reagents (e.g., one or more) for performing one of the assays described herein; and/or printed instructions for using the kit to quantify the expression of a biomarker gene (e.g., an IRS biomarker gene).
  • microarray refers to an arrangement of hybridizable array elements, e.g., probes (including primers), ligands, biomarker nucleic acid sequence or protein sequences on a substrate.
  • a reverse transcriptase may be used to reverse transcribe RNA transcripts, including mRNA, in a nucleic acid sample, to produce reverse transcribed transcripts, including reverse transcribed mRNA (also referred to as “cDNA”).
  • the nucleic acid sample is suitably derived from components of the immune system, representative examples of which include components of the innate and adaptive immune systems as broadly discussed for example above.
  • the reverse transcribed RNA is derived blood cells (e.g., peripheral blood cells).
  • the reverse transcribed RNA is derived leukocytes.
  • oligonucleotide primers that hybridize to the reverse transcribed transcript can be used to amplify at least a portion of the reverse transcribed transcript via a suitable nucleic acid amplification technique, e.g., RT-PCR or Q PCR techniques described herein.
  • oligonucleotide probes may be used to hybridize to the reverse transcribed transcript for the quantification, using a nucleic acid hybridization analysis technique (e.g., microarray analysis), as described for example above.
  • a respective oligonucleotide primer or probe is hybridized to a complementary nucleic acid sequence of a reverse transcribed transcript in the compositions of the invention.
  • the compositions typically comprise labeled reagents for detecting and/or quantifying the reverse transcribed transcripts.
  • Representative reagents of this type include labeled oligonucleotide primers or probes that hybridize to RNA transcripts or reverse transcribed RNA, labeled RNA, labeled reverse transcribed RNA as well as labeled oligonucleotide linkers or tags (e.g., a labeled RNA or DNA linker or tag) for labeling (e.g., end labeling such as 3′ end labeling) RNA or reverse transcribed RNA.
  • the primers, probes, RNA or reverse transcribed RNA i.e., cDNA
  • Representative reagents of this type include labeled oligonucleotide primers or probes that hybridize to reverse transcribed and transcripts as well as labeled reverse transcribed transcripts.
  • the label can be any reporter molecule as known in the art, illustrative examples of which are described above and elsewhere herein.
  • the present invention also encompasses non-reverse transcribed RNA embodiments in which cDNA is not made and the RNA transcripts are directly the subject of the analysis.
  • reagents are suitably used to quantify RNA transcripts directly.
  • oligonucleotide probes can be used to hybridize to transcripts for quantification of immune system biomarkers of the invention, using a nucleic acid hybridization analysis technique (e.g., microarray analysis), as described for example above.
  • a respective oligonucleotide probe is hybridized to a complementary nucleic acid sequence of an immune system biomarker transcript in the compositions of the invention.
  • compositions may comprise labeled reagents that hybridize to transcripts for detecting and/or quantifying the transcripts.
  • Representative reagents of this type include labeled oligonucleotide probes that hybridize to transcripts as well as labeled transcripts.
  • the primers or probes may be immobilized or free in solution.
  • immobilized means that a molecular species of interest is fixed to a solid support, suitably by covalent linkage. This covalent linkage can be achieved by different means depending on the molecular nature of the molecular species. Moreover, the molecular species may be also fixed on the solid support by electrostatic forces, hydrophobic or hydrophilic interactions or Van-der-Waals forces. The above described physico-chemical interactions typically occur in interactions between molecules.
  • the molecules remain immobilized or attached to a support under conditions in which it is intended to use the support, for example in applications requiring nucleic acid amplification and/or sequencing or in in antibody-binding assays.
  • oligonucleotides or primers are immobilized such that a 3′ end is available for enzymatic extension and/or at least a portion of the sequence is capable of hybridizing to a complementary sequence.
  • immobilization can occur via hybridization to a surface attached primer, in which case the immobilized primer or oligonucleotide may be in the 3′-5′ orientation.
  • immobilization can occur by means other than base-pairing hybridization, such as the covalent attachment.
  • solid support refers to a solid inert surface or body to which a molecular species, such as a nucleic acid and polypeptides can be immobilized.
  • solid supports include glass surfaces, plastic surfaces, latex, dextran, polystyrene surfaces, polypropylene surfaces, polyacrylamide gels, gold surfaces, and silicon wafers.
  • the solid supports are in the form of membranes, chips or particles.
  • the solid support may be a glass surface (e.g., a planar surface of a flow cell channel).
  • the solid support may comprise an inert substrate or matrix which has been “functionalized”, such as by applying a layer or coating of an intermediate material comprising reactive groups which permit covalent attachment to molecules such as polynucleotides.
  • such supports can include polyacrylamide hydrogels supported on an inert substrate such as glass.
  • the molecules e.g., polynucleotides
  • the intermediate material e.g., a hydrogel
  • the intermediate material can itself be non-covalently attached to the substrate or matrix (e.g., a glass substrate).
  • the support can include a plurality of particles or beads each having a different attached molecular species.
  • the present invention also extends to the management of inSIRS, ipSIRS or particular stages of ipSIRS, or prevention of further progression of inSIRS, ipSIRS or particular stages of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), or assessment of the efficacy of therapies in subjects following positive diagnosis for the presence of inSIRS, ipSIRS or particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock) in a subject.
  • inSIRS or ipSIRS conditions is generally highly intensive and can include identification and amelioration of the underlying cause and aggressive use of therapeutic compounds such as, vasoactive compounds, antibiotics, steroids, antibodies to endotoxin, anti-tumor necrosis factor agents, recombinant protein C.
  • palliative therapies as described for example in Cohen and Glauser (1991, Lancet 338: 736-739) aimed at restoring and protecting organ function can be used such as intravenous fluids and oxygen and tight glycemic control.
  • therapies for ipSIRS are reviewed in Healy (2002 , Ann Pharmacother. 36(4): 648-54) and Brindley (2005 , CJEM. 7(4): 227) and Jenkins (2006 , J Hosp Med. 1(5): 285-295).
  • the therapeutic agents will be administered in pharmaceutical (or veterinary) compositions together with a pharmaceutically acceptable carrier and in an effective amount to achieve their intended purpose.
  • the dose of active compounds administered to a subject should be sufficient to achieve a beneficial response in the subject over time such as a reduction in, or relief from, the symptoms of inSIRS, ipSIRS or particular stages of ipSIRS.
  • the quantity of the pharmaceutically active compounds(s) to be administered may depend on the subject to be treated inclusive of the age, sex, weight and general health condition thereof. In this regard, precise amounts of the active compound(s) for administration will depend on the judgment of the practitioner.
  • the medical practitioner or veterinarian may evaluate severity of any symptom associated with the presence of inSIRS, ipSIRS or particular stages of ipSIRS including, inflammation, blood pressure anomaly, tachycardia, tachypnea fever, chills, vomiting, diarrhea, skin rash, headaches, confusion, muscle aches, seizures.
  • severity of any symptom associated with the presence of inSIRS, ipSIRS or particular stages of ipSIRS including, inflammation, blood pressure anomaly, tachycardia, tachypnea fever, chills, vomiting, diarrhea, skin rash, headaches, confusion, muscle aches, seizures.
  • those of skill in the art may readily determine suitable dosages of the therapeutic agents and suitable treatment regimens without undue experimentation.
  • the therapeutic agents may be administered in concert with adjunctive (palliative) therapies to increase oxygen supply to major organs, increase blood flow to major organs and/or to reduce the inflammatory response.
  • adjunctive therapies include non-steroidal-anti-inflammatory drugs (NSAIDs), intravenous saline and oxygen.
  • the methods, apparatus and kits described above and elsewhere herein are contemplated for use in methods of treating, preventing or inhibiting the development of at least one condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis or septic shock) in a subject.
  • at least one condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS e.g., mild sepsis, severe sepsis or septic shock
  • These methods generally comprise: (a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker of a biological subject; (b) determining an indicator using a combination of the plurality of IRS biomarker values, the indicator being at least partially indicative of the presence, absence or degree of the at least one condition, wherein: (i) at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the indicator has a performance value greater than or equal to a performance threshold representing the ability of the indicator to diagnose the presence, absence or degree of the at least one condition, the performance threshold being indicative of an explained variance of at least 0.3; and (c) administering to the subject,
  • the treatment methods comprise: (1) determining a plurality of measured IRS biomarker values, each measured IRS biomarker value being a measured value of an IRS biomarker of the biological subject; and (2) applying a function to at least one of the measured IRS biomarker values to determine at least one derived IRS biomarker value, the at least one derived IRS biomarker value being indicative of a value of a corresponding derived IRS biomarker.
  • the function suitably includes at least one of: (a) multiplying two IRS biomarker values; (b) dividing two IRS biomarker values; (c) adding two IRS biomarker values; (d) subtracting two IRS biomarker values; (e) a weighted sum of at least two IRS biomarker values; (f) a log sum of at least two IRS biomarker values; and (g) a sigmoidal function of at least two IRS biomarker values.
  • the methods, apparatus and kits of the present invention are used for monitoring, treatment and management of conditions that can lead to inSIRS or ipSIRS, illustrative examples of which include retained placenta, meningitis, endometriosis, shock, toxic shock (i.e., sequelae to tampon use), gastroenteritis, appendicitis, ulcerative colitis, Crohn's disease, inflammatory bowel disease, acid gut syndrome, liver failure and cirrhosis, failure of colostrum transfer in neonates, ischemia (in any organ), bacteremia, infections within body cavities such as the peritoneal, pericardial, thecal, and pleural cavities, burns, severe wounds, excessive exercise or stress, hemodialysis, conditions involving intolerable pain (e.g., pancreatitis, kidney stones), surgical operations, and non-healing lesions.
  • inSIRS or ipSIRS illustrative examples of which include retained placenta, mening
  • the methods or kits of the present invention are typically used at a frequency that is effective to monitor the early development of inSIRS, ipSIRS or particular stages of ipSIRS, to thereby enable early therapeutic intervention and treatment of that condition.
  • the diagnostic methods or kits are used at least at 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 hour intervals or at least 1, 2, 3, 4, 5 or 6 day intervals, or at least weekly, fortnightly or monthly.
  • the present invention can be practiced in the field of predictive medicine for the purpose of diagnosis or monitoring the presence or development of a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS in a subject, and/or monitoring response to therapy efficacy.
  • biomarker signatures and corresponding indicators of the present invention further enable determination of endpoints in pharmacotranslational studies. For example, clinical trials can take many months or even years to establish the pharmacological parameters for a medicament to be used in treating or preventing inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock). However, these parameters may be associated with a biomarker signature and corresponding indicator of a health state (e.g., a healthy condition).
  • a health state e.g., a healthy condition
  • the clinical trial can be expedited by selecting a treatment regimen (e.g., medicament and pharmaceutical parameters), which results in a biomarker signature associated with a desired health state (e.g., healthy condition).
  • a treatment regimen e.g., medicament and pharmaceutical parameters
  • a biomarker signature associated with a desired health state e.g., healthy condition.
  • This may be determined for example by: a) determining a plurality of IRS biomarker values, each IRS biomarker value being indicative of a value measured or derived for at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker of a biological subject after treatment with a treatment regimen; (b) determining an indicator using a combination of the plurality of IRS biomarker values, the indicator being at least partially indicative of the presence, absence or degree of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, wherein: (i) at least two (e
  • this aspect of the present invention advantageously provides methods of monitoring the efficacy of a particular treatment regimen in a subject (for example, in the context of a clinical trial) already diagnosed with a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS.
  • These methods take advantage of measured or derived IRS biomarker values that correlate with treatment efficacy to determine, for example, whether measured or derived IRS biomarker values of a subject undergoing treatment partially or completely normalize during the course of or following therapy or otherwise shows changes associated with responsiveness to the therapy.
  • treatment regimen refers to prophylactic and/or therapeutic (i.e., after onset of a specified condition) treatments, unless the context specifically indicates otherwise.
  • treatment regimen encompasses natural substances and pharmaceutical agents (i.e., “drugs”) as well as any other treatment regimen including but not limited to dietary treatments, physical therapy or exercise regimens, surgical interventions, and combinations thereof.
  • the invention provides methods of correlating a biomarker signature with an effective treatment regimen for a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock), wherein the methods generally comprise: (a) determining a biomarker signature defining a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker values corresponding to values of at least two IRS biomarkers that can be measured for or derived from a biological subject having the condition and for whom an effective treatment has been identified, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of the condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence, absence or degree
  • correlating generally refers to determining a relationship between one type of data with another or with a state.
  • an indicator or biomarker signature is correlated to a global probability or a particular outcome, using receiver operating characteristic (ROC) curves.
  • ROC receiver operating characteristic
  • the invention further provides methods of determining whether a treatment regimen is effective for treating a subject with a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS (e.g., mild sepsis, severe sepsis and septic shock).
  • a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS e.g., mild sepsis, severe sepsis and septic shock.
  • These methods generally comprise: (a) determining a plurality of post-treatment IRS biomarker values, each post-treatment IRS biomarker value being indicative of a value measured or derived for at least one (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker of a biological subject after treatment with the treatment regimen; (b) determining a post-treatment indicator using a combination of the plurality of post-treatment IRS biomarker values, the post-treatment indicator being at least partially indicative of the presence, absence or degree of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, wherein: (i) at the least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarkers have a mutual correlation in respect of the at least one condition that lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the post-treatment indicator has a performance value greater than or equal to a performance threshold representing the
  • the invention can also be practiced to evaluate whether a subject is responding (i.e., a positive response) or not responding (i.e., a negative response) to a treatment regimen or has a side effect to a treatment regimen.
  • This aspect of the invention provides methods of correlating a biomarker signature with a positive or negative response or a side effect to a treatment regimen, which generally comprise: (a) determining a biomarker signature defining a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker values corresponding to values of at least two IRS biomarkers that can be measured for or derived from a biological subject following commencement of the treatment regimen, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, which lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii)
  • the term “positive response” means that the result of the treatment regimen includes some clinically significant benefit, such as the prevention, or reduction of severity, of symptoms, or a slowing of the progression of the condition.
  • the term “negative response” means that the treatment regimen provides no clinically significant benefit, such as the prevention, or reduction of severity, of symptoms, or increases the rate of progression of the condition.
  • the invention also encompasses methods of determining a positive or negative response to a treatment regimen and/or a side effect of a treatment regimen by a subject with a condition selected from inSIRS, ipSIRS or a particular stage of ipSIRS.
  • These methods generally comprise: (a) correlating a reference biomarker signature with a positive or negative response or a side effect to the treatment regimen, wherein the biomarker signature defines a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker values corresponding to values of at least two IRS biomarkers that are measured for or derived from a control biological subject or control group, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, which lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence, absence or degree of the at least one condition, or to provide a prognosis for the at least one condition, the performance threshold
  • the present invention further contemplates methods of determining a positive or negative response to a treatment regimen and/or a side effect to a treatment regimen by a biological subject.
  • These methods generally comprise: (a) determining a sample biomarker signature defining a combination of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) IRS biomarker values corresponding to values of at least two IRS biomarkers that are measured for or derived from a biological subject following commencement of the treatment regimen, wherein: (i) the at least two IRS biomarkers have a mutual correlation in respect of at least one condition selected from a healthy condition, inSIRS, ipSIRS or a particular stage of ipSIRS, which lies within a mutual correlation range, the mutual correlation range being between ⁇ 0.9; and (ii) the combination of at least two biomarker values has a performance value greater than or equal to a performance threshold representing the ability of the combination of at least two biomarker values to diagnose the presence, absence or degree of the
  • a sample IRS biomarker signature is obtained within about 2 hours, 4 hours, 6 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 6 weeks, 8 weeks, 10 weeks, 12 weeks, 4 months, six months or longer of commencing therapy.
  • the results set out in detail below highlight that as long as the above-described criteria are met, the resulting signatures provide the required discriminatory ability for use in diagnosing the presence, absence, degree or prognosis of at least one condition in a biological subject.
  • RNA from patient samples was then used in gene expression analysis (GeneChip® and/or quantitative PCR (qPCR)). Gene expression data were analyzed using a variety of statistical approaches to identify individual and derived markers. Derived markers were divided into groups based on how they correlated to each of the markers in the top-performing (based on AUC) ratio.
  • This ratio approach provides the best diagnostic power with respect to AUC for separating: healthy and post-surgical (PS) (also referred to herein as “inSIRS”) conditions; healthy and sepsis (also referred to herein as “ipSIRS”); inSIRS and ipSIRS; mild ipSIRS and severe ipSIRS; mild ipSIRS and septic shock; and severe ipSIRS and septic shock.
  • PS post-surgical
  • ipSIRS healthy and sepsis
  • inSIRS and ipSIRS inSIRS and ipSIRS
  • mild ipSIRS and severe ipSIRS mild ipSIRS and septic shock
  • severe ipSIRS and septic shock severe ipSIRS and septic shock.
  • Clinical trials were performed to determine whether certain mRNA transcripts could distinguish between healthy controls and various patient groups and within patient groups. Intensive care sepsis, post-surgical and inSIRS patients, as well as healthy controls were prospectively enrolled and attended a single visit where blood was collected for gene expression and mRNA analyses using Affymetrix exon arrays and/or quantitative real-time PCR (qRT-PCR). A definitive diagnosis of infection-positive SIRS (mild, severe or shock) or inSIRS was unlikely to be known at the time patients were enrolled, and thus confirmation of a diagnosis and the assignment of patients to the cohorts were made retrospectively.
  • SIRS infection-positive SIRS
  • inSIRS quantitative real-time PCR
  • Study participants were all over 18 years and either they or their surrogate decision maker signed and dated the clinical trial information sheet and consent form. All of the control participants were considered to be in good health based on a brief physical examination and their medical history at the time of enrolment.
  • inSIRS and ipSIRS participants needed a variable combination of clinical conditions including two or more of the following within the last 24 hours: temperature >38° C.
  • Demography vital signs measurements (blood pressure, heart rate, respiratory rate, oxygen saturation, temperature), hematology (full blood count), clinical chemistry (urea, electrolytes, liver function enzymes, blood glucose) as well as microbial status was recorded.
  • RNA is selectively bound to the silica-gel membrane as contaminants pass through. Remaining contaminants are removed in three efficient wash steps and RNA is then eluted in Buffer BR5. Determination of RNA quantity and quality was performed using an Agilent Bioanalyzer and Absorbance 260/280 ratio using a spectrophotometer.
  • Measurement of specific mRNA levels in a tissue sample can be achieved using a variety of technologies.
  • a common and readily available technology that covers most of the known human mRNAs is GeneChip® analysis using Affymetrix technology. Details on the technology and methodology can be found at www.affymetrix.com.
  • GeneChip® analysis has the advantage of being able to analyze thousands of RNA transcripts at a time.
  • Another common and readily available technology is qPCR (quantitative polymerase chain reaction), which has the advantage of being able to analyze, in real-time and quantitatively, hundreds of RNA transcripts at a time.
  • FIG. 8A plots these markers against the AUC
  • FIG. 8B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (AGFG1-ArfGAP with FG repeats 1). The conditions of Healthy and inSIRS are perfectly separated when using this mRNA biomarker alone.
  • FIGS. 8E and 8F demonstrate the correlation between the two groups based on their similarity to either AGFG1 or PVRIG.
  • the groups are referred to as either group 1 (AGFG1) or group 2 (PVRIG). It can be seen that each “group” contains those markers that are most highly correlated to each other.
  • each “group” also correlate strongly (as demonstrated by AUC greater than 0.7 for all markers) to the condition being studied (in this instance Healthy versus inSIRS (PS)) as shown in FIGS. 8G and 8H .
  • FIG. 9A plots these markers against the AUC
  • FIG. 9B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (LTBP3—latent transforming growth factor beta binding protein 3).
  • LTBP3 latent transforming growth factor beta binding protein 3
  • each “group” also correlate strongly (as demonstrated by AUC greater than 0.7 for all markers) to the condition being studied (in this instance Healthy versus ipSIRS (sepsis)), as shown in FIGS. 9G and 9H .
  • FIG. 10A plots these markers against the AUC
  • FIG. 10B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (PIWIL4—piwi-like RNA mediated gene silencing 4 ).
  • PS inSIRS
  • ipSIRS ipSIRS
  • the markers were broken into four groups—those that correlate to CEACAM4 (bucket 3), those that correlate to LAMP1 (bucket 4), those that correlate to PLA2G7 (bucket 1) and those that correlate to PLAC8 (bucket 2).
  • the plots in FIG. 10G demonstrate the markers in each group correlate strongly (as demonstrated by AUC greater than 0.7 for all markers) to the condition being studied (i.e., inSIRS (PS) versus ipSIRS (sepsis)).
  • FIG. 11A plots these markers against the AUC
  • FIG. 11B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (N4BP2L2-NEDD4 binding protein 2-like 2). The conditions of mild ipSIRS and severe ipSIRS are well separated when using this mRNA biomarker alone.
  • FIG. 12A plots these markers against the AUC
  • FIG. 12B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (CD6-CD6 molecule). The conditions of mild ipSIRS and ipSIRS shock are well separated when using this mRNA biomarker alone.
  • FIG. 13A plots these markers against the AUC
  • FIG. 13B is a box and whisker plot of the best mRNA biomarker for separating the two conditions (SIRPG—signal regulatory protein gamma)
  • SIRPG signal regulatory protein gamma
  • An assay capable of differentiating patients with inSIRS and ipSIRS can be used in multiple patient populations including:
  • ICU intensive care
  • ipSIRS patients admitted to intensive care
  • the ultimate aim of intensive care is to ensure the patient survives and is discharged to a general ward in the minimum time.
  • Patients in intensive care with diagnosed ipSIRS are usually administered a number of therapeutic compounds—many of which have opposing actions on the immune system and many of which could be counterproductive depending on the severity of ipSIRS (mild sepsis, severe sepsis, septic shock).
  • biomarkers of the present invention will allow medical practitioners to differentiate inSIRS from ipSIRS and determine the stage of ipSIRS and hence choice of therapies, when to start and stop therapies, and patient management procedures, and ultimately response to therapy. Information provided by these biomarkers will therefore allow medical intensivists to tailor and modify therapies to ensure patients survive and spend less time in intensive care. Less time in intensive care leads to considerable savings in medical expenses including through less occupancy time and appropriate use and timing of medications.
  • biomarkers of the present invention will allow nursing and medical practitioners to differentiate inSIRS and ipSIRS at an early stage and hence make informed decisions on choice of therapies and patient management procedures, and ultimately response to therapy. Information provided by these biomarkers will therefore allow medical practitioners to tailor and modify therapies to ensure patients recover quickly from surgery or other condition and do not develop ipSIRS. Less time in hospital and less complications leads to considerable savings in medical expenses including through less occupancy time and appropriate use and timing of medications.
  • patients presenting to emergency departments often have a fever, which is one (of four) of the clinical signs of inSIRS. Such patients need to be assessed to determine if they have either inSIRS or ipSIRS.
  • the treatment and management of pyretic, inSIRS and septic patients are different.
  • a patient with a fever without other inSIRS clinical signs and no obvious source of infection may be sent home, or provided with other non-hospital services, without further hospital treatment.
  • a patient with a fever may have early ipSIRS and not admitting such a patient may put their life at risk. Because these biomarkers can differentiate inSIRS and ipSIRS they will allow medical practitioners to triage emergency department patients quickly and effectively. Accurate triage decision-making insures that patients requiring hospital treatment are given it, and those that don't are provided with other appropriate services.
  • patients presenting to medical clinics often have any one of the four clinical signs of inSIRS (increased heart rate, increased respiratory rate, abnormal white blood cell count, fever or hypothermia).
  • Many different clinical conditions can present with one of the four clinical signs of inSIRS and such patients need to be assessed to determine if they have either inSIRS or ipSIRS and to exclude other differential diagnoses.
  • a patient with colic might also present with clinical signs of increased heart rate.
  • Differential diagnoses could be (but not limited to) appendicitis, urolithiasis, cholecystitis, pancreatitis, enterocolitis.
  • inSIRS systemic inflammatory response
  • ipSIRS systemic inflammatory response
  • the treatment and management of patients with and without systemic inflammation and/or infection are different. Because these biomarkers can differentiate patients with a systemic inflammatory response to infection from those with a systemic inflammatory response without infection (inSIRS and ipSIRS), and determine the degree of systemic involvement, the use of them will allow medical practitioners to determine the next medical procedure(s) to perform to satisfactorily resolve the patient issue.
  • a patient with respiratory distress is likely to present with clinical signs of increased respiratory rate.
  • Differential diagnoses could be (but not limited to) asthma, pneumonia, congestive heart failure, physical blockage of airways, allergic reaction, collapsed lung, pneumothorax. In each of these conditions it would be important to determine if there was a systemic inflammatory response (inSIRS) or whether an infection was contributing to the condition.
  • IMS systemic inflammatory response
  • the treatment and management of patients with and without systemic inflammation and/or infection are different.
  • biomarkers can differentiate patients with a systemic inflammatory response to infection from those with a systemic inflammatory response without infection (inSIRS and ipSIRS), and determine the degree of systemic involvement, the use of them will allow medical practitioners to determine the next medical procedure(s) to perform to satisfactorily resolve the patient issue.
  • Patients with a collapsed lung, pneumothorax or a physical blockage are unlikely to have a large systemic inflammatory response and patients with congestive heart failure, allergic reaction or asthma are unlikely to have a large systemic inflammatory response due to infection.
  • the extent of both inSIRS and ipSIRS, as indicated by biomarkers presented in this patent, also provides clinicians with information on next treatment and management steps.
  • a patient with respiratory distress and a strong biomarker response indicating ipSIRS is likely to be immediately hospitalized, placed on antibiotics and a chest X-ray performed.
  • a patient with respiratory distress and a strong biomarker response indicating inSIRS but not ipSIRS is likely to be hospitalized and chest X-rayed along with other investigative diagnostic procedures, such as MRI, ECG, and angiogram.
  • a patient with respiratory distress with a short history and no inSIRS or ipSIRS is likely to undergo further examination at a local clinic rather than requiring hospitalization.
  • inSIRS inSIRS
  • ipSIRS ipSIRS
  • a patient newly determined to have inSIRS that is not extensive may be able to be put on mild medication such a non-steroidal anti-inflammatory.
  • a patient newly determined to have extensive inSIRS e.g. trauma
  • ipSIRS it is also important to determine the extent of the inflammatory response to infection so that appropriate treatments and management regimens can be put in place or stopped.
  • the clinician may consider either changing, or adding to, the antibiotic treatment regimen in the absence of traditional bacterial culture and sensitivity results.
  • patients that are known to have had ipSIRS and have been on antimicrobial therapy for an extended period but have since demonstrated (by testing using biomarkers) that they no longer have either an inSIRS or ipSIRS can therefore be safely taken off intravenous antibiotics.
  • ipSIRS Patients admitted to intensive care (ICU) often have ipSIRS, or develop ipSIRS during their ICU stay. It is known that the severity of sepsis can be considered to be a continuum from less severe, or sepsis, to more severe, or severe sepsis, to the most severe, or septic shock. More severe sepsis (ipSIRS) requires more aggressive, immediate and tailored intervention compared to sepsis (although all are acute conditions). Patients in intensive care with diagnosed ipSIRS are usually administered a number of therapeutic compounds—many of which have opposing actions on the immune system and many of which could be counterproductive depending on the severity of ipSIRS (sepsis, severe sepsis, septic shock).
  • biomarkers of the present invention will allow medical practitioners to determine the severity of ipSIRS (mild, severe or shock) and hence choice of therapies and patient management procedures, and ultimately response to therapy. Information provided by these biomarkers disclosed herein will therefore allow medical practitioners to tailor, modify or cease therapies and/or care to ensure patients survive and spend less time in intensive care. Less time in intensive care leads to considerable savings in medical expenses including through less occupancy time and appropriate use and timing of medications.
  • the workflow involves up to seven steps depending upon availability of automated platforms.
  • the assay uses quantitative, real-time determination of the amount of each transcript in the sample based on the detection of fluorescence on a qRT-PCR instrument (e.g. Applied Biosystems 7500 Fast Dx Real-Time PCR Instrument, Applied Biosystems, Foster City, Calif., catalogue number 440685; K082562).
  • Transcripts are each amplified, detected, and quantified in a separate reaction well using a probe that is visualized in the FAM channel (by example).
  • the reported score is calculated using interpretive software provided separately to the kit but designed to integrate with RT-PCR machines.
  • the specimen used is a 2.5 mL sample of blood collected by venipuncture using the PAXgene® collection tubes within the PAXgene® Blood RNA System (Qiagen, kit catalogue #762164; Becton Dickinson, Collection Tubes catalogue number 762165; K042613).
  • An alternate collection tube is Tempus® (Life Technologies).
  • RNA Blood (2.5 mL) collected into a PAXgene RNA tube is processed according to the manufacturer's instructions. Briefly, 2.5 mL sample of blood collected by venipuncture using the PAXgeneTM collection tubes within the PAXgeneTM Blood RNA System (Qiagen, kit catalogue #762164; Becton Dickinson, Collection Tubes catalogue number 762165; K042613). Total RNA isolation is performed using the procedures specified in the PAXgeneTM Blood RNA kit (a component of the PAXgeneTM Blood RNA System). The extracted RNA is then tested for purity and yield (for example by running an A 260/280 ratio using a Nanodrop® (Thermo Scientific)) for which a minimum quality must be (ratio >1.6). RNA should be adjusted in concentration to allow for a constant input volume to the reverse transcription reaction (below). RNA should be processed immediately or stored in single-use volumes at or below ⁇ 70° C. for later processing.
  • the final reaction volume per well is 15 ⁇ L.
  • RNA sample 10 ⁇ L Total Volume (per well) 15 ⁇ L
  • qPCR master mix may be prepared to coincide roughly with the end of the RT reaction. For example, start about 15 minutes before this time. See below.
  • Software is specifically designed to integrate with the output of PCR machines and to apply an algorithm based on the use of multiple biomarkers.
  • the software takes into account appropriate controls and reports results in a desired format.
  • the data file will then be analyzed using the assay's software application for interpretation of results.
  • the Software will automatically generate classifier scores for controls and clinical specimens.
  • the Software compares each CON (control) specimen (CONH, CONL, CONN) to its expected result.
  • the controls are run in singleton.
  • Control specimen Designation Name Expected result CONH High Control Score range CONL Low Control Score range CONN Negative Control Score range NTC No Template Control Fail (no Ct for all targets)
  • NTC yields a result other than Fail (no Ct for all targets) the batch run is invalid and no data may be reported for the clinical specimens. This determination is made by visual inspection of the run data. The batch run should be repeated starting with either a new RNA preparation or starting at the RT reaction step.
  • a valid batch run may contain both valid and invalid specimen results.
  • Analytical criteria e.g. Ct values
  • Ct values that qualify each specimen as passing or failing (using pre-determined data) are called automatically by the software.
  • a singleton of the No Template Control is included in each batch run and Fail (no Ct for all targets) is a valid result indicating no amplifiable material was detectable in the well.
  • the negative control must yield a Negative result. If the negative control is flagged as Invalid, then the entire batch run is invalid.
  • the low positive and high positive controls must fall within the assigned ranges. If one or both of the positive controls are flagged as Invalid, then the entire batch run is invalid.
  • FIG. 15 A possible example output from the software is presented below in FIG. 15 .
  • the format of such a report depends on many factors including; quality control, regulatory authorities, cut-off values, the algorithm used, laboratory and clinician requirements, likelihood of misinterpretation.
  • the assay is called “SeptiCyte Lab Test”.
  • the result is reported as a number (5.8), a call (“Sepsis Positive”), a position on a 0-12 scale, and a probability of the patient having sepsis based on historical results and the use of a pre-determined cut-off (using results from clinical trials). Results of controls within the assay are also reported.
  • Other information that could be reported might include: previous results and date and time of such results, probability of severe sepsis or septic shock, a scale that provides cut-off values for historical testing results that separate the conditions of healthy, inSIRS and ipSIRS (mild, severe and shock) such that those patients with higher scores are considered to have more severe inSIRS or ipSIRS.
  • Machines have been, and are being, developed that are capable of processing a patient sample at point-of-care, or near point-of-care. Such machines require few molecular biology skills to run and are aimed at non-technical users. The idea is that the sample would be pipetted directly into a disposable cartridge that is then inserted into the machine. The user presses “Start” and within 2-3 hours a result is generated. The cartridge contains all of the required reagents to perform Steps 2-5 in the example workflow above and the machine has appropriate software incorporated to allow Steps 6 and 7 to be performed.
  • Fresh, whole, anti-coagulated blood can be pipetted into an Idylla Cartridge (Biocartis NV) or similar (Unyvero, Curetis AG; Enigma ML, Enigma Diagnostics; DiagCore, STAT Diagnostica; Savannah, Quidel Corp; ePlex, GenMark Dx), and on-screen instructions on the Idylla machine followed to test for differentiating inSIRS and ipSIRS (by example).
  • RNA is first extracted from the whole blood and is then converted into cDNA. The cDNA is then used in qRT-PCR reactions. The reactions are followed in real time and Ct values calculated.
  • On-board software generates a result output (see Figure XX). Appropriate quality control measures for RNA quality, no template controls, high and low template controls and expected Ct ranges ensure that results are not reported erroneously.
  • Example biomarker ratios (the top 12 based on AUC) that are capable of separating different conditions are shown in the box and whisker plots as listed below, with each showing perfect separation.
  • Biomarker ratios can be used in combination to increase the diagnostic power for separating various conditions. Determining which markers to use, and how many, for separating various conditions can be achieved by calculating Area Under Curve (AUC).
  • AUC Area Under Curve
  • FIG. 22 shows the effect on AUC (in this instance for separating inSIRS and ipSIRS) of adding biomarkers to the diagnostic signature.
  • Combinations of two, three, four and five biomarkers produced equally as good differentiation of inSIRS and ipSIRS without significant differences.
  • other factors come into play such as cost-effectiveness, assay complexity and capabilities of the qRT-PCR platform.
  • a 4-gene signature (0.986, 95% CI 0.964-1.00) offers the appropriate balance between simplicity, practicality and commercial risk for separating inSIRS and ipSIRS. Further, an equation using four markers weighs each biomarker equally which also provides additional robustness in cases of analytical or clinical variability.
  • the value for each biomarker is a Ct value from a PCR.
  • Ct values for each of the markers was found to fall between 26 and 34.
  • the first biomarker within each bracket pair has a higher value than the second biomarker within each bracket pair.
  • the “Diagnostic Score” has been found to have values between 0 and 12.
  • the “Diagnostic Score could potentially be highest Ct value +/ ⁇ highest Ct value.
  • Each patient was clinically and retrospectively (note, not at the time the sample was taken) confirmed as having either inSIRS (black dots) or ipSIRS (red dots).
  • Each patient sample has also had a SeptiCyte score calculated (Y axis on left hand side). On a scale of 0-12 it can be seen that patients with confirmed ipSIRS (red dots) obtain a higher Diagnostic Score compared to those with confirmed inSIRS.
  • an arbitrary cut-off line can be drawn that more or less separates the two conditions depending upon the desired false negative or false positive rate (compared to a retrospective diagnosis of inSIRS or ipSIRS using clinical data).
  • the line is drawn at a “SeptiCyte Score” of 4 such that the number of false negative ipSIRS calls in the Discovery Dataset is zero and the number of false negative ipSIRS calls in the Feasibility Dataset is 2.
  • the number of false positive ipSIRS calls in the Discovery Dataset is four and the number of false positive ipSIRS calls in the Feasibility Dataset is 9.
  • whether a patient sample is false positive or false negative depends on the artificial gold standard of a retrospective clinical call of inSIRS or ipSIRS.
  • the method when used for determining a likelihood of the subject having inSIRS or ipSIRS, can include determining a first pair of biomarker values indicative of a concentration of polynucleotide expression products of the PLA2G7 gene and PLAC8 gene, determining a second pair of biomarker values indicative of a concentration of polynucleotide expression products of the CEACAM4 gene and LAMP1 gene and then determining an indicator using the first and second pairs of biomarker values.
  • the indicator could then be compared to indicator references specifically established to distinguish between inSIRS and ipSIRS.
  • the processing system 201 determines reference data in the form of measured biomarker values obtained for a reference population.
  • the reference data may be acquired in any appropriate manner but typically this involves obtaining gene expression product data from a plurality of individuals.
  • gene expression product data are collected, for example by obtaining a biological sample, such as a peripheral blood sample, and then performing a quantification process, such as a nucleic acid amplification process, including PCR (Polymerase Chain Reaction) or the like, in order to assess the activity, and in particular, level or abundance of a number of reference biomarkers. Quantified values indicative of the relative activity are then stored as part of the reference data.
  • a biological sample such as a peripheral blood sample
  • a quantification process such as a nucleic acid amplification process, including PCR (Polymerase Chain Reaction) or the like
  • the measurements are received as raw data, which then undergoes preliminary processing.
  • raw data corresponds to information that has come from a source without modification, such as outputs from instruments such as PCR machines, array (e.g., microarray) scanners, sequencing machines, clinical notes or any other biochemical, biological, observational data, or the like.
  • This step can be used to convert the raw data into a format that is better suited to analysis. In one example this is performed in order to normalize the raw data and thereby assist in ensuring the biomarker values demonstrate consistency even when measured using different techniques, different equipment, or the like.
  • the goal of normalization is to remove the variation within the samples that is not directly attributable to the specific analysis under consideration. For example, to remove variances caused by differences in sample processing at different sites.
  • Classic examples of normalization include z-score transformation for generic data, or popular domain specific normalizations, such as RMA normalization for microarrays.
  • this step may not strictly be necessary, in which case the function can be a Null function producing an output identical to the input.
  • the preferred approach is a paired function approach over log normalized data.
  • Log normalization is a standard data transformation on microarray data, because the data follow a log-normal distribution when coming off the machine. Applying a log transform turns the data into process-friendly normal data.
  • the individuals are selected to include individuals diagnosed with one or more conditions of interest, as well as healthy individuals
  • the conditions are typically medical, veterinary or other health status conditions and may include any illness, disease, stages of disease, disease subtypes, severities of disease, diseases of varying prognoses or the like, and in the current example would include at least some individuals with inSIRS and some individuals with ipSIRS.
  • the individuals also typically undergo a clinical assessment allowing the conditions to be clinically identified, and with an indication of any assessment or condition forming part of the reference data.
  • biomarker values measured will depend on the predominant condition that is being assessed so, for example, in the case of determining the likelihood of a subject having inSIRS or ipSIRS, the biomarkers used will be LAMP1, CEACAM4, PLAC8 and PLA2G7, as discussed above.
  • the reference data can be stored in the database 211 allowing this to be subsequently retrieved by the processing system 201 for subsequent analysis, or could be provided directly to the processing system 201 for analysis.
  • the measurements are validated using traditional prior art techniques, to ensure that the measurements have been performed successfully, and hence are valid.
  • each individual with the reference population is typically allocated to a group.
  • the groups may be defined in any appropriate manner and may be defined based on any one or more of an indication of a presence, absence, degree, stage, severity, prognosis or progression of a condition, other tests or assays, or measured biomarkers associated with the individuals.
  • a first selection of groups may be to identify one or more groups of individuals suffering from SIRS, one or more groups of individuals suffering ipSIRS, and one or more groups of individuals suffering inSIRS. Further groups may also be defined for individuals suffering from other conditions.
  • the groups may include overlapping groups, so for example it may be desirable to define groups of healthy individuals and individuals having SIRS, with further being defined to distinguish inSIRS patients from ipSIRS patients, as well as different degree of inSIRS or ipSIRS, with these groups having SIRS in common, but each group of patients differing in whether a clinician has determined the presence of an infection or not.
  • further subdivision may be performed based on characteristics of the individuals, phenotypic traits, measurement protocols or the like, so groups could be defined based on these parameters so that a plurality of groups of individuals suffering from a condition are defined, with each group relating to a different phenotypic trait, measurement protocol or the like.
  • identification of different groups can be performed in other manners, for example on the basis of particular activities of biomarkers within the biological samples of the reference individuals, and accordingly, reference to conditions is not intended to be limiting and other information may be used as required.
  • classification into groups may vary depending on the preferred implementation. In one example, this can be performed automatically by the processing system 201 , for example, using unsupervised methods such as Principal Components Analysis (PCA), or supervised methods such as k-means or Self Organizing Map (SOM). Alternatively, this may be performed manually by an operator by allowing the operator to review reference data presented on a Graphical User Interface (GUI), and define respective groups using appropriate input commands.
  • PCA Principal Components Analysis
  • SOM Self Organizing Map
  • GUI Graphical User Interface
  • first and second derived biomarker values are determined representing respective indicator values.
  • the first and second indicator values In 1 , In 2 are determined on a basis of ratios of concentrations of first and second, and third and fourth biomarkers respectively:
  • the indicator values are then used to establish indicator references at step 2440 , which are then used in analyzing measured indicator values for a subject to establish a likelihood of the subject having a condition.
  • indicator values for each reference group are statistically analyzed to establish a range or distribution of indicator values that is indicative of each group, and an example distribution is shown in FIG. 26 , as will be discussed in more detail below.
  • FIGS. 25A and 25B A further example will now be described with reference to FIGS. 25A and 25B .
  • a sample is acquired from the subject.
  • the sample could be any suitable sample such as a peripheral blood sample, or the like, depending on the nature of the biomarker values being determined
  • the sample undergoes preparation allowing this to be provided to a measuring device and used in a quantification process at step 2510 .
  • the quantification process involves PCR amplification, with the measuring device being a PCR machine, although other suitable techniques could be used.
  • amplifications times At(PLA2G7), At(PLAC8), At(CEACAM4), At(LAMP1) are determined for each of the four biomarkers at step 2515 , with the amplification times being transferred from the measuring device to the processing system 201 allowing the processing system 201 to perform analysis of the corresponding biomarker values.
  • the processing system 201 calculates ratios using the amplifications times.
  • the amplification times represent a log value
  • the ratios are determined by subtracting amplifications times as will be appreciated by a person skilled in the art.
  • the indicator values would be determined as follows:
  • the processing system 201 determines an indicator value by combining the ratios for the indicator values, as follows:
  • the processing system 201 then compares the indicator value to one or more respective indicator references at step 2530 .
  • the indicator references are derived for a reference population and are used to indicate the likelihood of a subject suffering from inSIRS or ipSIRS.
  • the reference population is grouped based on a clinical assessment into groups having/not having the conditions or a measure of severity, risk or progression stage of the condition, with this then being used to assess threshold indicator values that can distinguish between the groups or provide a measure of severity, risk or progression stage.
  • the comparison is performed by comparing the indicator to an indicator distribution determined for each group in the reference population.
  • there are two reference groups with one corresponding to individuals diagnosed with inSIRS and the other for individuals diagnosed with ipSIRS.
  • the results of the comparison can be used to determine a likelihood of the individual having ipSIRS as opposed to inSIRS. This can be achieved using a number of different methods, depending on the preferred implementation.
  • FIG. 26 shows the distribution of indicator values for a reference population containing both inSIRS and ipSIRS samples.
  • the density (y axis) describes how common scores are in the reference population.
  • the most common values for the inSIRS population are in the range 1 to 8, and for the ipSIRS population are mostly in the range 5 to 13.
  • the calculated indicator value for a new sample is 4.
  • a value of 4 in the inSIRS population has a high density at this value (A)
  • the ipSIRS population has a low density at this value (B), meaning that this sample is more likely to be inSIRS.
  • this process can be performed by determining a basic probability based on score bands. For a given score band (i.e. 4-6), the proportion of individuals with SIRS or SEPSIS is calculated. For example, if 40% of the scores between 4 and 6 were SEPSIS, then if an subject has an indicator value between 4 and 6, they have a 40% probability of sepsis. Thus, for a given range within the reference distribution, the probability of belonging to one group or another (SIRS/SEPSIS) can simply be the proportion of that group within the range.
  • An alternative technique is a standard Bayes method.
  • the technique uses a distribution of inSIRS scores, a distribution of ipSIRS scores and an indicator value for the subject.
  • a standard score or equivalent is used to generate a probability of the indicator value belonging to the inSIRS distribution: pr(inSIRS) and separately to the ipSIRS distribution: pr(ipSIRS).
  • the Bayes method is used to generate the probability of ipSIRS given the individual distributions.
  • the probability of membership for a single unknown sample into each distribution can be calculated (p-value) using for example a standard score (z-score). Then the p-values for each distribution can be combined into an overall probability for each class (i.e. inSIRS/ipSIRS) using for example Bayes rule or any other probability calculation method (including frequentist or empirical or machine learned methods).
  • the results of this comparison are used by the processing system 201 to calculate a likelihood of the subject having ipSIRS at step 2535 , with this being used to generate a representation of the results at step 2540 , which is provided for display at step 2545 , for example to a clinician or medical practitioner.
  • This can be achieved by displaying the representation on a client device, such as part of an email, dashboard indication or the like.
  • FIGS. 27A and 27B An example of the representation is shown in FIGS. 27A and 27B .
  • the representation 2700 includes a pointer 2710 that moves relative to a linear scale 2720 .
  • the linear scale is divided into regions 2721 , 2722 , 2723 , 2724 which indicate whether the subject is suffering from level 1, 2, 3 or 4.
  • Corresponding indicator number values are displayed at step 2730 with an indication of whether the corresponding value represents a likelihood of SIRS (inSIRS) or SEPSIS (ipSIRS) being shown at step 2740 .
  • An alphanumeric indication of the score is shown at step 2751 together with an associated probability of the biological subject having SEPSIS at step 2752 .
  • a method can be provided for use in assessing the likelihood of a biological subject having inSIRS or ipSIRS the method including, in one or more processing devices:
  • apparatus for determining the likelihood of a biological subject having inSIRS or ipSIRS, the apparatus including:
  • a further method that can be provided includes differentiating between inSIRS and ipSIRS in a biological subject, the method including:
  • a method for determining an indicator used in assessing a likelihood of a biological subject having a presence, absence, degree or prognosis of at least one medical condition, the method including:

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