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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • C12Q1/701—Specific hybridization probes
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  • 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
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • 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
• • G—PHYSICS
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  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
  • G01N33/6863—Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors
  • G01N33/6866—Interferon
• • C—CHEMISTRY; METALLURGY
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  • C12Q2600/00—Oligonucleotides characterized by their use
  • C12Q2600/112—Disease subtyping, staging or classification
• • 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
  • C12Q2600/136—Screening for pharmacological compounds
• • 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
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/005—Assays involving biological materials from specific organisms or of a specific nature from viruses
  • G01N2333/08—RNA viruses
  • G01N2333/11—Orthomyxoviridae, e.g. influenza virus
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/52—Assays involving cytokines
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2469/00—Immunoassays for the detection of microorganisms
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/50—Determining the risk of developing a disease

Definitions

• the invention provides a method for identifying clinical risk in a patient having or suspected of having an influenza infection, the method comprising determining the expression level of interferon alpha inducible protein 27 (IF127) gene in a biological sample from said patient and comparing the determined level of IF127 gene product to a standard level.
• IF127 interferon alpha inducible protein 27
• the standard level is based on the level of IF127 in subjects infected with influenza virus who are asymptomatic and an elevated level of IFI27 in said patient sample compared to said standard level is indicative of clinical risk in said patient.
• the standard level of IF127 gene product is indicative of clinical risk
• an equal or elevated level of 1FI27 gene product in said patient sample compared to said standard level is indicative of clinical risk in said patient.
• the standard level of IF 127 gene product is based on the level of 1FI27 in healthy subjects and an elevated expression level of IF 127 in said patient sample compared to said standard level is indicative of influenza or viral pneumonia in said patient.
• a level of IF127 gene product that is at least 60 times higher than a standard level based on healthy subjects or subjects with bacterial pneumonia is indicative of a patient with influenza or viral pneumonia, and clinical risk.
• the method is performed entirely ex vivo.
• comparing the level of determined IFI27 gene product in a biological sample to a standard level is done with the assistance of a computer program.
• allocating a clinical risk to a patient on the basis of the comparison is done with the assistance of a computer program.
• the kit comprises one or more agents for normalisation of said method.
• the agent(s) for normalisation are selected from the group consisting of an agent or agents for the detection of a constitutively expressed gene product.
• the constitutively expressed gene product is GAPDH.
• the individual is exposed to an influenza virus prior to administration of said agent.
• the individual has an influenza infection when administered said agent.
• the individual is exposed to an influenza virus after said administration of said agent.
• the standard level indicative of clinical risk comprises a standard curve defining clinical risk.
• the methods of the invention comprise the use of a standard curve encompassing a range of amounts of IFI27, such as a range from negligible clinical risk to clinical risk of severe disease.
• the method is conducted as part of a research trai or clinical trial of a candidate anti-viral agent for the prevention or treatment of influenza.
• phosphate dehydrogenase GPDH
• transcript variant 1 mRNA. NCBI Reference Sequence: NM_002046.4 (SEQ ID NO.: 12A). Sites of primer annealing (SEQ ID NO.: 14 and SEQ ID NO.: 15) are highlighted and underlined.
• Samples may be obtained from the patient at appropriate intervals, such as intervals of one or several hours, or daily or weekly. Samples may be obtained after a certain treatment has been undertaken, such as the administration of a therapeutic agent to treat the disease cause by the influenza infection.
• a sample may be tested for the presence of an IFI27 gene product.
• the gene product may be an IFI27 mRNA or transcript.
• the full polynucleotide sequence of the 1FI27 mRNA has been determined and is reported, for example at Ensembl/1 lavana merge: ENSG00000165949.
• ENSG00000165949 As noted herein there are variants of the IFI27 transcript previously described.
• analyzing the sample for the presence of an IF127 gene comprises analyzing the sample for the presence of an IFI27 mRNA sequence, such as a sequence shown in SEQ ID NO: I or SEQ ID NO:2, or a fragment or variant thereof.
• RNA and cDNA sequences encoded by the DNA sequences disclosed herein may be derived using the genetic code.
• An RNA sequence may be derived from a given DNA sequence by generating a sequence that is complementary the particular DNA sequence.
• the complementary sequence may be generated by converting each cytosine ('C') base in the DNA sequence to a guanine ('G') base, each guanine ('G') base in the DNA sequence to a cytosine ('C') base, each thymidine (' ⁇ ') base in the DNA sequence to an adenine ( ⁇ ') base, and each adenine ( ⁇ ') base in the DNA sequence to a uracil ('LP) base.
• initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them.
• the word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always ⁇ 0). For amino acid sequences, a scoring matrix is used to calculate the cumulati ve score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
• a fragment, probe or primer is a fragment of the IFI27 gene, for example a sequence known in the art as specific for an IFI27 gene or fragment or variant thereof. The skilled addressee will be able to determine appropriate conditions for the use of such nucleic acid sequences in the methods of the invention.
• a fragment, probe or primer is a fragment of the IFI27 gene, for example the sequence TGC CTC GGG CAG CCT (SEQ ID NO:9) or the sequence TTG GTC AAT CCG GAG AGT CC (SEQ ID NO: 10).
• the antibodies may exist in a variety of forms, including for example as a whole antibody, or as an antibody fragment, or other immunologically active fragment thereof, such as complementarity determining regions.
• the antibody may exist as an antibody fragment having functional antigen-binding domains, that is, heavy and light chain variable domains.
• the antibody fragment may exist in a form selected from the group consisting of, but not limited to: Fv, F a (,, F(ab) 2 , scFv (single chain Fv), dAb (single domain antibody), chimeric antibodies, bi-specific antibodies, diabodies and triabodies.
• Methods for detecting the presence of or measuring the amount of, an antibody-marker complex include, for example, detection of fluorescence, chemi luminescence, luminescence, absorbance, birefringence, transmittance, reflectance, or refractive index such as surface plasmon resonance, biosensor, ellipsometry, a resonant mirror method, a grating coupler wave guide method or interferometry.
• Radio frequency methods include multipolar resonance spectroscopy.
• Electrochemical methods include amperometry and voltametry methods.
• Optical methods include imaging methods and non-imaging methods and microscopy.
• Quantifying, and hence determining the level may also include normalization of the sample or the method to account for differences within the assay specific to the sample. Typically this includes determining the level of another component detectable in the sample.
• samples may be normalized to account for inter- sample differences in performance of the invention.
• the internal reference marker may be any appropriate component in the sample, such as a gene product and would typically be a component the presence of which is uniform in samples from healthy subjects and in unhealthy subjects, or a component the presence of which is uniform in samples from subjects not infected with influenza and in subjects infected with influenza.
• a glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene product is used as an internal reference.
• Detection of polynucleotides and polypeptides disclosed herein may be performed using any suitable method.
• methods for the detection of an IFI27 gene product such as a polynucleotide and/or polypeptide may involve the use of a primer, probe or antibody specific for the 1FI27 gene product.
• Suitable techniques and assays in which the skilled addressee may utilise a primer, probe or antibody include, for example, the polymerase chain reaction (and related variations of this technique), antibody based assays such as ELISA and flow cytometry, and fluorescent microscopy.
• Methods by which the characteristic polypeptides disclosed herein may be identified are generally known in the art, and are described for example in Coligan J. E. et al.
• the detection of and determination of the level of an IFI27 gene product is achieved by amplification of nucleotide sequence from the sample of interest by polymerase chain reaction, using primers that hybridise specifically to a sequence, or a variant or fragment thereof, of the IF127 gene product and detecting the amplified sequence.
• a typical target sequence is an IF127 mRNA such as having a sequence shown in SEQ ID NO: I or SEQ ID NO:2, or a cDNA sequence of IF127 such as having a sequence shown in SEQ ID NO:5 or SEQ ID NO:6, or a fragment or variant of any thereof.
• multiple target sequences, fragments or variants thereof may be employed.
• PCR RNA elongation polymerase chain reaction
• nested primers single specific primers
• degenerate primers gene-specific primers
• vector-specific primers partially-mismatched primers
• Methods for designing PCR and RT-PCR primers are generally known in the art and are disclosed, for example, in Ausubel F. M. et al. (Eds) Current Protocols in Molecular Biology (2007), John Wiley and Sons, Inc; Maniatis et al. Molecular Cloning ( 1982), 280-281 ; Innis et al.
• Probes of the invention or for use in methods and kits of the invention may be labelled by incorporation of a marker to facilitate their detection.
• Techniques for labelling and detecting nucleic acids are described, for example, in Ausubel F. M. et al. (Eds) Current Protocols in Molecular Biology (2007), John Wiley and Sons, Inc.
• suitable markers include fluorescent molecules (e.g. acetylaminofluorene, 5-bromodeoxyuridine, digoxigenin, fluorescein) and radioactive isotopes (e.g. 32P, 35S, 3H, 33P).
• Detection of the marker may be achieved, for example, by chemical, photochemical, immunochemical, biochemical, or spectroscopic techniques.
• the kit may comprise one or more additional components selected from the group consisting of (i) one or more reference sample(s); (ii) one or more detectable moieties; (iii) one or more substance(s) for immobilising an agent for detecting an IFI27 gene product on a solid support; (iv) a solid support material; (v) one or more container(s) for collection and/or storage of a biological sample; (vi) one or more reagent(s) for use in preparation of a biological sample; (vii) one or more agents for the amplification of a nucleic acid sequence; and (viii) instructions for use of the kit or a component(s) thereof in a method for determining the level of an IFI27 gene product in a biological sample.
• additional components selected from the group consisting of (i) one or more reference sample(s); (ii) one or more detectable moieties; (iii) one or more substance(s) for immobilising an agent for detecting an IFI27 gene product on a
• Table 1 Demographic and clinical characteristics of individuals in development and validation sets.

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• 2013
  • 2013-07-10 CA CA2877400A patent/CA2877400A1/en not_active Abandoned
  • 2013-07-10 EP EP13817599.7A patent/EP2872891B1/en active Active
  • 2013-07-10 KR KR20157003223A patent/KR20150040289A/ko not_active Withdrawn
  • 2013-07-10 BR BR112015000685A patent/BR112015000685A2/pt not_active Application Discontinuation
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• 2018
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