US20140212871A1 - Nucleic Acid Extraction from Heterogeneous Biological Materials - Google Patents

Nucleic Acid Extraction from Heterogeneous Biological Materials Download PDF

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US20140212871A1
US20140212871A1 US14/116,372 US201214116372A US2014212871A1 US 20140212871 A1 US20140212871 A1 US 20140212871A1 US 201214116372 A US201214116372 A US 201214116372A US 2014212871 A1 US2014212871 A1 US 2014212871A1
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nucleic acid
containing materials
biological sample
kit
extraction
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Wayne Comper
Leileata M. Russo
Johan Karl Olov Skog
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Exosome Diagnostics Inc
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Exosome Diagnostics Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/02—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H1/00—Processes for the preparation of sugar derivatives
    • C07H1/06—Separation; Purification
    • C07H1/08—Separation; Purification from natural products
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C12N15/101—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by chromatography, e.g. electrophoresis, ion-exchange, reverse phase
    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Definitions

  • the present invention relates to the general field of nucleic acid analysis, particularly the procurement and analysis of high quality nucleic acids from a sample of heterogeneous biological materials.
  • Cancer-related biomarkers include, e.g., specific mutations in gene sequences (Cortez and Calin, 2009; Diehl et al., 2008; Network, 2008; Parsons et al., 2008), up- and down-regulation of mRNA and miRNA expression (Cortez and Calin, 2009; Itadani et al., 2008; Novakova et al., 2009), mRNA splicing variations, changes in DNA methylation patterns (Cadieux et al., 2006; Kristensen and Hansen, 2009), amplification and deletion of genomic regions (Cowell and Lo, 2009), and aberrant expression of repeated DNA sequences (Ting et al., 2011).
  • Various molecular diagnostic assays such as mutational analysis, methylation status of genomic DNA, and gene expression analysis may detect these biomarkers and provide valuable information for doctors, clinicians and researchers. These tests so far utilize cancer cells derived from surgically removed tumor tissue or from tissue obtained by biopsy.
  • a less invasive approach using a bodily fluid sample has wide ranging implications in terms of patient welfare, the ability to conduct longitudinal disease monitoring, and the ability to obtain expression profiles even when tissue cells are not easily accessible, e.g., in ovarian or brain cancer patients.
  • the present invention is directed to methods and systems for extracting high quality nucleic acid from a biological sample, preferably a fluid sample, and the resulting nucleic acid extractions.
  • the subject methods, systems and extractions may be used in support of patient diagnostics, prognostics, theranostics, monitoring, predictive medicine, personalized medicine, integrated medicine, pharmacodiagnostics and diagnostic/prescription partnering (companion diagnostics).
  • the present invention is a new method of extracting nucleic acid from a biological sample utilizing principles of extraction enhancement and affinity exclusion to reduce heterogeneity in a sample containing a heterogeneous collection of nucleic acid-containing materials.
  • extraction enhancement and affinity exclusion to reduce heterogeneity in a sample containing a heterogeneous collection of nucleic acid-containing materials.
  • nucleic acid-containing materials refer to cells, microvesicles, RNA-protein complexes, and other nucleic acid-containing particles naturally found in biological samples.
  • cells containing nucleic acids of special interest include, but are not limited to, circulating tumor cells and other cells that have undergone or are undergoing disease-related transformation, or other cells that contain genomic evidence of the physical status or health of an organism.
  • microvesicles examples include, but are not limited to, exosomes, membrane vesicles, shedding microvesicles, microparticles, nanovesicles, apoptotic bodies, nanoparticles and membrane vesicles, and will collectively be referred to throughout this specification as “microvesicles” unless otherwise expressly denoted.
  • Nucleic acid-containing materials may originate from, for example, a particular cell, organ or tissue of the body, or bodily fluid.
  • nucleic acid-containing materials can be detected or isolated from urine.
  • a nucleic acid-containing material may originate from, for example, a tumor, hyperplastic growth, nodule, neoplasm, cyst, or mass.
  • Nucleic acid-containing materials carry surface molecules, such as antigens, biomarkers, receptors, that may be used to identify, detect, isolate, enrich, or sort nucleic acid-containing materials from a specific donor cell type, tissue or organ of the body, or bodily fluid. Individual species of nucleic acid-containing materials may co-purify during extraction methods, as described herein. For example, circulating tumor cells may co-purify with microvesicles.
  • a “heterogeneous collection of nucleic acid-containing materials,” as used herein, is a mixture of any of the foregoing species of nucleic acid-containing materials, e.g., cells, any species of microvesicle, RNA-protein complexes, and any other species of nucleic acid-containing particles, or any combination thereof.
  • a heterogeneous collection of nucleic acid-containing materials of the present invention includes cells or microvesicles, or both.
  • a heterogeneous collection of nucleic acid-containing materials of the present invention is circulating tumor cells and microvesicles.
  • the mixture will comprise one or more cells in addition to any or all of the other species of nucleic acid-containing materials.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials; performing an extraction enhancement operation; and extracting nucleic acid from the resulting materials.
  • this method will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • the heterogeneous collection of nucleic acid-containing materials includes, but is not limited to, a mixture of nucleic acid-containing materials, which include, but are not limited to, cells or microvesicles, or both.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials; performing an affinity exclusion operation on the heterogeneous collection of nucleic acid-containing materials; and extracting nucleic acid from the resulting materials.
  • this method will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • the heterogeneous collection of nucleic acid-containing materials includes, but is not limited to, a mixture of nucleic acid-containing materials, which include, but are not limited to, cells or microvesicles or both.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials; performing an extraction enhancement operation; performing an affinity exclusion operation on the resulting materials; and extracting nucleic acid from the remaining materials.
  • the affinity exclusion operation is performed at any time after the pre-processing step.
  • this method will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • the heterogeneous collection of nucleic acid-containing materials includes, but is not limited to, a mixture of nucleic acid-containing materials, which include, but are not limited to, cells or microvesicles, or both.
  • the invention is a nucleic acid extraction from a heterogeneous collection of nucleic acid-containing materials obtained from a eukaryotic biological sample, wherein 18S rRNA and 28S rRNA are detectable in the extraction.
  • the quantitative ratio of 18S rRNA to 28S rRNA detectable in the nucleic acid extractions is within the range of approximately 1:1 to approximately 1:2; and is preferably approximately 1:2. Nucleic acid extractions of this nature are obtainable using any of the above-described methods.
  • the invention is a nucleic acid extraction from a heterogeneous collection of nucleic acid-containing materials obtained from a bodily fluid sample with a protein concentration of less than 10 mg/ml, such as urine, where the nucleic acid extraction has a nucleic acid yield of great than or equal to 50 pg/ml from 20 ml of biological sample. Nucleic acid extractions of this nature are obtainable using any of the above-described methods.
  • the invention is a nucleic acid extraction from a heterogeneous collection of nucleic acid-containing materials obtained from a bodily fluid sample with a protein concentration of greater than 10 mg/ml, such as serum or plasma, wherein the nucleic acid extraction has a nucleic acid yield of greater than or equal to 50 pg/ml from 1 ml of biological sample.
  • the heterogeneous collection of nucleic acid-containing materials includes, but is not limited to, a mixture of nucleic-acid containing materials, which include, but are not limited to, cells or microvesicles. Nucleic acid extractions of this nature are obtained by using any of the above-described methods.
  • nucleic acid profiles are obtained by analyzing the nucleic acid extractions resulting from any of the foregoing methods.
  • the invention is a kit for extracting nucleic acids from biological samples or heterogeneous nucleic acid-containing collection.
  • the heterogeneous collection of nucleic acid-containing materials includes, but is not limited to, a mixture of nucleic-acid containing materials, which include, but are not limited to, cells or microvesicles, or both.
  • All of the foregoing embodiments may include a sample pre-processing step which includes techniques for separating nucleic acid-containing materials from a biological sample. For example, methods of centrifugation, filtration concentration, and/or anion exchange and/or gel permeation chromatography can be used.
  • Extraction enhancement agents may include, but are not limited to, RNase inhibitor, protease, reducing agent, decoy substrate (e.g., synthetic RNA), soluble receptor, small interfering RNA, RNA binding molecule (e.g., anti-RNA antibody, chaperone protein, RNase inhibitory protein), or RNase denaturing substance (e.g., high osmolarity solution detergent), or any combination of the foregoing agents.
  • decoy substrate e.g., synthetic RNA
  • soluble receptor e.g., small interfering RNA
  • RNA binding molecule e.g., anti-RNA antibody, chaperone protein, RNase inhibitory protein
  • RNase denaturing substance e.g., high osmolarity solution detergent
  • All of the foregoing embodiments may include an affinity exclusion operation, as described below, for reducing the heterogeneity of the fraction of nucleic acid-containing materials obtained from the preprocessing step.
  • the affinity exclusion operation may remove nucleic acid-containing materials that are not of interest.
  • the depletion may be complete or partial. For example, in some instances a depletion of 50% of the undesirable materials would be sufficient to achieve a high quality nucleic acid extraction.
  • All of the foregoing embodiments may include an affinity enrichment operation, as described below, wherein affinity selection methods are used to enrich for nucleic acid-containing materials of a certain type or originating from a particular cell, tissue or organ of the body.
  • affinity selection methods are used to enrich for nucleic acid-containing materials of a certain type or originating from a particular cell, tissue or organ of the body.
  • nucleic acid-containing materials from specific donor cells can be detected, selected, or enriched by the specific surface molecules known to be present.
  • the invention provides a use for any of the nucleic acid extraction methods disclosed herein in any of a variety of known methods and techniques for analyzing nucleic acids in support of patient diagnostics, prognostics, theranostics, monitoring, predictive medicine, personalized medicine, integrated medicine, pharmacodiagnostics and diagnostic/prescription partnering (companion diagnostics).
  • the nucleic acid obtained from the practice of the extraction method is analyzed for the presence or absence of a genetic aberration associated with a disease or medical condition.
  • a nucleic acid is, for example, DNA or RNA.
  • the RNA can be, for example, coding RNA, e.g. messenger RNA which may encode proteins, or non-coding RNA (ncRNA), e.g., ribosomal RNA, transfer RNA, microRNA, and other non-coding transcripts that may originate from genomic DNA.
  • Non-coding RNA transcripts may include, but are not limited to, transcripts that are transcribed from satellite repeats and transposons, which may be DNA transposons or retrotransposons.
  • the DNA can be, for example, single stranded DNA, e.g. cDNA that is reverse transcribed from RNA or generated from DNA replication; double-stranded DNA; genomic DNA; non-coding DNA (ncDNA), e.g. satellite repeats, transposons, or retrotransposons; or any fragment or combination thereof.
  • the biological sample can be any sample from an organism, for example, a mammal, and in particular, a human.
  • the biological sample is a bodily fluid such as urine, blood, serum or plasma, and may also include sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intraorgan system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.
  • a biological sample may come from a subject.
  • subjects include, but are not limited to, all animals shown to or expected to have nucleic acid-containing materials.
  • the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mouse, rat, guinea pig, etc.).
  • FIG. 1 is a flow chart depicting a first aspect of the present invention directed to a new method of nucleic acid extraction from a biological sample.
  • FIG. 2 is a flow chart depicting a second aspect of the present invention directed to a new method of nucleic acid extraction from a biological sample.
  • FIG. 3 is a flow chart depicting a third aspect of the present invention directed to a new method of nucleic acid extraction from a biological sample.
  • Nucleic acid-containing biological materials are often used as starting materials for nucleic acid extraction and analysis.
  • Cells are an example of a nucleic acid-containing biological material.
  • Examples of cells containing nucleic acids of special interest include, but are not limited to, circulating tumor cells and other cells that have undergone or are undergoing disease-related transformation, or other cells that contain genomic evidence of the physical status or health of an organism.
  • nucleic acids can be found in smaller materials ranging in size from about 10 nm in diameter to about 10000 nm in diameter.
  • “exosomes” have diameters of approximately 30 to 200 nm, with shedding microvesicles and apoptotic bodies often described as larger (Orozco and Lewis, 2010).
  • nucleic acid-containing materials such as RNA-protein complexes, may co-isolate with cells and microvesicles using the various methods and techniques described herein. Accordingly, the generic term “nucleic acid-containing materials” will be used herein to refer to cells, microvesicles, RNA-protein complexes, and other nucleic acid containing particles naturally found in biological samples.
  • a “heterogeneous collection of nucleic acid-containing materials,” as used herein, is a mixture of any of the foregoing species of nucleic acid-containing materials, e.g., cells, any species of microvesicle, RNA-protein complexes, and any other species of nucleic acid-containing particles.
  • the mixture will comprise one or more cells in addition to any or all of the other species of nucleic acid-containing materials.
  • Nucleic acid-containing materials may originate from particular cells, tissues or organs of the body, or bodily fluids. In particular, nucleic acid-containing materials may be isolated from urine, plasma, or serum. In some embodiments, nucleic acid-containing materials may originate from a tumor, hyperplastic growth, nodule, neoplasm, cyst, or mass. Nucleic acid-containing materials often carry surface molecules such as antigens, biomarkers, or receptors from their donor cells. These surface molecules may be used to detect, identify, isolate, sort, and/or enrich nucleic acid-containing materials from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008).
  • nucleic acid-containing materials originating from distinct cell populations can be analyzed for their nucleic acid content.
  • tumor (malignant and non-malignant) nucleic acid-containing materials carry tumor-associated surface antigen and may be detected, isolated, or enriched via these specific tumor-associated surface antigens.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials (preferably said heterogeneous collection comprises cells in addition to other nucleic acid-containing materials); performing an extraction enhancement operation; and extracting nucleic acid from the resulting materials.
  • a sample pre-processing step and the extraction enhancement operation there is no specified order to the performance of the sample pre-processing step and the extraction enhancement operation, and indeed, the two may be performed simultaneously.
  • this method will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • FIG. 1 One variation of this first embodiment is shown in FIG. 1 , wherein the method comprises the steps of obtaining a biological sample ( 100 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 110 ), performing an extraction enhancement operation on the fraction ( 120 ), and extracting nucleic acid from the fraction ( 130 ).
  • the extraction enhancement operation is performed prior to the sample pre-processing, or the pre-processing and extraction enhancement operations are performed simultaneously.
  • nucleic acids there may be an additional step of removing nucleic acids that are not located inside the cells or microvesicles that may be part of the heterogeneous collection of nucleic acid-containing materials.
  • Methods of removing nucleic acids are well known in the art.
  • an enzyme digestion step may be performed at any point in the process, e.g., prior to sample pre-processing, prior to performance of the enhancement extraction operation, or prior to nucleic acid extraction.
  • Such enzymes may be a type of ribonuclease that catalyzes the enzymatic digestion of ribonucleic acids or a type of deoxyribonuclease that catalyzes the enzymatic digestion of deoxyribonucleic acids.
  • the biological sample can be any sample from an organism, for example, a mammal, and in particular, a human.
  • the biological sample is a bodily fluid such as urine, blood, serum or plasma, and may also include sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intraorgan system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.
  • a biological sample may sometimes come from a subject.
  • subject is intended to include all animals shown to or expected to have nucleic acid-containing materials.
  • the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mouse, rat, guinea pig, etc.).
  • rodent e.g. mouse, rat, guinea pig, etc.
  • the terms “subject,” “individual” and “patient” are used interchangeably herein and have the same meaning.
  • the sample pre-processing step provides certain advantages not present in nucleic acid extraction methods of the prior art that do not employ a pre-processing step to obtain from the sample a fraction comprising a heterogeneous collection of nucleic acid-containing materials.
  • a pre-processing step (1) tend to produce significantly higher yields of extracted nucleic acid with higher integrity; (2) provide advantages associated with scalability, e.g., when used in support of an assay to detect nucleic acids expressed in a subject at low levels, the sensitivity of the assay can be increased by isolating, in the pre-processing step, more nucleic acid-containing materials from a larger volume of sample fluid; (3) purer nucleic acids in that protein and lipids, debris from dead cells, and other potential contaminants and PCR inhibitors can be excluded from the nucleic acid-containing materials isolated in the preprocessing step; and (4) more choices in nucleic acid extraction tools and techniques as the fraction comprising nucleic acid
  • the sample pre-processing step may be any of several known techniques for separating nucleic acid-containing materials from a biological sample.
  • a method of isolating circulating tumor cells is described in a paper by Stott et al. (Stott et al., 2010)
  • a method of differential centrifugation is described in a paper by Raposo et al. (Raposo et al., 1996)
  • a paper by Skog et. al. Skog et. al.
  • Skog et al. Skog et al. al.
  • Nilsson et al. Nilsson et al.
  • sucrose density gradients or organelle electrophoresis are described in U.S. Pat. No. 7,198,923.
  • a method of magnetic activated cell sorting (MACS) is described in a paper by Taylor and Gercel-Taylor (Taylor and Gercel-Taylor, 2008).
  • Methods of filtration concentration are described in a paper by Cheruvanky et al. (Cheruvanky et al., 2007) and in PCT Publication No. WO2011/009104 (Russo et al.).
  • microvesicles can be identified and isolated from bodily fluid of a subject by a newly developed microchip technology that uses a unique microfluidic platform to efficiently and selectively separate tumor-derived microvesicles (Chen et al., 2010).
  • a newly developed microchip technology that uses a unique microfluidic platform to efficiently and selectively separate tumor-derived microvesicles (Chen et al., 2010).
  • the purpose of the extraction enhancement step is to remove or mitigate adverse factors that prevent high quality nucleic acid extraction from a biological sample.
  • factors such as excessive circulating DNA may affect the quality of nucleic acid extraction from such samples and contaminate DNA extracted from within nucleic acid-containing materials.
  • factors such as excessive levels of endogenous RNase may affect the quality of nucleic acid extraction from such samples.
  • Many agents and methods may be used to remove these adverse factors. These methods and agents are referred to collectively herein as an “extraction enhancement operation.”
  • the extraction enhancement operation may involve the addition of nucleic acid extraction enhancement agents to the biological sample or various derivatives of the sample at any given stage of the process.
  • extraction enhancement agents may include, but are not limited to, a commercially available RNase inhibitor such as Superase-In (Ambion Inc.), RNaseIN (Promega Corp.), or other agents that function in a similar fashion; a protease; a reducing agent; a decoy substrate such as a synthetic RNA; a soluble receptor that can bind RNase; a small interfering RNA (siRNA); an RNA binding molecule, such as an anti-RNA antibody, or a chaperone protein; an RNase denaturing substance, such as a high osmolarity solution, a detergent, or a combination thereof.
  • RNase inhibitor such as Superase-In (Ambion Inc.), RNaseIN (Promega Corp.), or other agents that function in a similar fashion
  • a protease such as Superase-
  • enhancement agents may exert their functions in various ways, for example, but not limited to, through inhibiting RNase activity (e.g., RNase inhibitors), through a ubiquitous degradation of proteins (e.g., proteases), or through a chaperone protein (e.g., a RNA-binding protein) that binds and protects RNA.
  • RNase activity e.g., RNase inhibitors
  • a ubiquitous degradation of proteins e.g., proteases
  • a chaperone protein e.g., a RNA-binding protein
  • the extraction enhancement operation may involve the performance of one or more process steps.
  • Such processes include extensive or substantially thorough washing of nucleic acid-containing components of the fraction or sample; size separation of RNases from the biological sample; denaturation of proteins in the biological sample by various techniques including, but not limited to, generating a particular pH condition, a temperature condition, (e.g., the maintenance of a decreasing or lower temperature), freeze/thaw cycles, and combinations thereof.
  • the extraction enhancement operation is comprised of: (a) the addition of one or more enhancement agents to the biological sample; or (b) the performance of one or more enhancement steps prior to nucleic acid extraction; or (c) a combination of enhancement agents and enhancement steps.
  • the enhancement agents may include: (i) RNase inhibitor; (ii) protease; (iii) reducing agent; (iv) decoy substrate, such as synthetic RNA; (v) soluble receptor; (vi) small interfering RNA; (vii) RNA binding molecule, such as anti-RNA antibody, chaperone protein, or an RNase inhibitory protein; and (ix) RNase denaturing substance, such as high osmolarity solution or detergent.
  • the extraction enhancement steps may include: (x) washing; (xi) size-separating RNase from the sample; (xii) effecting RNase denaturation through a physical change, such as by decreasing temperature, or executing a freeze/thaw cycle.
  • the RNase inhibitor may be added to the biological sample or to the fraction comprising a heterogeneous collection of nucleic acid-containing materials prior to extracting nucleic acid.
  • the RNase inhibitor has a concentration of greater than 0.027 AU (1 ⁇ ) for a sample equal to or more than 1 ⁇ l; alternatively, greater than or equal to 0.135 AU (5 ⁇ ) for a sample equal to or more than 1 ⁇ l; alternatively, greater than or equal to 0.27 AU (10 ⁇ ) for a sample equal to or more than 1 ⁇ l; alternatively, greater than or equal to 0.675 AU (25 ⁇ ) for a sample equal to or more than 1 ⁇ l; and alternatively, greater than or equal to 1.35 AU (50 ⁇ ) for a sample equal to or more than wherein the 1 ⁇ protease concentration refers to an enzymatic condition wherein 0.027 AU or more protease is used to treat microvesicles isolated from 1 ⁇ l
  • the nucleic acid extraction step may be performed using procedures that are well-known in the art. Persons of skill will select a particular extraction procedure as appropriate for the particular biological sample. Examples of extraction procedures are provided in patent publications WO/2009/100029 and WO/2011/009104, each of which is incorporated by reference herein for its teaching of these procedures as well as any other procedures mentioned herein. In some instances, with some techniques, it may also be possible to analyze the nucleic acid without first extracting it from the nucleic acid-containing materials.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials; performing an affinity exclusion operation on the heterogeneous collection of nucleic acid-containing materials; and extracting nucleic acid from the resulting materials.
  • the biological sample, pre-processing step, and nucleic acid extraction step are all as described above in relation to the first embodiment.
  • this method will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • FIG. 2 One variation of this second embodiment is shown in FIG. 2 , wherein the method comprises the steps of obtaining a biological sample ( 200 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 210 ), performing an affinity exclusion operation ( 220 ), and extracting nucleic acids from the affinity reduced fraction ( 230 ).
  • the affinity exclusion operation is a novel means for reducing the heterogeneity of the fraction of nucleic acid-containing materials obtained from the preprocessing step. Instead of using affinity selection techniques to enrich for nucleic-acid containing materials of interest, in the affinity exclusion operation, affinity techniques are used to remove nucleic-acid containing materials that are not of interest (e.g., nucleic acid containing materials originating from a cell type that is not of interest in a biomarker assay to be performed on the extracted nucleic acid).
  • affinity techniques are used to remove nucleic-acid containing materials that are not of interest (e.g., nucleic acid containing materials originating from a cell type that is not of interest in a biomarker assay to be performed on the extracted nucleic acid).
  • epithelial cells may be eliminated from the sample prior to execution of the nucleic acid extraction step.
  • the depletion may be complete or partial. For example, in some instances a depletion of 50% of the undesirable materials would be sufficient to achieve a high quality nucleic acid extraction.
  • the surface molecule used in the affinity exclusion operation is a molecule specific to cell type, e.g., but not limited to, any of the cell-type markers listed in Table 1.
  • the surface molecule used in the affinity exclusion operation may be a surface molecule listed in Table 2 if nucleic acid-containing materials originating from a specific tumor cell type are to be excluded in the assay.
  • Erythrocyte (RBC) markers AE1 (Band 3) (Ding et al., 2004) BGP1 (Lewis et al, 1988) CD47 (Oldenborg et al., 2000) Globin (Min-Oo et al., 2004) Glycophorin A (GPA) (Shan et al., 1998; Telen and Chasis, 1990) Rh polypeptides and Rh glycoprotein (Agre et al., 1990; Avent et al., 1996) TER119 (Jiang et al., 2005; Kobayashi et al., 2004) Transferrin receptor (CD71) (Min-Oo et al., 2004; Tao et al., 2000) B.
  • Glycophorin A Glycophorin A
  • Rh polypeptides and Rh glycoprotein Rh glycoprotein
  • TER119 Jiang et al., 2005; Kobayashi et al., 2004
  • Leukocyte (WBC) markers Beta2 Leukocyte Integrins (CD11/CD18) (Flaherty et al., 1997) CD45RA/CD45RB/CD45RO (Bembridge et al., 1993; Lai et al., 1991; Masuoka et al., 1992) CD166 (ALCAM, activated leukocyte cell (Lunter et al., 2005) adhesion molecule) HLA (human leukocyte antigen) (Guerini et al., 2006) LAM-1 (leukocyte adhesion molecule-1) (Kansas et al., 1991) L-selectin (Tu et al., 2002; Venturi et al., 2003) LSP1 (leukocyte-specific protein-1) (Hannigan et al, 2001; Marafioti et al, 2004) Ly-9 (de la Fuente et al, 2001) M6 (leukocyte activation antigen) (Kasin
  • Lymphocyte markers T-cells: CD3, CD5, T cell receptor (TCR) (Berrington et al., 2005) B-cells: MHC class II, CD19, CD21 (Berrington et al., 2005) NK-cells: CD16, CD56, NKp46, NKp44 (Berrington et al., 2005) D.
  • Monocyte/Macrophase markers 125I-WVH-1 (Fayle et al, 1985) CD11b - also a neutrophil marker (Fink et al., 2003) CD14 (Jonas et al., 1990; Ruppert et al., 1991) FcRI and FcRII (Clement et al., 1985) HLA-DR Ki-M1p (Rudolph et al., 1997) p-selectin E.
  • Basophil markers 2D7 (Agis et al., 2006b; Kepley et al., 1995) Basogranulin (BB1) (Agis et al., 2006a) Bsp-1 (Valent et al., 1990) CCR-3 (eotaxin receptor) (Ducrest et al., 2005) CD203-C (E-NPP3) (Sainte-Laudy and Belon, 2006) CDw-17 (lactosylceramide) (Yokohama et al., 2002) CD88 (Yokohama et al., 2002) F. Thrombocyte (platelet) marker: CD36 (Thibert et al., 1995) G.
  • Dendritic cell marker CD83 CD11c CD1a H. Endothelial cells CD31 IV.
  • Other type markers A. Fibroblast marker: Fibroblast-specific protein 1 (FSP1) (Nishitani et al, 2005; Strutz et al, 1995) MAb AS02 Thy. 1
  • FSP1 Fibroblast-specific protein 1
  • Mesenchymal marker CD29 (Siegel et al., 2009) N-cadherin (Li et al., 2011) Vimentin (Punnoose et al., 2010)
  • Glioblastoma cells marker EGFRvIII protein (Al-Nedawi et al., 2008) PDGFR IL13Ra2 CD 133 chondroitin proteoglycan Sulfate 3′-isoLM1 3′6′-isoLD1 GPNMB MRP3 podoplanin D.
  • the method may additionally comprise an extraction enhancement operation, as described above in relation to the first embodiment.
  • the extraction enhancement operation may be performed at any time in the process prior to the final nucleic acid extraction step.
  • nucleic acids there may be an additional step of removing nucleic acids that are not located inside the cells or microvesicles that may be part of the heterogeneous collection of nucleic acid-containing materials.
  • Methods of removing nucleic acids are well known in the art.
  • an enzyme digestion step may be performed at any point in the process.
  • Such enzymes may be a type of ribonuclease that catalyzes the enzymatic digestion of ribonucleic acids or a type of deoxyribonuclease that catalyzes the enzymatic digestion of deoxyribonucleic acids.
  • the invention is a method of extracting nucleic acid from a biological sample, comprising the steps of: obtaining a biological sample; performing a sample pre-processing step on the biological sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials; performing an extraction enhancement operation; performing an affinity exclusion operation; and extracting nucleic acid from the resulting materials.
  • the biological sample, pre-processing step, extraction enhancement operation, affinity exclusion operation, and nucleic acid extraction step are all as described above in relation to the first and second embodiments.
  • the sample pre-processing step must occur before the affinity exclusion operation, but the extraction enhancement operation may occur at any time prior to the nucleic acid extraction step.
  • this embodiment too will result in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • FIG. 3 One variation of the method described in this embodiment is shown in FIG. 3 , wherein the method comprises the steps of obtaining a biological sample ( 300 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 310 ), performing an affinity exclusion operation ( 320 ), performing an extraction enhancement operation ( 330 ), and extracting nucleic acids.
  • this third embodiment may further comprise an additional step of removing nucleic acids that are not located inside the cells or microvesicles that may be part of the heterogeneous collection of nucleic acid-containing materials.
  • Methods of removing nucleic acids are well known in the art.
  • an enzyme digestion step may be performed at any point in the process, e.g., prior to sample preprocessing, prior to performance of the enhancement extraction operation, or prior to nucleic acid extraction.
  • Such enzymes may be a type of ribonuclease that catalyzes the enzymatic digestion of ribonucleic acids or a type of deoxyribonuclease that catalyzes the enzymatic digestion of deoxyribonucleic acids.
  • nucleic acid extraction methods described above may further comprise an affinity enrichment operation, wherein affinity selection methods are used to enrich for nucleic acid-containing materials of a certain type or originating from a particular cell, tissue or organ of the body, e.g., lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, or fetus cells.
  • affinity selection methods are used to enrich for nucleic acid-containing materials of a certain type or originating from a particular cell, tissue or organ of the body, e.g., lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, or fetus cells.
  • nucleic acid-containing materials often carry surface molecules such as antigens from their donor cells
  • surface molecules may be used to identify, isolate and/or enrich for nucleic acid-containing materials from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008).
  • nucleic acid-containing materials originating from distinct cell populations can be analyzed for their nucleic acid content.
  • tumor (malignant and non-malignant) nucleic acid-containing materials carry tumor-associated surface antigens and may be detected, isolated, or enriched via these specific tumor-associated surface antigens.
  • the surface antigen is epithelial-cell-adhesion-molecule (EpCAM), which is specific to nucleic acid-containing materials from carcinomas of lung, colorectal, breast, prostate, head and neck, and hepatic origin, but not of hematological cell origin (Balzar et al., 1999; Went et al., 2004).
  • EpCAM epithelial-cell-adhesion-molecule
  • the surface antigen is CD24, which is a glycoprotein specific to urine nucleic acid-containing materials (Keller et al., 2007).
  • the surface antigen is selected from a group of molecules such as CD70, carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fas ligand, TRAIL, transferrin receptor, p38.5, p97 and HSP72.
  • tumor specific nucleic acid-containing materials may be characterized by the lack of surface markers, such as CD80 and CD86.
  • the surface antigens are any one of the tumor markers, listed in Table 2.
  • the surface antigens in Table 2 may be used to perform an affinity enrichment operation so that nucleic acid-containing materials from a specific tumor cell type are enriched.
  • the surface antigen in the affinity enrichment operation may be any of the surface markers listed in the foregoing Table 1.
  • the surface markers described in Tables 1 and 2 may be used interchangeably for an affinity exclusion operation or an affinity enrichment operation depending on the objectives of a given assay and nucleic acid extraction method practiced according to the teachings of this disclosure.
  • the surface markers for fibroblasts may be used to exclude fibroblast-derived nucleic acid-containing materials when a procedure for evaluating glioblastoma biomarkers is performed.
  • the surface markers for fibroblasts may be used to enrich fibroblast-derived nucleic acid-containing materials when a procedure for evaluating fibroblastoma is performed.
  • affinity procedure for depletion or enrichment of nucleic acid-containing materials from a specific cell type may be accomplished, for example, by using antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen (hereinafter “affinity agent(s)”).
  • affinity agent(s) antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen.
  • the surface antigen is specific for a cancer type.
  • the surface antigen is specific for a cell type which is not necessarily cancerous.
  • nucleic acid extractions obtained by the novel methods described herein are characterized by high yield and high integrity, making the extracted nucleic acids useful for various applications in which high quality nucleic acid extractions are required or preferred.
  • the performance of any of the various nucleic acid extraction methods according to the present invention preferably results in a nucleic acid extraction that meets one or more of the quality standards described below in terms of the quantitative ratio of 18S rRNA to 28S rRNA, or nucleic acid yield.
  • the nucleic acid extraction methods of this invention will result in a nucleic acid extraction in which one can detect significant quantities of ribosomal RNA (rRNA), specifically 18S and 28S rRNA, preferably in a ratio of approximately 1:1 to approximately 1:2; and more preferably, in a ratio of approximately 1:2.
  • rRNA ribosomal RNA
  • nucleic acid extraction methods of the present invention will preferably result in improved yields of extracted nucleic acid.
  • a nucleic acid yield of greater than or equal to 50 pg/ml from a 20 ml low protein biological sample such as urine.
  • a nucleic acid yield of greater than or equal to 50 pg/ml from 1 ml of a high protein biological sample, such as scrum or plasma.
  • the novel nucleic acid extractions obtained by the methods described herein preferably meet one or more of the following quality standards: (1) the detection of 18S and 28S rRNA, preferably in a ratio of approximately 1:1 to approximately 1:2; and more preferably, approximately 1:2; and/or (2) a nucleic acid yield of greater than or equal to 50 pg/ml from a 20 ml low protein biological sample or a 1 ml high protein biological sample.
  • nucleic acid extraction methods Use of the nucleic acid extraction methods, and resulting nucleic acid extractions, in nucleic acid analysis for research and clinical applications.
  • the nucleic acid extraction methods of the present invention may be used to produce novel and improved nucleic acid extractions for various applications, including but not limited to analysis of nucleic acid for research (e.g., research in support of the discovery of new biomarkers or biomarker associations) or clinical analysis of nucleic acid in aid of patient diagnostics, prognostics, theranostics, monitoring, predictive medicine, personalized medicine, integrated medicine, pharmacodiagnostics and diagnostic/prescription partnering (companion diagnostics).
  • analysis of nucleic acid for research e.g., research in support of the discovery of new biomarkers or biomarker associations
  • clinical analysis of nucleic acid in aid of patient diagnostics, prognostics, theranostics, monitoring, predictive medicine, personalized medicine, integrated medicine, pharmacodiagnostics and diagnostic/prescription partnering (companion diagnostics).
  • the extracted nucleic acids are analyzed directly without an amplification step.
  • Direct analysis may be performed with different methods including, but not limited to, nanostring technology.
  • NanoString technology enables identification and quantification of individual target molecules in a biological sample by attaching a color coded fluorescent reporter to each target molecule. This approach is similar to the concept of measuring inventory by scanning barcodes. Reporters can be made with hundreds or even thousands of different codes allowing for highly multiplexed analysis. The technology is described in a publication by Geiss et al. (Geiss et al., 2008) and is incorporated herein by reference for this teaching.
  • nucleic acid amplification it may be beneficial or otherwise desirable to amplify the nucleic acid prior to analyzing it.
  • Methods of nucleic acid amplification are commonly used and generally known in the art, many examples of which are described herein. If desired, the amplification can be performed such that it is quantitative. Quantitative amplification will allow quantitative determination of relative amounts of the various nucleic acids, to generate a profile as described below.
  • the extracted nucleic acid is RNA.
  • the RNA is then preferably reverse-transcribed into complementary DNA (cDNA) before further amplification.
  • cDNA complementary DNA
  • Such reverse transcription may be performed alone or in combination with an amplification step.
  • a method combining reverse transcription and amplification steps is reverse transcription polymerase chain reaction (RT-PCR), which may be further modified to be quantitative, e.g., quantitative RT-PCR as described in U.S. Pat. No. 5,639,606, which is incorporated herein by reference for this teaching.
  • Nucleic acid amplification methods include, without limitation, polymerase chain reaction (PCR) (U.S. Pat. No. 5,219,727) and its variants such as in situ polymerase chain reaction (U.S. Pat. No. 5,538,871), quantitative polymerase chain reaction (U.S. Pat. No. 5,219,727), nested polymerase chain reaction (U.S. Pat. No.
  • PCR polymerase chain reaction
  • U.S. Pat. No. 5,219,727 in situ polymerase chain reaction
  • quantitative polymerase chain reaction U.S. Pat. No. 5,219,727
  • nested polymerase chain reaction U.S. Pat. No.
  • the analysis of nucleic acids present in the nucleic acid-containing materials may be quantitative and/or qualitative.
  • the amounts (expression levels), either relative or absolute, of specific nucleic acids of interest within the nucleic acid-containing materials are measured with methods known in the art (described below).
  • the species of specific nucleic acids of interest within the nucleic acid-containing materials, whether wild type or variants, are identified with methods known in the art.
  • the invention further includes a novel, high-quality profile of nucleic acids from a biological sample.
  • profiles are generated by performing any of the various embodiments and variations of the nucleic acid extraction methods disclosed herein, and analyzing the resulting nucleic acid.
  • a profile refers to a collection of characteristics, which can be determined through the quantitative or qualitative analysis of one or more biological components or materials (such as nucleic acid) contained in a sample (such as a nucleic acid extraction obtained by any of the methods disclosed herein).
  • a reference profile is a profile obtained from an independent subject or from the same subject at a different time point.
  • RNA can be coding RNA, e.g., messenger RNA which may encode proteins.
  • RNA can also be non-coding RNA (ncRNA), e.g., ribosomal RNA, transfer RNA, microRNA, and other non-coding transcripts that may originate from genomic DNA.
  • ncRNA non-coding RNA
  • These non-coding RNA transcripts may include transcripts that are transcribed from satellite repeats and transposons, which may be DNA transposons or retrotransposons.
  • the nucleic acids can also be DNA.
  • DNA can be single-stranded DNA, e.g., cDNA, that is reverse transcribed from RNA.
  • the DNA can also be single-stranded DNA that is generated during DNA replication. Genomic DNA replicates in the nucleus while the cell is dividing. Some of the replicated DNA may come off its template, be exported out of nucleus, and packaged in microvesicles. It is also possible for the DNA to be double-stranded DNA.
  • the DNA can be non-coding DNA (ncDNA).
  • High quality nucleic acid profiles are highly desirable for many uses, such as for research (e.g., research in support of the discovery of new biomarkers or biomarker associations) or clinical uses such as patient diagnostics, prognostics, theranostics, monitoring, predictive medicine, personalized medicine, integrated medicine, pharmacodiagnostics and diagnostic/prescription partnering (companion diagnostics). It is desirable in that such profiles are consistent between samples. Such consistency cannot be achieved without high quality nucleic acid extractions.
  • the nucleic acid profile includes one or more genetic aberrations, which is used herein to refer to nucleic acid amounts as well as nucleic acid variants.
  • the nucleic acid is endogenous to the subject.
  • Genetic aberrations include, without limitation, over-expression of one or more genomic elements, underexpression of one or more genomic elements, alternative production of splice variants of one or more genomic elements, copy number variants (CNV) of one or more genomic elements (e.g.
  • DNA double minutes DNA double minutes
  • nucleic acid modifications e.g., methylation, acetylation and phosphorylations
  • single nucleotide polymorphisms SNPs
  • chromosomal rearrangements e.g., inversions, deletions and duplications
  • mutations insertions, deletions, duplications, missense, nonsense, synonymous or any other nucleotide changes of one or more genomic elements, which mutations, in many cases, ultimately affect the activity and function of the genome, lead to alternative transcriptional splice variants and/or changes of gene expression level.
  • the nucleic acids in the nucleic acid-containing materials can be any type of nucleic acid, including but not limited to the examples provided herein.
  • the nucleic acids can be coding RNA, e.g., messenger RNA which may encode proteins; non-coding RNA (ncRNA), e.g., ribosomal RNA, transfer RNA, microRNA, and other non-coding transcripts that may originate from genomic DNA.
  • Non-coding RNA transcripts may include transcripts that are transcribed from satellite repeats and transposons, which may be DNA transposons or retrotransposons.
  • the nucleic acids can include single-stranded DNA (ssDNA), e.g., cDNA, which is reverse transcribed from RNA and ssDNA that is generated during DNA replication; double-stranded DNA (dsDNA); DNA that codes for proteins (coding DNA); and DNA that does not code for proteins, i.e., non-coding DNA (ncDNA).
  • ssDNA single-stranded DNA
  • dsDNA double-stranded DNA
  • coding DNA DNA that codes for proteins
  • ncDNA non-coding DNA
  • nucleic acid modifications can be assayed by methods described in, e.g., U.S. Pat. No.
  • methylation profiles may be determined by, e.g., the Illumina DNA Methylation OMA003 Cancer Panel.
  • SNPs and mutations can be detected by hybridization with allele-specific probes, enzymatic mutation detection, chemical cleavage of mismatched heteroduplex (Cotton et al., 1988), ribonuclease cleavage of mismatched bases (Myers et al., 1985), mass spectrometry (U.S. Pat. Nos.
  • nucleic acid sequencing single strand conformation polymorphism (SSCP) (Orita et al., 1989), denaturing gradient gel electrophoresis (DGGE) (Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), temperature gradient gel electrophoresis (TGGE) (Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), restriction fragment length polymorphisms (RFLP) (Kan and Dozy, 1978a; Kan and Dozy, 1978b), oligonucleotide ligation assay (OLA), allele-specific PCR (ASPCR) (U.S. Pat. No.
  • DGGE denaturing gradient gel electrophoresis
  • TGGE temperature gradient gel electrophoresis
  • RFLP restriction fragment length polymorphisms
  • OLA oligonucleotide ligation assay
  • ASPCR allele-specific PCR
  • gene expression levels may be determined by the serial analysis of gene expression (SAGE) technique (Velculescu et al., 1995).
  • SAGE serial analysis of gene expression
  • the present invention is also directed to a kit for obtaining nucleic acids from biological samples.
  • the kit may comprise an affinity agent; an extraction enhancement agent; and a lysis buffer.
  • the affinity agent is capable of binding to one or more markers listed in Table 1 or Table 2.
  • the kit may further comprise instructions for using the kit.
  • Instructions for using the kit may be put in the package with the other kit components or in a different location accessible to a kit user (e.g., on a website or webpage accessible to the kit purchaser).
  • the content of the instructions may include, but is not limited to, instructions for how to use the affinity agent, how to perform an affinity exclusion operation, how to reconstitute reagents, how to do the nucleic acid enhancement, how to use the lysis buffer, and how to carry out the whole procedure of obtaining nucleic acids by using the kit.
  • the extraction enhancement agent may be RNase inhibitor; protease; reducing agent; decoy substrate; soluble receptor; small interfering RNA; RNA binding molecule; RNase denaturing substance; or any combination of any of the foregoing.
  • affinity agent is suitable for performing an exclusion operation
  • instructions included in or with the kit comprise instructions for using the affinity agent in an affinity exclusion operation.
  • Kits of this nature may further comprise a second affinity agent, and instructions for using the second affinity agent in an affinity enrichment operation.
  • the kit may further comprise DNase, RNase, or both, and instructions for their use.
  • DNase, RNase, or both may be used to eliminate DNA or RNA that is of no interest in the intended assay, e.g., DNA or RNA that clings to the outside of the nucleic acid-containing materials in the extraction.
  • the amount of DNase or RNase may depend on the source of the biological sample. In some samples, the amount of DNA or RNA of no interest is relatively high, and therefore, more DNase or RNase will need to be added in the extraction process.
  • FIG. 1 One variation of the invention is shown in FIG. 1 , where the method comprises the steps of obtaining a biological sample ( 100 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 110 ), performing an extraction enhancement operation on the fraction ( 120 ), and extracting nucleic acid from the fraction ( 130 ).
  • FIG. 2 One variation of the invention is shown in FIG. 2 , where the method comprises the steps of obtaining a biological sample ( 200 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 210 ), performing an affinity exclusion operation ( 220 ), and extracting nucleic acids from the affinity reduced fraction ( 230 ).
  • FIG. 3 One variation of the invention is shown in FIG. 3 , where the method comprises the steps of obtaining a biological sample ( 300 ), pre-processing the sample to obtain a fraction comprising a heterogeneous collection of nucleic acid-containing materials ( 310 ), performing an affinity exclusion operation ( 320 ), performing an extraction enhancement operation ( 330 ), and extracting nucleic acids.
  • Heterogeneous collections of nucleic acid-containing materials can be isolated from a biological sample from a subject that has or is suspected to have cancer.
  • a urine sample is collected from the subject.
  • a fraction containing nucleic acid-containing materials is enriched by centrifugation or filtration from the urine.
  • the resulting fraction contains a heterogeneous collection of nucleic acid-containing materials, which includes a mixture of microvesicles and cells in addition to other nucleic acid-containing materials.
  • This fraction is then incubated with extraction enhancement agents, such as RNase inhibitors, to prevent or mitigate those factors that may prevent high quality nucleic acid extraction.
  • the fraction is subjected to an affinity enrichment operation to enrich for the potential circulating tumor cells and microvesicles of particular interest.
  • a surface antigen carried by both the circulating tumor cells and microvesicles is used to select for and purify these particular nucleic acid-containing materials from the remaining mixture.
  • Nucleic acids from the purified circulating tumor cells and microvesicles are extracted and analyzed for the presence, absence, or levels of genetic aberrations that are associated with the presence or absence of malignant cancer; or stage or grade of the tumor from which the cells and microvesicles may have originated from.

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