WO2013172934A1 - Variants génétiques d'intégrine et récurrence de tumeurs spécifique au stade chez des patients atteints d'un cancer du côlon au stade ii et iii - Google Patents

Variants génétiques d'intégrine et récurrence de tumeurs spécifique au stade chez des patients atteints d'un cancer du côlon au stade ii et iii Download PDF

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WO2013172934A1
WO2013172934A1 PCT/US2013/030301 US2013030301W WO2013172934A1 WO 2013172934 A1 WO2013172934 A1 WO 2013172934A1 US 2013030301 W US2013030301 W US 2013030301W WO 2013172934 A1 WO2013172934 A1 WO 2013172934A1
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cancer
patient
experience
tumor recurrence
genotype
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WO2013172934A8 (fr
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Heinz-Josef Lenz
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University Of Southern California
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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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • This invention relates to the field of pharmaco genomics and specifically to the application of genetic polymorphisms to predict outcome of a clinical procedure.
  • polymorphism In nature, organisms of the same species usually differ from each other in some aspects, e.g., their appearance. The differences are genetically determined and are referred to as polymorphism. Genetic polymorphism is the occurrence in a population of two or more genetically determined alternative phenotypes due to different alleles. Polymorphism can be observed at the level of the whole individual (phenotype), in variant forms of proteins and blood group substances (biochemical polymorphism), morphological features of chromosomes (chromosomal polymorphism) or at the level of DNA in differences of nucleotides (DNA polymorphism).
  • Polymorphism also plays a role in determining differences in an individual's response to drugs.
  • Pharmacogenetics and pharmacogenomics are multidisciplinary research efforts to study the relationship between genotype, gene expression profiles, and phenotype, as expressed in variability between individuals in response to or toxicity from drugs. Indeed, it is now known that cancer chemotherapy is limited by the predisposition of specific populations to drug toxicity or poor drug response.
  • germline polymorphisms in clinical oncology, see Lenz (2004) J. Clin. Oncol. 22(13):2519-2521; Park et al. (2006) Curr. Opin. Pharma.
  • CRC colorectal cancer
  • GA gastric adenocarcinoma
  • CFR case-fatality ratio
  • T stage, N stage remains the main prognostic determinant for CRC and GA. Patients in early stages who are fortunate enough to undergo surgery, are considered candidates for cure. However, ⁇ 30%-40% of CRC patients and ⁇ 40%-60% of GA patients who underwent surgery followed by adjuvant (radio)chemotherapy will develop recurrence.
  • compositions, methods and kits for determining the likely tumor recurrence in cancer patients by screening one or more of the ITGB3, ITGB1 or ITGB4 polymorphisms in samples isolated from the patient.
  • a method for aiding in the determination of or determining whether a cancer patient is likely to, or identifying a patient or population of patients that is likely to, experience a longer or shorter time to tumor recurrence comprising, or alternatively consisting essentially of, or yet alternatively consisting of, screening a tissue or cell sample isolated from the patient for the ITGB3 rs4642 A/G polymorphism, wherein a (A/ A) genotype determines that the patient is likely to experience a longer time to tumor recurrence, or a (G/G or A/G) genotype determines that the patient is likely to experience a shorter time to tumor recurrence.
  • a method for aiding in the determination of or determining whether a cancer patient is likely to experience a longer or shorter time to tumor recurrence comprising screening a tissue or cell sample isolated from the patient for at least one of the integrin beta 1 (ITGB1) rs2298141 A/G polymorphism or the integrin beta 4 (ITGB4) rs7562325 C/T polymorphism, wherein the presence:
  • the patient suffers from at least one cancer of the type of the group of lung cancer, non-small cell lung cancer, breast cancer, head and neck cancer, ovarian cancer, colon cancer, rectal cancer, Stage II or Stage III colon cancer, localized gastric cancer, gastric adenocarcinoma, colorectal cancer, esophageal cancer, gastric cancer, liver cancer, bone cancer, spleen cancer, pancreatic cancer, or gallbladder cancer.
  • the patient suffers from one or more gastrointestinal cancer.
  • the gastrointestinal cancer is colon cancer or gastric cancer.
  • a patient includes but is not limited to a human, a simian, a murine, a bovine, an equine, a porcine, a feline, a canine, or an ovine.
  • FIG. 1 shows the time to tumor recurrence (TTR) as correlated with ITGB3 rs4642 in stage II colon cancer.
  • FIG. 2 shows the TTR as correlated with ITGB1 rs2298141 and IGTA4 rs7562325 in stage III colon cancer.
  • BIOLOGY F. M. Ausubel et al. eds. (2007)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc., N.Y.); PCR 1 : A PRACTICAL APPROACH (M. MacPherson et al. IRL Press at Oxford University Press (1991)); PCR 2: A PRACTICAL APPROACH (M.J.
  • a cell includes a single cell as well as a plurality of cells, including mixtures thereof.
  • compositions and methods include the recited elements, but not excluding others.
  • Consisting essentially of when used to define compositions and methods shall mean excluding other elements of any essential significance to the composition or method.
  • Consisting of shall mean excluding more than trace elements of other ingredients for claimed compositions and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this disclosure. Accordingly, it is intended that the methods and compositions can include additional steps and components (comprising) or alternatively including steps and compositions of no significance (consisting essentially of) or alternatively, intending only the stated method steps or
  • compositions consisting of.
  • alleles refers to alternative forms of a gene or portions thereof. Alleles occupy the same locus or position on homologous chromosomes. When a subject has two identical alleles of a gene, the subject is said to be homozygous for the gene or allele. When a subject has two different alleles of a gene, the subject is said to be heterozygous for the gene. Alleles of a specific gene can differ from each other in a single nucleotide, or several nucleotides, and can include substitutions, deletions and insertions of nucleotides. An allele of a gene can also be a form of a gene containing a mutation.
  • a polymorphic locus is a single nucleotide polymorphic
  • SNP locus If the allelic composition of a SNP locus is heterozygous, the genotype of the SNP locus will be identified as "X/Y" wherein X and Y are two different nucleotides, e.g., G/C for the ITGB3 rs4642 A/G SNP. If the allelic composition of a SNP locus is homozygous, the genotype of the SNP locus will be identified as "X X" wherein X identifies the nucleotide that is present at both alleles, e.g., G/G for the ITGB3 rs4642 A/G SNP.
  • genetic marker refers to an allelic variant of a polymorphic region of a gene of interest and/or the expression level of a gene of interest.
  • polymorphism refers to the coexistence of more than one form of a gene or portion thereof.
  • a portion of a gene of which there are at least two different forms, i.e., two different nucleotide sequences, is referred to as a "polymorphic region of a gene.”
  • polymorphic region can be a single nucleotide, the identity of which differs in different alleles.
  • a "polymorphic gene” refers to a gene having at least one polymorphic region.
  • genotype refers to the specific allelic composition of an entire cell or a certain gene and in some aspects a specific polymorphism associated with that gene, whereas the term “phenotype” refers to the detectable outward manifestations of a specific genotype.
  • the phrase "genotypes are determined” includes screening methods such as PCR, direct sequencing, ligation amplification (or ligase chain reaction, LCR) and amplification methods. These methods are known and widely practiced in the art. See, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202 and Innis et al, 1990 (for PCR); and Wu, D.Y. et al. (1989) Genomics 4:560-569 (for LCR).
  • the PCR procedure describes a method of gene amplification which is comprised of (i) sequence-specific hybridization of primers to specific genes within a DNA sample (or library), (ii) subsequent amplification involving multiple rounds of annealing, elongation, and denaturation using a DNA polymerase, and (iii) screening the PCR products for a band of the correct size.
  • the primers used are oligonucleotides of sufficient length and appropriate sequence to provide initiation of polymerization, i.e. each primer is specifically designed to be complementary to each strand of the genomic locus to be amplified.
  • Reagents and hardware for conducting PCR are commercially available. Primers useful to amplify sequences from a particular gene region are preferably complementary to, and hybridize specifically to sequences in the target region or in its flanking regions. Nucleic acid sequences generated by amplification may be sequenced directly. Alternatively the amplified sequence(s) may be cloned prior to sequence analysis. A method for the direct cloning and sequence analysis of enzymatically amplified genomic segments is known in the art.
  • encode refers to a polynucleotide which is said to "encode” a polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, it can be transcribed and/or translated to produce the mRNA for the polypeptide and/or a fragment thereof.
  • the antisense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.
  • isolated or recombinant refers to molecules separated from other DNAs or RNAs, respectively that are present in the natural source of the macromolecule as well as polypeptides.
  • isolated or recombinant nucleic acid is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state.
  • isolated is also used herein to refer to polynucleotides, polypeptides and proteins that are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides.
  • the term "isolated or recombinant” means separated from constituents, cellular and otherwise, in which the cell, tissue, polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof, which are normally associated in nature.
  • an isolated cell is a cell that is separated from tissue or cells of dissimilar phenotype or genotype.
  • An isolated polynucleotide is separated from the 3' and 5' contiguous nucleotides with which it is normally associated in its native or natural environment, e.g., on the chromosome.
  • a non-naturally occurring polynucleotide, peptide, polypeptide, protein, antibody or fragment(s) thereof does not require "isolation" to distinguish it from its naturally occurring counterpart.
  • a "patient” as used herein intends an animal patient, a mammal patient or yet further a human patient.
  • a patient includes but is not limited to a simian, a human, a murine, a bovine, an equine, a porcine, a feline, a canine, or an ovine.
  • Gastrointestinal cancer refers to malignant conditions of the gastrointestinal tract.
  • gastrointestinal cancer includes gastrointestinal stromal tumors (GIST), esophageal cancer, stomach cancer (also called gastric cancer), liver cancer (also called hepatocellular carcinoma, HCC, or hepatoma), gallbladder cancer, pancreatic cancer, colorectal cancer (e.g., called colon cancer, bowel cancer, and rectal cancer) and anal cancer.
  • GIST gastrointestinal stromal tumors
  • esophageal cancer also called gastric cancer
  • liver cancer also called hepatocellular carcinoma, HCC, or hepatoma
  • gallbladder cancer pancreatic cancer
  • colorectal cancer e.g., called colon cancer, bowel cancer, and rectal cancer
  • gastrointestinal cancer includes esophageal cancer, stomach cancer, liver cancer and colorectal cancer. In another aspect, gastrointestinal cancer includes stomach cancer and colorectal cancer.
  • Colorectal cancer or "bowel cancer” refers to a cancer in the colon, rectum, appendix or anus.
  • colorectal cancer includes both colon cancer and rectal cancer.
  • surgical resection refers to surgical removal of a tumor of concern.
  • Tumor Recurrence as used herein and as defined by the National Cancer Institute is cancer that has recurred (come back), usually after a period of time during which the cancer could not be detected. The cancer may come back to the same place as the original (primary) tumor or to another place in the body. It is also called recurrent cancer.
  • TTR Time to Tumor Recurrence
  • OS Global System for Mobile Communications
  • Relative Risk in statistics and mathematical epidemiology, refers to the risk of an event (or of developing a disease) relative to exposure. Relative risk is a ratio of the probability of the event occurring in the exposed group versus a non-exposed group.
  • the term "determine” or “determining” is to associate or affiliate a patient closely to a group or population of patients who likely experience the same or a similar clinical response.
  • Stage I cancer typically identifies that the primary tumor is limited to the organ of origin.
  • Stage II intends that the primary tumor has spread into surrounding tissue and lymph nodes immediately draining the area of the tumor.
  • Stage III intends that the primary tumor is large, with fixation to deeper structures.
  • Stage IV intends that the primary tumor is large, with fixation to deeper structures. See pages 20 and 21, CANCER BIOLOGY, 2 nd Ed., Oxford University Press (1987).
  • a "tumor” is an abnormal growth of tissue resulting from uncontrolled, progressive multiplication of cells and serving no physiological function.
  • a “tumor” is also known as a neoplasm.
  • Having a/the same cancer is used when comparing one patient to another or alternatively, one patient population to another patient population.
  • the two patients or patient population will each have or be suffering from colon cancer.
  • blood refers to blood which includes all components of blood circulating in a subject including, but not limited to, red blood cells, white blood cells, plasma, clotting factors, small proteins, platelets and/or cryoprecipitate. This is typically the type of blood which is donated when a human patent gives blood.
  • a "normal cell corresponding to the tumor tissue type” refers to a normal cell from a same tissue type as the tumor tissue.
  • a non-limiting examples is a normal lung cell from a patient having lung tumor, or a normal colon cell from a patient having colon tumor.
  • a "blood cell” refers to any of the cells contained in blood.
  • a blood cell is also referred to as an erythrocyte or leukocyte, or a blood corpuscle.
  • Non-limiting examples of blood cells include white blood cells, red blood cells, and platelets.
  • Plasma is known in the art as the yellow liquid component of blood, in which the blood cells in whole blood are typically suspended. It makes up about 55% of the total blood volume.
  • Blood plasma can be prepared by spinning a tube of fresh blood containing an anti-coagulant in a centrifuge until the blood cells fall to the bottom of the tube. The blood plasma is then poured or drawn off. Blood plasma has a density of approximately 1025 kg/m3, or 1.025 kg/1.
  • a "native” or “natural” or “wild-type” antigen is a polypeptide, protein or a fragment which contains an epitope and which has been isolated from a natural biological source. It also can specifically bind to an antigen receptor.
  • the disclosure further provides diagnostic, prognostic and therapeutic methods, which are based, at least in part, on determination of the identify of a genotype of interest identified herein.
  • information obtained using the diagnostic assays described herein is useful for determining whether a subject is likely to experience a longer time to tumor recurrence.
  • a patient's likely clinical outcome following a clinical procedure such as surgery can be expressed in relative terms.
  • a patient having a particular genotype or expression level may experience relatively longer overall survival than a patient or patients not having the genotype or expression level.
  • the patient having the particular genotype or expression level alternatively, can be considered as likely to survive.
  • a patient having a particular genotype or expression level may experience relatively shorter time to tumor recurrence than a patient or patients not having the genotype or expression level.
  • the patient having the particular genotype or expression level alternatively, can be considered as not likely to suffer tumor recurrence.
  • information obtained using the diagnostic assays described herein may be used alone or in combination with other information, such as, but not limited to, genotypes or expression levels of other genes, clinical chemical parameters, histopathological parameters, or age, gender and weight of the subject.
  • the information obtained using the diagnostic assays described herein is useful in determining or identifying the clinical outcome of a treatment, selecting a patient for a treatment, or treating a patient, etc.
  • the information obtained using the diagnostic assays described herein is useful in aiding in the determination or identification of clinical outcome of a treatment, aiding in the selection of a patient for a treatment, or aiding in the treatment of a patient and etc.
  • the genotypes or expression levels of one or more genes as disclosed herein are used in a panel of genes, each of which contributes to the final diagnosis, prognosis or treatment.
  • the methods of this disclosure are useful for the diagnosis and prognosis of patients suffering from at least one or more cancer of the group: lung cancer, non- small cell lung cancer,
  • a patient includes but is not limited to a human, a simian, a murine, a bovine, an equine, a porcine, a feline, a canine or an ovine.
  • a method for aiding in the determination of or determining whether a cancer patient is likely to, or identifying a patient or population of patients that is likely to, experience a longer or shorter time to tumor recurrence comprising, or alternatively consisting essentially of, or yet alternatively consisting of, screening a tissue or cell sample isolated from the patient for the ITGB3 rs4642 A/G polymorphism, wherein a (A/ A) genotype determines that the patient is likely to experience a longer time to tumor recurrence, or a (G/G or A/G) genotype determines that the patient is likely to experience a shorter time to tumor recurrence.
  • a method for aiding in the determination of or determining whether a cancer patient is likely to, or identifying a patient or population of patients that is likely to, experience a longer or shorter time to tumor recurrence comprising, or alternatively consisting essentially of, or yet alternatively consisting of, screening a tissue or cell sample isolated from the patient for the ITGB3 rs4642 A/G polymorphism.
  • the cancer is one or more gastrointestinal cancer.
  • the cancer is one or more colorectal cancer.
  • the colorectal cancer is colon cancer, or in particular Stage II colon cancer, or adjuvant colon cancer.
  • a (A/ A) genotype determines that the patient is likely to experience a longer time to tumor recurrence.
  • a patient likely to experience a longer time to tumor recurrence is a patient likely to experience a longer time to tumor recurrence than a patient suffering from a same cancer and having a (G/G or A/G) genotype.
  • a (G/G or A/G) genotype determines that the patient is likely to experience a shorter time to tumor recurrence.
  • a patient likely to experience a shorter time to tumor recurrence is a patient likely to experience a shorter time to tumor recurrence than a patient suffering from a same cancer and having a (A/ A) genotype.
  • a method for aiding in the determination of or determining whether a cancer patient is likely to experience a longer or shorter time to tumor recurrence comprising screening a tissue or cell sample isolated from the patient for at least one of the integrin beta 1 (ITGB1) rs2298141 A/G polymorphism or the integrin beta 4 (ITGB4) rs7562325 C/T polymorphism, wherein the presence:
  • the presence of (a) or (b) genotype determines that the patient is likely to experience a longer time to tumor recurrence.
  • a patient likely to experience a longer time to tumor recurrence is as compared to a patient suffering from a same cancer and not having an (a) or (b) genotype.
  • the presence of neither (a) nor (b) genotype determines that the patient is likely to experience a shorter time to tumor recurrence.
  • a patient likely to experience a shorter time to tumor recurrence is as compared to a patient suffering from a same cancer and having an (a) or (b) genotype.
  • Also provided is a method for aiding in the determination of or determining whether a cancer patient is likely to experience a longer or shorter time to tumor recurrence comprising screening a tissue or cell sample isolated from the patient for at least one of the integrin beta 1 (ITGB1) rs2298141 A/G polymorphism or the integrin beta 4 (ITGB4) rs7562325 C/T polymorphism, wherein the presence:
  • a (T/T) genotype of the rs7562325 C/T polymorphism determines that the patient is likely to experience a longer time to tumor recurrence, or the presence of neither (a) nor (b) determines that the patient is likely to experience a shorter time to tumor recurrence. In one aspect, neither the presence of (a) nor (b) genotype determines that the patient is likely to experience a longer time to tumor recurrence.
  • the patient suffers from at least one cancer of the type of the group of lung cancer, non-small cell lung cancer, breast cancer, head and neck cancer, ovarian cancer, colon cancer, a stage of cancer that is excludes Stage II colon cancer,
  • Stage II or Stage III colon cancer localized gastric cancer, gastric adenocarcinoma, rectal cancer, colorectal cancer, esophageal cancer, gastric cancer, liver cancer, bone cancer, spleen cancer, pancreatic cancer, or gallbladder cancer.
  • the patient suffers from one or more gastrointestinal cancer.
  • the colon cancer is stage II or III colon cancer.
  • the gastric cancer is localized gastric adenocarcinoma.
  • the patient has is an adjuvant patient having received surgical resection.
  • the patient is a Stage II or Stage III cancer patient.
  • Suitable patient samples in the methods include, but are not limited to a sample that comprises, or alternatively consisting essentially of, or yet further consisting of, at least one of blood, a tumor cell, a normal cell adjacent to a tumor, a normal cell corresponding to the tumor tissue type, a blood cell, a peripheral blood lymphocyte, or combinations thereof.
  • the samples can be at least one of an original sample recently isolated from the patient, a fixed tissue, a frozen tissue, a biopsy tissue, a resection tissue, a microdissected tissue, or combinations thereof.
  • genotype is determined by a method comprising, or alternatively consisting essentially of, or yet further consisting of, polymerase chain reaction analysis (PCR), sequencing analysis, restriction enzyme analysis, mismatch cleavage analysis, single strand conformation polymorphism analysis, denaturing gradient gel electrophoresis, selective oligonucleotide hybridization, selective PCR amplification, selective primer extension, oligonucleotide ligation assay, exonuclease-resistant nucleotide analysis, Genetic Bit Analysis, primer-guided nucleotide incorporation analysis PCR, PCR-restriction fragment length polymorphism (PCR-RFLP), direct DNA sequencing, whole genome sequencing, and/or microarray.
  • PCR polymerase chain reaction analysis
  • a patient includes but is not limited to a human, a simian, a murine, a bovine, an equine, a porcine, a feline, a canine, or an ovine.
  • diagnosis methods described in the present disclosure can provide useful information for optimizing treatment strategy. For example, patients at high risk of tumor recurrence or having a low expectation of survival may be treated with more aggressive therapy
  • information obtained using the diagnostic assays described herein is useful for determining if a subject will likely, more likely, or less likely to survive or experience tumor recurrence.
  • a doctor can recommend a therapeutic protocol, useful for treating reducing the malignant mass or tumor in the patient or treat cancer in the individual.
  • knowledge of the identity of a particular allele in an individual allows customization of therapy for a particular disease to the individual's genetic profile, the goal of "pharmacogenomics".
  • an individual's genetic profile can enable a doctor: 1) to more effectively prescribe a drug that will address the molecular basis of the disease or condition; 2) to better determine the appropriate dosage of a particular drug and 3) to identify novel targets for drug development.
  • the identity of the genotype or expression patterns of individual patients can then be compared to the genotype or expression profile of the disease to determine the appropriate drug and dose to administer to the patient.
  • Detection of point mutations or additional base pair repeats can be accomplished by molecular cloning of the specified allele and subsequent sequencing of that allele using techniques known in the art, in some aspects, after isolation of a suitable nucleic acid sample using methods known in the art.
  • the gene sequences can be amplified directly from a genomic DNA preparation from the tumor tissue using PCR, and the sequence composition is determined from the amplified product.
  • numerous methods are available for isolating and analyzing a subject's DNA for mutations at a given genetic locus such as the gene of interest.
  • a detection method is allele specific hybridization using probes overlapping the polymorphic site and having about 5, or alternatively 10, or alternatively 20, or alternatively 25, or alternatively 30 nucleotides around the polymorphic region.
  • oligonucleotides can be bound to a solid support by a variety of processes, including lithography.
  • a chip can hold up to 250,000 oligonucleotides (GeneChip, Affymetrix). Mutation detection analysis using these chips comprising oligonucleotides, also termed "DNA probe arrays" is described e.g., in Cronin et al. (1996) Human Mutation 7:244.
  • Amplification can be performed, e.g., by PCR and/or LCR, according to methods known in the art.
  • genomic DNA of a cell is exposed to two PCR primers and amplification for a number of cycles sufficient to produce the required amount of amplified DNA.
  • Alternative amplification methods include: self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques known to those of skill in the art. These detection schemes are useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
  • any of a variety of sequencing reactions known in the art can be used to directly sequence at least a portion of the gene of interest and detect allelic variants, e.g., mutations, by comparing the sequence of the sample sequence with the corresponding wild-type (control) sequence.
  • Exemplary sequencing reactions include those based on techniques developed by Maxam and Gilbert (1997) Proc. Natl. Acad. Sci, USA 74:560) or Sanger et al. (1977) Proc. Nat. Acad. Sci, 74:5463).
  • any of a variety of automated sequencing procedures can be utilized when performing the subject assays (Biotechniques (1995) 19:448), including sequencing by mass spectrometry (see, for example, U.S. Patent No. 5,547,835 and International Patent Application Publication Number WO 94/16101, entitled DNA Sequencing by Mass Spectrometry by Koster; U.S. Patent No. 5,547,835 and international patent application Publication Number WO 94/21822 entitled "DNA Sequencing by Mass Spectrometry Via Exonuclease Degradation" by Koster; U.S. Patent No. 5,605,798 and
  • the presence of the specific allele in DNA from a subject can be shown by restriction enzyme analysis.
  • the specific nucleotide polymorphism can result in a nucleotide sequence comprising a restriction site which is absent from the nucleotide sequence of another allelic variant.
  • protection from cleavage agents can be used to detect mismatched bases in RNA/RNA DNA/DNA, or RNA/DNA heteroduplexes (see, e.g., Myers et al. (1985) Science 230:1242).
  • the technique of "mismatch cleavage” starts by providing heteroduplexes formed by hybridizing a control nucleic acid, which is optionally labeled, e.g., RNA or DNA, comprising a nucleotide sequence of the allelic variant of the gene of interest with a sample nucleic acid, e.g., RNA or DNA, obtained from a tissue sample.
  • a control nucleic acid which is optionally labeled, e.g., RNA or DNA
  • sample nucleic acid e.g., RNA or DNA
  • RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with SI nuclease to enzymatically digest the mismatched regions.
  • either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine whether the control and sample nucleic acids have an identical nucleotide sequence or in which nucleotides they are different. See, for example, U.S. Patent No. 6,455,249, Cotton et al. (1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) Methods Enzy. 217:286- 295.
  • the control or sample nucleic acid is labeled for detection.
  • alterations in electrophoretic mobility is used to identify the particular allelic variant.
  • SSCP single strand conformation polymorphism
  • SSCP single strand conformation polymorphism
  • the DNA fragments may be labeled or detected with labeled probes.
  • the sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence.
  • the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
  • the identity of the allelic variant is obtained by analyzing the movement of a nucleic acid comprising the polymorphic region in polyacrylamide gels containing a gradient of denaturant, which is assayed using denaturing gradient gel
  • DGGE electrophoresis
  • Examples of techniques for detecting differences of at least one nucleotide between 2 nucleic acids include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension.
  • oligonucleotide probes may be prepared in which the known polymorphic nucleotide is placed centrally (allele-specific probes) and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324: 163); Saiki et al. (1989) Proc. Natl. Acad. Sci. USA 86:6230 and Wallace et al. (1979) Nucl. Acids Res. 6:3543).
  • oligonucleotide hybridization techniques may be used for the detection of the nucleotide changes in the polymorphic region of the gene of interest.
  • oligonucleotides having the nucleotide sequence of the specific allelic variant are attached to a hybridizing membrane and this membrane is then hybridized with labeled sample nucleic acid.
  • hybridization signal will then reveal the identity of the nucleotides of the sample nucleic acid.
  • allele specific amplification technology which depends on selective PCR amplification may be used in conjunction with the instant disclosure.
  • Oligonucleotides used as primers for specific amplification may carry the allelic variant of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11:238 and Newton et al. (1989) Nucl. Acids Res. 17:2503). This technique is also
  • identification of the allelic variant is carried out using an oligonucleotide ligation assay (OLA), as described, e.g., in U.S. Patent No. 4,998,617 and in Landegren et al. (1988) Science 241: 1077-1080.
  • OLA oligonucleotide ligation assay
  • the OLA protocol uses two oligonucleotides which are designed to be capable of hybridizing to abutting sequences of a single strand of a target.
  • One of the oligonucleotides is linked to a separation marker, e.g., biotinylated, and the other is detectably labeled.
  • oligonucleotides will hybridize such that their termini abut, and create a ligation substrate. Ligation then permits the labeled oligonucleotide to be recovered using avidin, or another biotin ligand.
  • Nickerson et al. have described a nucleic acid detection assay that combines attributes of PCR and OLA (Nickerson et al. (1990) Proc. Natl. Acad. Sci. (U.S.A.) 87:8923-8927). In this method, PCR is used to achieve the exponential amplification of target DNA, which is then detected using OLA.
  • each OLA reaction can be detected by using hapten specific antibodies that are labeled with different enzyme reporters, alkaline phosphatase or horseradish peroxidase.
  • This system permits the detection of the two alleles using a high throughput format that leads to the production of two different colors.
  • the single base polymorphism can be detected by using a specialized exonuclease-resistant nucleotide, as disclosed, e.g., in Mundy, C. R. (U.S. Patent No. 4,656,127).
  • a primer complementary to the allelic sequence immediately 3 ' to the polymorphic site is permitted to hybridize to a target molecule obtained from a particular animal or human. If the polymorphic site on the target molecule contains a nucleotide that is complementary to the particular exonuclease-resistant nucleotide derivative present, then that derivative will be incorporated onto the end of the hybridized primer. Such incorporation renders the primer resistant to exonuclease, and thereby permits its detection.
  • a solution-based method is used for determining the identity of the nucleotide of the polymorphic site.
  • Cohen, D. et al. (French Patent 2,650,840; PCT Appln. No. WO91/02087).
  • a primer is employed that is complementary to allelic sequences immediately 3' to a polymorphic site. The method determines the identity of the nucleotide of that site using labeled dideoxynucleotide derivatives, which, if complementary to the nucleotide of the polymorphic site will become incorporated onto the terminus of the primer.
  • GBA TM Genetic Bit Analysis
  • Goelet, P. et al. PCT Appln. No. 92/157112.
  • This method uses mixtures of labeled terminators and a primer that is complementary to the sequence 3' to a polymorphic site.
  • the labeled terminator that is incorporated is thus determined by, and complementary to, the nucleotide present in the polymorphic site of the target molecule being evaluated.
  • the method of Goelet, P. et al. supra is preferably a heterogeneous phase assay, in which the primer or the target molecule is immobilized to a solid phase.
  • the polymorphic region is located in the coding region of the gene of interest, yet other methods than those described above can be used for determining the identity of the allelic variant. For example, identification of the allelic variant, which encodes a mutated signal
  • 4813-1952-0531.1 -18- peptide can be performed by using an antibody specifically recognizing the mutant protein in, e.g., immunohistochemistry or immunoprecipitation.
  • Antibodies to the wild-type or signal peptide mutated forms of the signal peptide proteins can be prepared according to methods known in the art.
  • a solid phase support is used as a support capable of binding of a primer, probe, polynucleotide, an antigen or an antibody.
  • Well-known supports include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite.
  • the nature of the support can be either soluble to some extent or insoluble for the purposes of the present disclosure.
  • the support material may have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody.
  • the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod.
  • the surface may be flat such as a sheet, test strip, etc. or alternatively polystyrene beads.
  • suitable supports for binding antibody or antigen or will be able to ascertain the same by use of routine experimentation.
  • the methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits, such as those described below, comprising at least one probe or primer nucleic acid described herein, which may be conveniently used, e.g., to determine whether a subject is likely to experience tumor recurrence following therapy as described herein or has or is at risk of developing disease such as colon cancer.
  • Sample nucleic acid for use in the above-described diagnostic and prognostic methods can be obtained from any suitable cell type or tissue of a subject.
  • a subject's bodily fluid e.g. blood
  • known techniques e.g., venipuncture
  • nucleic acid tests can be performed on dry samples (e.g., hair or skin). Diagnostic procedures can also be performed in situ directly upon tissue sections (fixed and/or frozen) of patient tissue obtained from biopsies or resections, such that no nucleic acid purification is necessary. Nucleic acid reagents can be used as probes and/or primers for such in situ procedures (see, for example, Nuovo, G. J. (1992) PCR IN SITU HYBRIDIZATION:
  • Fingerprint profiles can be generated, for example, by utilizing a differential display procedure, Northern analysis and/or RT-PCR.
  • Amplification can be performed, e.g., by PCR and/or LCR, according to methods known in the art.
  • PCR e.g., by PCR and/or LCR, according to methods known in the art.
  • Various non- limiting examples of PCR include the herein described methods.
  • Allele-specific PCR is a diagnostic or cloning technique is used to identify or utilize single-nucleotide polymorphisms (SNPs). It requires prior knowledge of a DNA sequence, including differences between alleles, and uses primers whose 3' ends encompass the SNP. PCR amplification under stringent conditions is much less efficient in the presence of a mismatch between template and primer, so successful amplification with an SNP-specific primer signals presence of the specific SNP in a sequence (See, Saiki et al. (1986) Nature
  • Assembly PCR or Polymerase Cycling Assembly is the artificial synthesis of long DNA sequences by performing PCR on a pool of long oligonucleotides with short overlapping segments.
  • the oligonucleotides alternate between sense and antisense directions, and the overlapping segments determine the order of the PCR fragments thereby selectively producing the final long DNA product (See, Stemmer et al. (1995) Gene 164(l):49-53 and U.S. Patent Nos.: 6,335,160; 7,058,504 or 7,323,336)
  • Asymmetric PCR is used to preferentially amplify one strand of the original DNA more than the other. It finds use in some types of sequencing and hybridization probing where having only one of the two complementary stands is required. PCR is carried out as usual, but with a great excess of the primers for the chosen strand. Due to the slow amplification later in the reaction after the limiting primer has been used up, extra cycles of PCR are required (See, Innis et al. (1988) Proc Natl Acad Sci U.S.A. 85(24):9436-9440 and U.S.
  • Colony PCR uses bacterial colonies, for example E. coli, which can be rapidly screened by PCR for correct DNA vector constructs. Selected bacterial colonies are picked with a sterile toothpick and dabbed into the PCR master mix or sterile water. The PCR is started with an extended time at 95 °C when standard polymerase is used or with a shortened denaturation step at 100°C and special chimeric DNA polymerase (Pavlov et al. (2006) "Thermostable DNA
  • Helicase-dependent amplification is similar to traditional PCR, but uses a constant temperature rather than cycling through denaturation and annealing/extension cycles.
  • DNA Helicase an enzyme that unwinds DNA, is used in place of thermal denaturation (See, Myriam et al. (2004) EMBO reports 5(8):795-800 and U.S. Patent No. 7,282,328).
  • Hot-start PCR is a technique that reduces non-specific amplification during the initial set up stages of the PCR.
  • the technique may be performed manually by heating the reaction components to the melting temperature (e.g., 95 °C) before adding the polymerase (Chou et al. (1992) Nucleic Acids Research 20: 1717-1723 and U.S. Patent Nos.: 5,576,197 and 6,265,169).
  • Specialized enzyme systems have been developed that inhibit the polymerase's activity at ambient temperature, either by the binding of an antibody (Sharkey et al. (1994) Bio/Technology 12:506-509) or by the presence of covalently bound inhibitors that only dissociate after a high- temperature activation step.
  • Hot-start/cold-finish PCR is achieved with new hybrid polymerases that are inactive at ambient temperature and are instantly activated at elongation temperature.
  • Intersequence-specific (ISSR) PCR method for DNA fingerprinting that amplifies regions between some simple sequence repeats to produce a unique fingerprint of amplified fragment lengths (Zietkiewicz et al. (1994) Genomics 20(2): 176-83).
  • Inverse PCR is a method used to allow PCR when only one internal sequence is known. This is especially useful in identifying flanking sequences to various genomic inserts. This involves a series of DNA digestions and self ligation, resulting in known sequences at either end of the unknown sequence (Ochman et al. (1988) Genetics 120:621-623 and U.S. Patent Nos.: 6,013,486; 6,106,843 or 7,132,587).
  • Ligation-mediated PCR uses small DNA linkers ligated to the DNA of interest and multiple primers annealing to the DNA linkers; it has been used for DNA sequencing, genome walking, and DNA footprinting (Mueller et al. (1988) Science 246:780-786).
  • Methylation-specific PCR is used to detect methylation of CpG islands in genomic DNA (Herman et al. (1996) Proc Natl Acad Sci U.S.A. 93(13):9821-9826 and U.S. Patent Nos.: 6,811,982; 6,835,541 or 7,125,673). DNA is first treated with sodium bisulfite, which converts unmethylated cytosine bases to uracil, which is recognized by PCR primers as thymine. Two PCRs are then carried out on the modified DNA, using primer sets identical except at any CpG islands within the primer sequences. At these points, one primer set recognizes DNA with cytosines to amplify methylated DNA, and one set recognizes DNA with
  • MSP using qPCR can also be performed to obtain quantitative rather than qualitative information about methylation.
  • MPA Multiplex Ligation-dependent Probe Amplification
  • Multiplex -PCR uses of multiple, unique primer sets within a single PCR mixture to produce amplicons of varying sizes specific to different DNA sequences (See, U.S. Patent Nos.: 5,882,856; 6,531,282 or 7,118,867). By targeting multiple genes at once, additional information may be gained from a single test run that otherwise would require several times the reagents and more time to perform. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes, i.e., their base pair length, should be different enough to form distinct bands when visualized by gel electrophoresis.
  • Nested PCR increases the specificity of DNA amplification, by reducing background due to non-specific amplification of DNA.
  • Two sets of primers are being used in two successive PCRs. In the first reaction, one pair of primers is used to generate DNA products, which besides the intended target, may still consist of non-specifically amplified DNA fragments.
  • the product(s) are then used in a second PCR with a set of primers whose binding sites are completely or partially different from and located 3 ' of each of the primers used in the first reaction (See, U.S. Patent Nos.: 5,994,006; 7,262,030 or 7,329,493).
  • Nested PCR is often more successful in specifically amplifying long DNA fragments than conventional PCR, but it requires more detailed knowledge of the target sequences.
  • Overlap-extension PCR is a genetic engineering technique allowing the construction of a DNA sequence with an alteration inserted beyond the limit of the longest practical primer length.
  • Quantitative PCR also known as RQ-PCR, QRT-PCR and RTQ-PCR, is used to measure the quantity of a PCR product following the reaction or in real-time. See, U.S.
  • Q-PCR is the method of choice to
  • RT-PCR refers to reverse transcription PCR
  • QRT-PCR methods use fluorescent dyes, such as Sybr Green, or fluorophore-containing DNA probes, such as TaqMan, to measure the amount of amplified product in real time.
  • RT-PCR Reverse Transcription PCR
  • RACE-PCR Rapid Amplification of cDNA Ends
  • TAIL-PCR Thermal asymmetric interlaced PCR
  • Touchdown PCR a variant of PCR that aims to reduce nonspecific background by gradually lowering the annealing temperature as PCR cycling progresses.
  • the annealing temperature at the initial cycles is usually a few degrees (3-5 °C) above the T m of the primers used, while at the later cycles, it is a few degrees (3-5 °C) below the primer T m .
  • the higher temperatures give greater specificity for primer binding, and the lower temperatures permit more efficient amplification from the specific products formed during the initial cycles (Don et al. (1991) Nucl Acids Res 19:4008 and U.S. Patent No. 6,232,063).
  • probes are labeled with two fluorescent dye molecules to form so-called “molecular beacons” (Tyagi, S. and Kramer, F.R. (1996) Nat.
  • molecular beacons signal binding to a complementary nucleic acid sequence through relief of intramolecular fluorescence quenching between dyes bound to opposing ends on an oligonucleotide probe.
  • the use of molecular beacons for genotyping has been described (Kostrikis, L.G. (1998) Science 279: 1228-9) as has the use of multiple beacons simultaneously (Marras, S.A. (1999) Genet. Anal. 14:151-6).
  • a quenching molecule is useful with a particular fluorophore if it has sufficient spectral overlap to substantially inhibit fluorescence of the fluorophore when the two are held proximal to one another, such as in a molecular beacon, or when attached to the ends of an oligonucleotide probe from about 1 to about 25 nucleotides.
  • Labeled probes also can be used in conjunction with amplification of a gene of interest.
  • U.S. Patent No. 5,210,015 by Gelfand et al. describe fluorescence-based approaches to provide real time measurements of amplification products during PCR.
  • Such approaches have either employed intercalating dyes (such as ethidium bromide) to indicate the amount of double-stranded DNA present, or they have employed probes containing fluorescence-quencher pairs (also referred to as the "Taq- Man” approach) where the probe is cleaved during amplification to release a fluorescent molecule whose concentration is proportional to the amount of double-stranded DNA present.
  • the probe is digested by the nuclease activity of a polymerase when hybridized to the target sequence to cause the fluorescent molecule to be separated from the quencher molecule, thereby causing fluorescence from the reporter molecule to appear.
  • the Taq-Man approach uses a probe containing a reporter molecule—quencher molecule pair that specifically anneals to a region of a target polynucleotide containing the polymorphism.
  • Probes can be affixed to surfaces for use as "gene chips.” Such gene chips can be used to detect genetic variations by a number of techniques known to one of skill in the art. In one technique, oligonucleotides are arrayed on a gene chip for determining the DNA sequence of a by the sequencing by hybridization approach, such as that outlined in U.S. Patent Nos.
  • the probes of the disclosure also can be used for fluorescent detection of a genetic sequence. Such techniques have been described, for example, in U.S. Patent Nos. 5,968,740 and 5,858,659.
  • a probe also can be affixed to an electrode surface for the electrochemical detection of nucleic acid sequences such as described by Kayem et al. U.S. Patent No. 5,952,172 and by Kelley, S.O. et al. (1999) Nucleic Acids Res. 27:4830-4837.
  • This disclosure also provides for a prognostic panel of genetic markers selected from, but not limited to the genetic polymorphisms identified herein.
  • the prognostic panel comprises probes or primers or microarrays that can be used to amplify and/or for determining the molecular structure of the polymorphisms identified herein.
  • the probes or primers can be attached or supported by a solid phase support such as, but not limited to a gene chip or microarray.
  • the panel contains the herein identified probes or primers as wells as other probes or primers.
  • the panel includes one or more of the above noted probes or primers and others.
  • the panel consist only of the above- noted probes or primers.
  • Primers or probes can be affixed to surfaces for use as "gene chips” or "microarray.” Such gene chips or microarrays can be used to detect genetic variations by a number of techniques known to one of skill in the art. In one technique, oligonucleotides are arrayed on a gene chip for determining the DNA sequence of a by the sequencing by hybridization approach, such as that outlined in U.S. Patent Nos. 6,025,136 and 6,018,041. The probes of the disclosure also can be used for fluorescent detection of a genetic sequence. Such techniques have been described, for example, in U.S. Patent Nos. 5,968,740 and 5,858,659.
  • a probe also can be affixed to an electrode surface for the electrochemical detection of nucleic acid sequences such as described by Kayem et al. U.S. Patent No. 5,952,172 and by Kelley et al. (1999) Nucleic Acids Res. 27:4830-4837.
  • GeneChip (Affymetric, Inc); LabChip (Caliper Technologies Corp); a low-density array with electrochemical sensing (Clinical Micro Sensors); LabCD System (Gamera Bioscience Corp.); Omni Grid (Gene Machines); Q Array (Genetix Ltd.); a high-throughput, automated mass spectrometry systems with liquid-phase expression technology (Gene Trace Systems, Inc.); a thermal jet spotting system (Hewlett Packard Company); Hyseq HyChip (Hyseq, Inc.);
  • BeadArray (Illumina, Inc.); GEM (Incyte Microarray Systems); a high-throughput
  • microarraying system that can dispense from 12 to 64 spots onto multiple glass slides
  • probes or primers for the gene of interest are provided alone or in combination with other probes and/or primers.
  • a suitable sample is obtained from the patient extraction of genomic DNA, RNA, or any combination thereof and amplified if necessary.
  • the DNA or RNA sample is contacted to the gene chip or microarray panel under conditions suitable for hybridization of the gene(s) of interest to the probe(s) or primer(s) contained on the gene chip or microarray.
  • the probes or primers may be detectably labeled thereby identifying the polymorphism in the gene(s) of interest.
  • a chemical or biological reaction may be used to identify the probes or primers which hybridized with the DNA or RNA of the gene(s) of interest.
  • the genetic profile of the patient is then determined with the aid of the aforementioned apparatus and methods.
  • the nucleic acid sequences of the gene of interest, or portions thereof can be the basis for probes or primers, e.g., in methods for determining expression level of the gene of interest or the allelic variant of a polymorphic region of a gene of interest identified in the experimental section below.
  • they can be used in the methods of the disclosure to determine which therapy is most likely to treat an individual's cancer.
  • the methods of the disclosure can use nucleic acids isolated from vertebrates.
  • the vertebrate nucleic acids are mammalian nucleic acids.
  • the nucleic acids used in the methods of the disclosure are human nucleic acids.
  • Primers for use in the methods of the disclosure are nucleic acids which hybridize to a nucleic acid sequence which is adjacent to the region of interest or which covers the region of interest and is extended.
  • a primer can be used alone in a detection method, or a primer can be used together with at least one other primer or probe in a detection method.
  • Primers can also be used to amplify at least a portion of a nucleic acid.
  • Probes for use in the methods of the disclosure are nucleic acids which hybridize to the gene of interest and which are not further extended.
  • a probe is a nucleic acid which hybridizes to the gene of interest, and which by hybridization or absence of hybridization to the DNA of a subject will be indicative of the identity of the allelic variant of the expression levels of the gene of interest.
  • Primers and/or probes for use in the methods can be provided as isolated single stranded oligonucleotides or alternatively, as isolated double stranded oligonucleotides.
  • primers comprise a nucleotide sequence which comprises a region having a nucleotide sequence which hybridizes under stringent conditions to about: 6, or alternatively 8, or alternatively 10, or alternatively 12, or alternatively 25, or alternatively 30, or alternatively 40, or alternatively 50, or alternatively 75 consecutive nucleotides of the gene of interest.
  • Primers can be complementary to nucleotide sequences located close to each other or further apart, depending on the use of the amplified DNA.
  • primers can be chosen such that they amplify DNA fragments of at least about 10 nucleotides or as much as several kilobases.
  • the primers of the disclosure will hybridize selectively to nucleotide sequences located about 100 to about 1000 nucleotides apart.
  • a forward primer i.e., 5' primer
  • a reverse primer i.e., 3' primer
  • Forward and reverse primers hybridize to complementary strands of a double stranded nucleic acid, such that upon extension from each primer, a double stranded nucleic acid is amplified.
  • primers of the disclosure are nucleic acids which are capable of selectively hybridizing to the gene.
  • primers can be specific for the gene of interest sequence, so long as they have a nucleotide sequence which is capable of hybridizing to the gene of interest.
  • the probe or primer may further comprises a label attached thereto, which, e.g., is capable of being detected, e.g. the label group is selected from amongst radioisotopes, fluorescent compounds, enzymes, and enzyme co-factors.
  • nucleic acids used as probes or primers may be modified to become more stable.
  • exemplary nucleic acid molecules which are modified include
  • nucleic acids used in the methods of the disclosure can also be modified at the base moiety, sugar moiety, or phosphate backbone, for example, to improve stability of the molecule.
  • the nucleic acids, e.g., probes or primers may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane. See, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. U.S.A. 86:6553-6556;
  • nucleic acid used in the methods of the disclosure may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent, etc.
  • the isolated nucleic acids used in the methods of the disclosure can also comprise at least one modified sugar moiety selected from the group including but not limited to arabinose, 2-fluoroarabinose, xylulose, and hexose or, alternatively, comprise at least one modified phosphate backbone selected from the group consisting of a phosphorothioate, a
  • phosphorodithioate a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, and a formacetal or analog thereof.
  • nucleic acids, or fragments thereof, to be used in the methods of the disclosure can be prepared according to methods known in the art and described, e.g., in Sambrook et al. (2001) supra.
  • discrete fragments of the DNA can be prepared and cloned using restriction enzymes.
  • discrete fragments can be prepared using the Polymerase Chain Reaction (PCR) using primers having an appropriate sequence under the manufacturer's conditions, (described above).
  • Oligonucleotides can be synthesized by standard methods known in the art, e.g. by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc.).
  • an automated DNA synthesizer such as are commercially available from Biosearch, Applied Biosystems, etc.
  • phosphorothioate oligonucleotides can be synthesized by the method of Stein et al. (1988) Nucl. Acids Res. 16:3209
  • methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports. Sarin et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85:7448-7451.
  • the diagnostic methods described in the present disclosure can provide useful information for optimizing treatment strategy. For example, patients at high risk of tumor recurrence or having a low expectation of survival may be treated with more aggressive therapy and/or sooner. Conversely, those at relatively lower risk of tumor recurrence or having a high expectation of survival may be more suitable for a more conservative and/or less toxic therapy.
  • the following therapies are available for cancer patients, such as colorectal cancer patients, to prevent or reduce tumor recurrence: 5 -fluorouracil (5-FU), capecitabine (Xeloda), Leucovorin (LV, folinic Acid), Oxaliplatin (Eloxatin), the combination of infusional 5- fluorouracil, leucovorin, and oxaliplatin (FOLFOX) with bevacizumab or infusional 5- fluorouracil, leucovorin, and irinotecan (FOLFIRI) with bevacizumab, Tegafur-uracil, Irinotecan (Camptosar), Oxaliplatin (Eloxatin), Bevacizumab (Avastin), Cetuximab (Erbitux),
  • 5 -fluorouracil 5 -fluorouracil
  • capecitabine Xeloda
  • Leucovorin LV, folinic Acid
  • Panitumumab (Vectibix), Bortezomib (Velcade), Oblimersen (Genasense, G3139), Gefitinib and erlotinib (Tarceva) or Topotecan (Hycamtin).
  • Therapeutic and adverse effects of these therapies have been studied.
  • the therapy can further comprise radiation therapy.
  • the diagnostic methods provided in the present disclosure therefore, are useful in optimal selection of these therapies.
  • this disclosure also provides methods for treating a cancer patient.
  • a cancer patient which is predicted to experience a relatively shorter time to tumor recurrence or relatively more likely to experience tumor recurrence, is treated with a more aggressive therapy such as a therapy at a higher dose or a higher frequency.
  • a cancer patient which is predicted to experience a relatively longer time to tumor
  • 4813-1952-0531.1 -28- recurrence or relatively less likely to experience tumor recurrence is treated with a safer therapy or a therapy causing less adverse effects, such as a therapy at a lower dose or a lower frequency.
  • the methods are useful to treat patients that include but are not limited to animals, such as mammals which can include simians, ovines, bovines, murines, canines, equines, felines, canines, and humans.
  • animals such as mammals which can include simians, ovines, bovines, murines, canines, equines, felines, canines, and humans.
  • the therapies can be administered by any suitable formulation. Accordingly, a formulation comprising the necessary therapy is further provided herein.
  • the formulation can further comprise one or more preservatives or stabilizers. Any suitable concentration or mixture can be used as known in the art, such as 0.001-5%, or any range or value therein, such as, but not limited to 0.001, 0.003, 0.005, 0.009, 0.01, 0.02, 0.03, 0.05, 0.09, 0.1, 0.2, 0.3, O.4., 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.3, 4.5, 4.6, 4.7, 4.8, 4.9, or any range or value there
  • Non-limiting examples include, no preservative, 0.1-2% m-cresol (e.g., 0.2, 0.3. 0.4, 0.5, 0.9, 1.0%), 0.1-3% benzyl alcohol (e.g., 0.5, 0.9, 1.1., 1.5, 1.9, 2.0, 2.5%), 0.001-0.5% thimerosal (e.g., 0.005, 0.01), 0.001-2.0% phenol (e.g., 0.05, 0.25, 0.28, 0.5, 0.9, 1.0%), 0.0005- 1.0% alkylparaben(s) (e.g., 0.00075, 0.0009, 0.001, 0.002, 0.005, 0.0075, 0.009, 0.01, 0.02, 0.05, 0.075, 0.09, 0.1, 0.2, 0.3, 0.5, 0.75, 0.9, and 1.0%).
  • 0.1-2% m-cresol e.g., 0.2, 0.3. 0.4, 0.5, 0.9, 1.0%
  • compositions typically intends a combination of the active agent and another carrier, e.g., compound or composition, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers.
  • another carrier e.g., compound or composition, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers.
  • Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, terra-, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in combination 1-99.99% by weight or volume.
  • Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like.
  • amino acid/antibody components which can also function in a buffering capacity, include alanine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like.
  • Carbohydrate excipients are also intended within the scope of this disclosure, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-
  • disaccharides such as lactose, sucrose, trehalose, cellobiose, and the like; polysaccharides, such as raffmose, melezitose, maltodextrins, dextrans, starches, and the like; and alditols, such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
  • disaccharides such as lactose, sucrose, trehalose, cellobiose, and the like
  • polysaccharides such as raffmose, melezitose, maltodextrins, dextrans, starches, and the like
  • alditols such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoi
  • the term carrier further includes a buffer or a pH adjusting agent; typically, the buffer is a salt prepared from an organic acid or base.
  • Representative buffers include organic acid salts such as salts of citric acid, ascorbic acid, gluconic acid, carbonic acid, tartaric acid, succinic acid, acetic acid, or phthalic acid; Tris, tromethamine hydrochloride, or phosphate buffers.
  • Additional carriers include polymeric excipients/additives such as polyvinylpyrrolidones, ficolls (a polymeric sugar), dextrates (e.g., cyclodextrins, such as 2-hydroxypropyl-. quadrature. - cyclodextrin), polyethylene glycols, flavoring agents, antimicrobial agents, sweeteners, antioxidants, antistatic agents, surfactants (e.g., polysorbates such as "TWEEN 20" and
  • TWEEN 80 lipids (e.g., phospholipids, fatty acids), steroids (e.g., cholesterol), and chelating agents (e.g., EDTA).
  • lipids e.g., phospholipids, fatty acids
  • steroids e.g., cholesterol
  • chelating agents e.g., EDTA
  • the term "pharmaceutically acceptable carrier” encompasses any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, and emulsions, such as an oil/water or water/oil emulsion, and various types of wetting agents.
  • the compositions also can include stabilizers and preservatives and any of the above noted carriers with the additional proviso that they be acceptable for use in vivo.
  • stabilizers and adjuvants see Martin REMINGTON'S PHARM. SCI., 15th Ed. (Mack Publ. Co., Easton (1975) and Williams & Williams, (1995), and in the "PHYSICIAN'S DESK REFERENCE", 52 nd ed., Medical Economics, Montvale, N.J. (1998).
  • capecitabine/docetaxel the "Cooper regimen” fluorouracil-levamisole, fluorouracil-leucovorin, fluorouracil/oxaliplatin, methotrexate-leucovorin, and the like.
  • Combinations of chemotherapies and molecular targeted therapies, biologic therapies, and radiation therapies are also well known to the art; including therapies such as trastuzumab plus paclitaxel, alone or in further combination with platinum compounds such as oxaliplatin, for certain breast cancers, and many other such regimens for other cancers; and the "Dublin regimen” 5-fluorouracil IV over 16 hours on days 1-5 and 75 mg/m cisplatin IV or oxaliplatin over 8 hours on day 7, with repetition at 6 weeks, in combination with 40 Gy radiotherapy in 15 fractions over the first 3 weeks) and the "Michigan regimen” (fluorouracil plus cisplatin or
  • the method for treating a patient further comprises, or alternatively consists essentially of, or yet further consists of surgical resection of a metastatic or non-metastatic solid malignant tumor and, in some aspects, in combination with radiation.
  • Methods for treating these tumors as Stage I, Stage II, Stage III, or Stage IV by surgical resection and/or radiation are known to one skilled in the art. Guidelines describing methods for treatment by surgical resection and/or radiation can be found at the National Comprehensive Cancer Network's web site, nccn.org, last accessed on May 27, 2008.
  • the disclosure provides an article of manufacture, comprising packaging material and at least one vial comprising a solution of the chemotherapy as described herein and/or or at least one antibody or its biological equivalent with the prescribed buffers and/or preservatives, optionally in an aqueous diluent, wherein said packaging material comprises a label that indicates that such solution can be held over a period of 1, 2, 3, 4, 5, 6, 9, 12, 18, 20, 24, 30, 36,40, 48, 54, 60, 66, 72 hours or greater.
  • the disclosure further comprises an article of manufacture, comprising packaging material, a first vial comprising the chemotherapy and/or at least one lyophilized antibody or its biological equivalent and a second vial comprising an aqueous diluent of prescribed buffer or preservative, wherein said packaging material comprises a label that instructs a patient to reconstitute the therapeutic in the aqueous diluent to form a solution that can be held over a period of twenty- four hours or greater.
  • Chemotherapeutic formulations of the present disclosure can be prepared by a process which comprises mixing at least one antibody or biological equivalent and a preservative selected from the group consisting of phenol, m-cresol, p-cresol, o-cresol, chlorocresol, benzyl alcohol, alkylparaben, (methyl, ethyl, propyl, butyl and the like), benzalkonium chloride, benzethonium chloride, sodium dehydroacetate and thimerosal or mixtures thereof in an aqueous diluent.
  • a preservative selected from the group consisting of phenol, m-cresol, p-cresol, o-cresol, chlorocresol, benzyl alcohol, alkylparaben, (methyl, ethyl, propyl, butyl and the like), benzalkonium chloride, benzethonium chloride, sodium dehydroacetate and thimerosal or mixtures thereof in an
  • a measured amount of at least one antibody in buffered solution is combined with the desired preservative in a buffered solution in quantities sufficient to provide the antibody and preservative at the desired concentrations.
  • Variations of this process would be recognized by one of skill in the art, e.g., the order the components are added, whether additional additives are used, the temperature and pH at which the formulation is prepared, are all factors that can be optimized for the
  • compositions and formulations can be provided to patients as clear solutions or as dual vials comprising a vial of lyophilized antibody that is reconstituted with a second vial containing the aqueous diluent.
  • Either a single solution vial or dual vial requiring reconstitution can be reused multiple times and can suffice for a single or multiple cycles of patient treatment and thus provides a more convenient treatment regimen than currently available.
  • Recognized devices comprising these single vial systems include those pen-injector devices for delivery of a solution such as BD Pens, BD Autojectore, Humaject® NovoPen®, B-D®Pen, AutoPen®, and OptiPen®, GenotropinPen®, Genotronorm Pen®, Humatro Pen®, Reco-Pen®, Roferon Pen®, Biojector®, iject®, J-tip Needle-Free Injector®, Intraject®, Medi-Ject®, e.g., as made or developed by Becton Dickensen (Franklin Lakes, N.J.
  • chemotherapeutic agent of the disclosure e.g., encapsulation in liposomes, microparticles, microcapsules, expression by recombinant cells, receptor-mediated endocytosis. See e.g., Wu and Wu (1987) J. Biol. Chem. 262:4429-4432 for construction of a therapeutic nucleic acid as part of a retroviral or other vector, etc.
  • Methods of delivery include but are not limited to intra-arterial, intramuscular, intravenous, intranasal and oral routes.
  • agents identified herein as effective for their intended purpose can be administered to subjects or individuals identified by the methods herein as suitable for the therapy.
  • Therapeutic amounts can be empirically determined and will vary with the pathology being treated, the subject being treated and the efficacy and toxicity of the agent.
  • a therapy or a medicament comprising an effective amount of a chemotherapeutic as described herein for treatment of a human cancer patient having the appropriate expression level of the gene of interest as identified in the experimental examples.
  • a therapy comprising a platinum drug, or alternatively a platinum drug therapy, for use in treating a human cancer patient having the appropriate expression level of the gene of interest as identified in the experimental examples.
  • compositions are well known to those of ordinary skill in the art and include, but are not limited to, oral, microinjection, intravenous or parenteral administration.
  • the compositions are intended for topical, oral, or local
  • Administration as well as intravenously, subcutaneously, or intramuscularly. Administration can be effected continuously or intermittently throughout the course of the treatment. Methods of determining the most effective means and dosage of administration are well known to those of skill in the art and will vary with the cancer being treated and the patient and the subject being treated. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician.
  • kits for use in aiding in the determination of or determining whether a cancer patient is likely to, or identifying a patient or population of patients that is likely to, experience a longer or shorter time to tumor recurrence comprising, or alternatively consisting essentially of, or yet alternatively consisting of, suitable primers or probes or a microarray for screening a tissue or cell sample isolated from the patient for the ITGB3 (integrin beta 3) rs4642 A/G, integrin beta 1 (ITGB1) rs2298141 A/G and the integrin beta 4 (ITGB4) rs7562325 C/T polymorphisms, and instructions for use therein.
  • the patient suffers from one or more cancer selected from lung cancer, non-small cell lung cancer, breast cancer, head and neck cancer, ovarian cancer, colon cancer, Stage II or Stage III colon cancer, localized gastric cancer, gastric adenocarcinoma, rectal cancer, colorectal cancer, esophageal cancer, gastric cancer, liver cancer, bone cancer, spleen cancer, pancreatic cancer, or gallbladder cancer.
  • lung cancer non-small cell lung cancer
  • breast cancer breast cancer
  • head and neck cancer ovarian cancer
  • colon cancer Stage II or Stage III colon cancer
  • localized gastric cancer gastric adenocarcinoma
  • rectal cancer colorectal cancer
  • esophageal cancer gastric cancer
  • gastric cancer liver cancer
  • bone cancer bone cancer
  • spleen cancer pancreatic cancer
  • pancreatic cancer pancreatic cancer
  • gallbladder cancer gallbladder cancer
  • Suitable patient samples for the methods as described herein the sample comprises, or alternatively consisting essentially of, or yet further consisting of, at least one of blood, plasma, a tumor cell, a normal cell adjacent to a tumor, a normal cell corresponding to the tumor tissue type, a blood cell, a peripheral blood lymphocyte, or combinations thereof.
  • the samples can be any one or more of a fixed tissue, a frozen tissue, a biopsy tissue, a resection tissue, a
  • microdissected tissue or combinations thereof.
  • genotype is determined by a method comprising, or alternatively consisting essentially of, or yet further consisting of, polymerase chain reaction analysis (PCR), sequencing analysis, restriction enzyme analysis, mismatch cleavage analysis, single strand conformation
  • PCR polymerase chain reaction analysis
  • a patient includes but is not limited to a simian, a murine, a bovine, an equine, a porcine, a feline, a canine, or an ovine.
  • the disclosure provides diagnostic methods for determining the polymorphic region of the gene of interest.
  • the methods use probes or primers or microarrays comprising nucleotide sequences which are complementary to the gene of interest.
  • the disclosure provides kits for performing these methods as well as instructions for carrying out the methods of this disclosure such as collecting tissue and/or performing the screen, and/or analyzing the results. These can be used alone or in combination with other suitable chemotherapy or biological therapy.
  • the kit can comprise at least one probe or primer which is capable of specifically hybridizing to the gene of interest and instructions for use.
  • the kits preferably comprise at least one of the above described nucleic acids.
  • Preferred kits for amplifying at least a portion of the gene of interest comprise two primers, at least one of which is capable of hybridizing to the allelic variant sequence.
  • Such kits are suitable for detection of genotype by, for example, fluorescence detection, by electrochemical detection, or by other detection.
  • Oligonucleotides whether used as probes or primers, contained in a kit can be detectably labeled. Labels can be detected either directly, for example for fluorescent labels, or indirectly. Indirect detection can include any detection method known to one of skill in the art, including biotin-avidin interactions, antibody binding and the like. Fluorescently labeled oligonucleotides also can contain a quenching molecule. Oligonucleotides can be bound to a surface. In one embodiment, the preferred surface is silica or glass. In another embodiment, the surface is a metal electrode.
  • kits of the disclosure comprise at least one reagent necessary to perform the assay.
  • the kit can comprise an enzyme.
  • the kit can comprise a buffer or any other necessary reagent.
  • Conditions for incubating a nucleic acid probe with a test sample depend on the format employed in the assay, the detection methods used, and the type and nature of the nucleic acid probe used in the assay.
  • One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the nucleic acid probes for use in the present disclosure. Examples of such assays can be found in Chard, T. (1986) AN INTRODUCTION TO RADIOIMMUNOASSAY AND RELATED TECHNIQUES Elsevier Science Publishers, Amsterdam, The Netherlands; Bullock, G.R.
  • test samples used in the diagnostic kits include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine.
  • the test samples may also be a tumor cell, a normal cell adjacent to a tumor, a normal cell corresponding to the tumor tissue type, a blood cell, a peripheral blood lymphocyte, or combinations thereof.
  • the test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are known in the art and can be readily adapted in order to obtain a sample which is compatible with the system utilized.
  • kits can include all or some of the positive controls, negative controls, reagents, primers, sequencing markers, probes and antibodies described herein for determining the subject's genotype in the polymorphic region of the gene of interest.
  • these suggested kit components may be packaged in a manner customary for use by those of skill in the art.
  • these suggested kit components may be provided in solution or as a liquid dispersion or the like.
  • the identification of the polymorphic region or the expression level of the gene of interest can also be useful for identifying an individual among other individuals from the same species.
  • DNA sequences can be used as a fingerprint for detection of different individuals within the same species. Thompson, J. S. and Thompson, eds., (1991) GENETICS IN MEDICINE, W B Saunders Co., Philadelphia, Pa. This is useful, e.g., in forensic studies.
  • Integrins are key elements in cancer biology regulating tumor growth, angiogenesis and lymphangiogenesis through interactions of the tumor cells with the microenvironment.
  • the predominant role of ITGB3 rs4642 in stage II diseases was confirmed using recursive partitioning, showing that ITGB3 rs4642 was the most important factor in stage II diseases (FIG. 1, Table 3).
  • the interaction between stage and the combined ITGB1 rs2298141 and ITGA4 rs7562325 was significant (p 0.025) (FIG. 2).
  • A/G 2.300 (1.358, 3.894) 0.002 5.939(2.110,16.718) ⁇ 0.001 1.594(0.842,3.016) 0.15 G/G 1.141 (0.482(2.700) 0.76 1.388 (0.266,7.247) 0.70 1.093 (0.393.3.040 0.86

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Abstract

La présente invention concerne des compositions et des méthodes qui permettent de déterminer la probabilité de récurrence de tumeurs chez des patients atteints de cancer au moyen d'une recherche d'au moins un polymorphisme ITGB3, ITGBl ou ITGA4 dans des échantillons isolés provenant du patient.
PCT/US2013/030301 2012-05-15 2013-03-11 Variants génétiques d'intégrine et récurrence de tumeurs spécifique au stade chez des patients atteints d'un cancer du côlon au stade ii et iii WO2013172934A1 (fr)

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CN107365837A (zh) * 2017-07-06 2017-11-21 郑州大学 用BanII鉴定人胃癌ZNF33B‑2:1基因rs579501多态性的方法

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