Genetic Variants Predictive of Cancer Risk
AssigneedeCODE Genetics ehf.
InventorsThorunn Rafnar, Patrick Sulem, Simon Stacey
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Abstract
The invention discloses genetic variants that have been determined to be susceptibility variants of cancer. Methods of disease management, including determining increased susceptibility to cancer, methods of predicting response to therapy and methods of predicting prognosis of cancer using such variants are described. The invention further relates to kits useful in the methods of the invention.
Claims68
A method for determining a susceptibility to cancer in a human individual, comprising determining whether at least one allele of at least one polymorphic marker is present in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is selected from the group consisting of rs401681, rs2736100 and rs2736098, and markers in linkage disequilibrium therewith, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2,
- determining a susceptibility to cancer in the subject from the presence or absence of the at least one allele, and wherein the presence of the at least one allele is indicative of a susceptibility to cancer for the individual.
A method of determining a susceptibility to cancer in a human individual, the method comprising determining whether at least one allele of at least one polymorphic marker is present in a nucleic acid sample obtained from the individual, wherein the at least one polymorphic marker is associated with the TERT gene, and wherein the presence of the at least one allele is indicative of a susceptibility to cancer for the individual.
A method of determining a susceptibility to cancer in a human individual, the method comprising:
- obtaining nucleic acid sequence data about a human individual identifying at least one allele of at least one polymorphic marker selected from the group consisting of rs401681, rs2736100 and rs2736098, and markers in linkage disequilibrium therewith, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2, and wherein different alleles of the at least one polymorphic marker are associated with different susceptibilities to cancer in humans, and
- determining a susceptibility to cancer from the nucleic acid sequence data.
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A method of identification of a marker for use in assessing susceptibility to cancer, the method comprising:
- a. identifying at least one polymorphic marker in linkage disequilibrium with at least one of rs401681, rs2736100 and rs2736098, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2;
- b. determining the genotype status of a sample of individuals diagnosed with, or having a susceptibility to, cancer;
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- c. determining the genotype status of a sample of control individuals;
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- d. identifying the at least one polymorphic marker for use in assessing susceptibility to thyroid cancer from (b) and (c),
- wherein a significant difference in frequency of at least one allele in at least one polymorphism in individuals diagnosed with, or having a susceptibility to, cancer, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one polymorphism being useful for assessing susceptibility to cancel;
- wherein an increase in frequency of the at least one allele in the at least one polymorphism in individuals diagnosed with, or having a susceptibility to, cancer, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one polymorphism being useful for assessing increased susceptibility to cancer, and
- wherein a decrease in frequency of the at least one allele in the at least one polymorphism in individuals diagnosed with, or having a susceptibility to, cancer, as compared with the frequency of the at least one allele in the control sample is indicative of the at least one polymorphism being useful for assessing decreased susceptibility to, or protection against, cancer.
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A method of genotyping a nucleic acid sample obtained from a human individual comprising determining whether at least one allele of at least one polymorphic marker is present in a nucleic acid sample from the individual sample, wherein the at least one marker is selected from rs401681, rs2736100 and rs2736098, and markers in linkage disequilibrium therewith, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2, and wherein determination of the presence of the at least one allele in the sample is indicative of a susceptibility to cancer in the individual.
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A computer-readable medium having computer executable instructions for determining susceptibility to cancer in a human individual, the computer readable medium comprising:
- data indicative of at least one polymorphic marker;
- a routine stored on the computer readable medium and adapted to be executed by a processor to determine risk of developing cancer in an individual for the at least one polymorphic marker;
- wherein the at least one polymorphic marker is selected from rs401681, rs2736100 and rs2736098, and markers in linkage disequilibrium therewith, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2.
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An apparatus for determining a genetic indicator for cancer in a human individual, comprising:
- a processor a computer readable memory having computer executable instructions adapted to be executed on the processor to analyze marker and/or haplotype information for at least one human individual with respect to at least one polymorphic marker selected from rs401681, rs2736100 and rs2736098, and markers in linkage disequilibrium therewith, wherein the linkage disequilibrium is characterized by a value for r2 of at least 0.2, and
- generate an output based on the marker or haplotype information, wherein the output comprises a risk measure of the at least one marker or haplotype as a genetic indicator of cancer for the human individual.
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Dependencies are inferred from the claim text.