Molecular diagnostic test for cancer
First Claim
1. A method of diagnosing and treating an individual as having a DNA damage response deficient (DDRD) cancer comprising;
- a. measuring expression levels of at least two genes in a test sample of tumour cells obtained from the individual to determine a test score, wherein the at least two genes are selected from the group consisting of CXCL10, IDO1, CD2, GBP5, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1; and
b. treating the individual with a DNA-damage therapeutic agent, wherein the individual is diagnosed as having the DDRD cancer because a test score of the test sample exceeds a threshold score, and said exceeding occurs if the test score, based on the expression levels of the at least two genes, exceeds a threshold score based on the same genes.
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Abstract
Methods and compositions are provided for the identification of a molecular diagnostic test for cancer. The test defines a novel DNA damage repair deficient molecular subtype and enables classification of a patient within this subtype. The present invention can be used to determine whether patients with cancer are clinically responsive or non-responsive to a therapeutic regimen prior to administration of any chemotherapy. This test may be used in different cancer types and with different drugs that directly or indirectly affect DNA damage or repair, such as many of the standard cytotoxic chemotherapeutic drugs currently in use. In particular, the present invention is directed to the use of certain combinations of predictive markers, wherein the expression of the predictive markers correlates with responsiveness or non-responsiveness to a therapeutic regimen.
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Citations
28 Claims
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1. A method of diagnosing and treating an individual as having a DNA damage response deficient (DDRD) cancer comprising;
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a. measuring expression levels of at least two genes in a test sample of tumour cells obtained from the individual to determine a test score, wherein the at least two genes are selected from the group consisting of CXCL10, IDO1, CD2, GBP5, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1; and b. treating the individual with a DNA-damage therapeutic agent, wherein the individual is diagnosed as having the DDRD cancer because a test score of the test sample exceeds a threshold score, and said exceeding occurs if the test score, based on the expression levels of the at least two genes, exceeds a threshold score based on the same genes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A method of treating cancer, comprising administering a DNA-damage therapeutic agent to an individual, wherein:
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a. the individual has been selected for the treatment because the combined expression level of at least two genes in a cancer sample from the individual is higher than an established threshold value, thereby diagnosing the individual as having a DDRD cancer; and b. the combined expression level of the at least two genes is based on the expression of at least two genes selected from the group consisting of CXCL10, IDO1, CD2, GBP5, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1. - View Dependent Claims (13, 14, 15, 16, 17, 18, 19, 20, 21, 22)
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23. A method of treating cancer, comprising administering a modulator of DNA-damage-related immune signalling to an individual, wherein:
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a. the individual has been selected for the treatment because the combined expression level of at least two genes in a cancer sample from the individual is higher than an established threshold value, thereby diagnosing the individual as having a DDRD cancer; and b. the combined expression level of the at least two genes is based on the expression of at least two genes selected from the group consisting of CXCL10, IDO1, CD2, GBP5, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1. - View Dependent Claims (24, 25, 26, 27, 28)
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Specification