Methods for detecting inactivation of the homologous recombination pathway (brca1/2) in human tumors

Abstract

Methods for detecting inactivation of the DNA Homologous Recombination pathway in a patient, and in particular for detecting BRCA1 inactivation, are provided.

1 . A method for predicting tumor deficiency in the DNA homologous recombination (HR) pathway in a patient suffering from cancer, comprising the step of quantifying the number of rearrangements in the genomic DNA of a tumor sample obtained from said patient, wherein the number of rearrangements corresponds to the number, per genome, of breakpoints resulting in segments of at least 3 megabases. 
     
     
         2 . A method according to  claim 1 , wherein the deficiency in the DNA Homologous Recombination pathway is an inactivation of at least one gene selected from the group consisting of BRCA1, BRCA2, PALP2/FANCN, BRIP1/FANCJ, BARD1, RAD51 and RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3). 
     
     
         3 . A method according to  claim 1 , wherein the deficiency is due to germline mutation or somatic mutation of BRCA1, germline mutation or somatic mutation of BRCA2 or promoter methylation of BRCA1. 
     
     
         4 . A method according to  claim 1 , wherein the cancer is selected from breast cancer, ovary cancer, pancreas cancer, head and neck carcinoma and melanoma. 
     
     
         5 . A method according to  claim 1 , wherein the cancer is breast cancer, preferably basal-like, luminal, or HER2-overexpressing breast carcinoma. 
     
     
         6 . A method according to  claim 1 , wherein the number of breakpoints resulting in segments of at least 3 megabases per genome is quantified by quantifying the number of copy number variations per genome. 
     
     
         7 . A method according to  claim 1 , wherein the number of breakpoints resulting in segments of at least 3 megabases per genome is quantified by quantifying the number of copy number variations per genome by comparative genomic hybridization (CGH) array or Single Nucleotide Polymorphism (SNP) array. 
     
     
         8 . A method according to  claim 1 , further comprising the step of evaluating the ploidy of the tumor sample. 
     
     
         9 . A method according to  claim 1 , further comprising the step of evaluating the ploidy of the tumor sample by a method selected from the group consisting of fluorescence activated cell sorting (FACS), fluorescent in situ hybridization (FISH), and Single Nucleotide Polymorphism array (SNP array). 
     
     
         10 . A method according to  claim 1  wherein the number of rearrangements in the genomic DNA is compared to a reference. 
     
     
         11 . A method for predicting tumor deficiency in the DNA homologous recombination (HR) pathway in a patient suffering from cancer, comprising the steps consisting of:
 determining the ploidy of the tumor sample;   quantifying the number of rearrangements in the genomic DNA of a tumor sample obtained from said patient;   comparing the number of rearrangements per genome to a reference, wherein a number of rearrangements resulting in segments of at least 3 megabases superior to said reference is indicative of HR deficiency.   
     
     
         12 . A method according to  claim 1 , wherein the step of quantifying the number of rearrangements in the genomic DNA of a tumor sample obtained from said patient and/or the step of evaluating the ploidy of the tumor sample is performed by SNP array. 
     
     
         13 . A method for predicting the efficacy of a treatment in a patient suffering from cancer, wherein said treatment comprises a PARP inhibitor and/or an alkylating agent,
 and wherein said method comprises the step consisting of predicting deficiency in the DNA homologous recombination (HR) pathway in said patient according to the method of  claim 1 .   
     
     
         15 . A method for treating cancer in a patient, comprising administering a therapeutically effective amount of a PARP inhibitor and/or an alkylating agent, wherein said patient has been classified as having a deficiency in the HR pathway according to the method of  claim 1 . 
     
     
         16 . A method for treating cancer in a patient, comprising the steps of:
 quantifying the number of rearrangements in the genomic DNA of a tumor sample obtained from said patient, wherein the number of rearrangements corresponds to the number, per genome, of breakpoints resulting in segments of at least 3 megabases, preferably at least 4 megabases, even more preferably at least 5, 6, 7, 8 9, 10, 11 12, 13, 14, 15, 16, 17, 18, 19 or 20 megabases.   comparing said number of rearrangements to a predetermined reference;   administering a therapeutically effective amount of a PARP inhibitor and/or an alkylating agent, if said patient has a number of rearrangements superior to said reference.   
     
     
         17 . A method according to  claim 16 , wherein said PARP inhibitor and/or alkylating agent is selected from the group consisting of iniparib, olaparib, rocaparib, CEP 9722, MK 4827, BMN-673, 3-aminobenzamide, platinium complexes such as cisplatin, carboplatin and oxaliplatin, chlormethine, chlorambucil, melphalan, cyclophosphamide, ifosfamide, estramustine, carmustine, lomustine, fotemustine, streptozocin, busulfan, pipobroman, procarbazine, dacarabazine, thiotepa and temozolomide. 
     
     
         18 . The method of  claim 16 , wherein the cancer is selected from breast cancer, ovary cancer, pancreas cancer, head and neck carcinoma and melanoma. 
     
     
         19 . The method according to  claim 16 , wherein the cancer is breast cancer, preferably basal-like, luminal, or HER2-overexpressing breast carcinoma.