Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing

Abstract

Inherited loss-of-function mutations in BRCA1 and BRCA2 and other tumor suppressor genes predispose to ovarian carcinomas, but the overall burden of disease due to inherited mutations is not known. Using targeted capture and massively parallel genomic sequencing, we screened for germ-line mutations in 21 tumor suppressor genes in genomic DNA from women with primary ovarian, peritoneal, or fallopian tube carcinoma. Subjects were consecutively enrolled at diagnosis and not selected for age or family history. All classes of mutations, including point mutations and large genomic deletions and insertions, were detected. Of 360 subjects, 24% carried germ-line loss-of-function mutations: 18% in BRCA1 or BRCA2 and 6% in BARD1, BRIP1, CHEK2, MRE11A, MSH6, NBN, PALB2, RAD50, RAD51C, or TP53. Six of these genes were not previously implicated in inherited ovarian carcinoma. Primary carcinomas were generally characterized by genomic loss of normal alleles of the mutant genes. Of women with inherited mutations, >30% had no family history of breast or ovarian carcinoma, and >35% were 60 y or older at diagnosis. More patients with ovarian carcinoma carry cancer-predisposing mutations and in more genes than previously appreciated. Comprehensive genetic testing for inherited carcinoma is warranted for all women with ovarian, peritoneal, or fallopian tube carcinoma, regardless of age or family history. Clinical genetic testing is currently done gene by gene, with each test costing thousands of dollars. In contrast, massively parallel sequencing allows such testing for many genes simultaneously at low cost. O varian carcinoma is the most deadly of gynecological malignancies; the majority of women are diagnosed with advanced stage disease when the chance of cure is small. Inherited mutations in BRCA1 and BRCA2 create a lifetime risk of ovarian carcinoma of between 20% (for BRCA2) and 50% or even higher (for BRCA1) (1). It has been previously estimated that 13-15% of patients with ovarian carcinoma in North America carry germ-line mutations in BRCA1 or BRCA2 (2, 3). Hereditary ovarian carcinoma also occurs in the context of Lynch syndrome [hereditary nonpolyposis colorectal cancer (HNPCC)], but the proportion of ovarian carcinoma explained by germ-line mutations in the mismatch repair genes has not been determined. Inherited mutations in RAD51C, RAD51D, and PALB2 have also been reported in patients with familial ovarian carcinoma (4-6). The overall proportion of ovarian carcinoma due to germ-line mutations in these genes and the roles of other tumor suppressor genes, particularly those implicated in inherited breast cancer, remain unknown.Women with early stage ovarian carcinoma have far better survival than women whose carcinomas are diagnosed at later stages, but current methods of early detection have not proven effective (7). In contrast, risk-reducing salpingo-oophorectomy in women with BRCA1 or BRCA2 mutations dramatically reduces risk of ovarian carcinoma and significantly decreases overall mortality (8-10). It is critically i...

Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

“…38,39 The detection, among 708 patients suspected of HBOC, of 20 inactivating mutations within PALB2, RAD51C, CHEK2 and ATM ( Table 2), indicates that their collective contribution can be estimated at least to 3% and provides another argument highlighting the genetic heterogeneity of HBOC. 19,40 Within families harbouring these mutations, segregation studies will be performed to estimate their causality and penetrance. At the present time, published data concerning the causality of these mutations are still insufficient to integrate these genes into a routine HBOC diagnostic panel.…”

DNA mismatch repair deficiency and hereditary syndromes in Latino patients with colorectal cancer

“…Genomic regions were captured using biotinylated RNA oliognucleotides (SureSelect), prepared in paired-end libraries with ∼200 bp insert size, and sequenced on an Illumina HiSeq2000 instrument with 100 bp read lengths, in a modification of a procedure described by Pritchard et al 2012 27 . Large deletions and duplications were detected using methods described by Nord et al 2011 28 .…”

Mapping genetic alterations causing chemoresistance in cancer: identifying the roads by tracking the drivers

“…210,211 In addition, germline mutations in RAD51C and RAD51D, more recently shown to interact with the Fanconi pathway 212 as well as RAD51 and the BRCA1 co-factor BARD, have all been associated with predisposition to breast and/or ovarian cancer. [213][214][215] These findings, revealing defects in the Fanconi pathway beyond BRCA1/2 mutations to be associated with cancer risk, advocate disturbances in other Fanconi complex components to be examined with respect to drug sensitivity/resistance as well (see below).…”