Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking KnownBRCAMutations

Abstract

BRCA1 and BRCA2 testing for hereditary breast and ovarian cancer (HBOC) does not identify all pathogenic variants. Sequencing of 20 complete genes in HBOC patients with uninformative test results (N = 287), including noncoding and flanking sequences of ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD51B, STK11, TP53, and XRCC2, identified 38,372 unique variants. We apply information theory (IT) to predict and prioritize noncoding variants of uncertain significance in regulatory, coding, and intronic regions based on changes in binding sites in these genes. Besides mRNA splicing, IT provides a common framework to evaluate potential affinity changes in transcription factor (TFBSs), splicing regulatory (SRBSs), and RNA-binding protein (RBBSs) binding sites following mutation. We prioritized variants affecting the strengths of 10 splice sites (four natural, six cryptic), 148 SRBS, 36 TFBS, and 31 RBBS. Three variants were also prioritized based on their predicted effects on mRNA secondary (2°) structure and 17 for pseudoexon activation. Additionally, four frameshift, two in-frame deletions, and five stop-gain mutations were identified. When combined with pedigree information, complete gene sequence analysis can focus attention on a limited set of variants in a wide spectrum of functional mutation types for downstream functional and co-segregation analysis.

Comprehensive Analysis of Germline Variants in Mexican Patients with Hereditary Breast and Ovarian Cancer Susceptibility

“…Interestingly, half of the pathogenic variants, 50% (26/52), have not been reported before in any Latin-American population, which highlights the current need to expand the evaluation of the genetic diversity of under-studied, mixed populations such as Mexicans and its association to HBOC. These results also confirm the high level of locus heterogeneity that has been described for HBOC [ 6 , 23 , 31 ] ( Table 1 ).…”

“…It is also possible that patients who tested negative for any of the genes evaluated may harbor variants in noncoding regions that we did not analyzed. Additional mechanisms of pathogenesis that may play a role in susceptibility to BC might include pathogenic variants affecting splicing mechanisms that disrupt RNA-binding protein (RBBSs) and splicing regulatory (SRBSs) binding sites as well as transcription factor binding site disruption or promoter mutations [ 31 , 61 ].…”

Discovery and validation of information theory-based transcription factor and cofactor binding site motifs

“…To test this, the iPWMs were applied to mutation analyses of regulatory SNPs (Supplementary Data). We have recently used this approach to identify and prioritize variants affecting TF binding in 20 risk genes of 287 hereditary breast and ovarian cancer patients (116) and 7 genes from 102 such patients (117). In present study, the iPWMs were also used to delineate known and novel TF-cofactor interactions.…”

Dualistic Role of BARD1 in Cancer

“…Although variants in protein-coding regions have received the most attention, numerous studies have noted the importance of non-coding variants in cancer. A sequencing of 20 complete genes, including noncoding and flanking sequences, in hereditary breast and ovarian cancer patients ( n = 287) identified a single nucleotide variants in 5’ UTR (c.-53G > T; rs143914387) of BARD1 predicted to alter the mRNA structure [ 37 ]. Further complete gene sequencing or whole genome sequencing projects are warranted to investigate the contribution of rare non-coding variants of BARD1 in conferring cancer risk.…”