Abstract 4175: Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer
Authors: Purrington Kristen , Dyson Gregory , Craig Douglas , Boerner Julie , Madden Julie , Beebe-Dimmer Jennifer , Schwartz Ann G. , Simon Michael 
Published: August 2019

Abstract
Mutations in twenty genes have been associated with heritable breast cancer (BCA), yet the prevalence and clinical implications of most of these genes have not been well described in African American women (AAW). AAW who harbor inherited mutations in BCA susceptibility (BCS) genes are less likely to be identified and thus less likely to receive standard of surgical and preventive care for heritable BCA. A better understanding of heritable mutations in AAW with BCA would ultimately help to define guidelines for clinical management of high risk AAW. We performed targeted sequencing for 288 AAW diagnosed with invasive BCA unselected for family history, age, or BCA subtype. Participants were enrolled in the Detroit Research on Cancer Survivors (ROCS) cohort study or the Karmanos Cancer Institute Biobank. A custom sequencing panel captured the coding sequence of 43 genes (Known: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MRE11A, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53; Candidate: MLH1, MSH2, PMS1, SEC23B, BLM, ATR, BAP1, BBC3, CDKN1A, FAM175A, FANCA, FANCC, FANCI, FANCL, FANCM, GEN1, RAD51B, RBBP8, RECQL, RINT1, TP53BP1, XRCC1, XRCC3). Samples were sequenced using the Illumina MiSeq platform multiplexed for 100X mean depth of coverage. Intronic or synonymous exonic variants and those with &lt;40 reads, or alternative allele frequency &gt;3% in African populations in the 1000 Genomes, ExAC, or NHLBI ESP6500SI databases were filtered. Only variants in known BCS genes could be considered definitively pathogenic (DP), defined as missense variants categorized as pathogenic in ClinVar and all frameshift, nonsense, and splice site variants. All other variants were defined as variants of uncertain significance (VUS). We identified 54 women harboring DP mutations in 15 known BCS genes. Mutations in BRCA1/2 accounted for 32% of all DP mutations. Notably, nearly 17% of DP mutations were in MSH6, a gene only recently described as associated with increased risk of BCA in the general population. Among women with these DP mutations, nearly 25% had no high-risk characteristics. Ten VUS in known BCS genes were identified, where 4 were reported in ClinVar (BARD1, RAD5C, BRCA2, PMS2) and 6 were novel (PMS2, BRCA1, MUTYH, MSH6, NBN, MRE11). Among the candidate BCS genes, 63 VUS were identified: 51 frameshift variants, 5 nonsense variants, 3 splice site variants, and 4 missense mutations predicted to be pathogenic by ≥8/9 algorithms. Nearly 60% of participants had neither a DP mutation or VUS. These data suggest that AAW with BCA have a unique mutation spectrum and may benefit from BCS gene sequencing regardless of family history, age, or subtype. Additional sequencing in AAW will lay the foundation for identification of germline factors associated with BCA risk and prognosis specifically in AAW and offer opportunities for personalized risk assessment.
Citation Format: Kristen Purrington, Gregory Dyson, Douglas Craig, Julie Boerner, Julie Madden, Jennifer Beebe-Dimmer, Ann G. Schwartz, Michael Simon. Spectrum of heritable mutations in 43 known and candidate breast cancer susceptibility genes in African American women with breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4175.