Ancestry-specific predisposing germline variants in cancer.

TitleAncestry-specific predisposing germline variants in cancer.
Publication TypeJournal Article
Year of Publication2020
AuthorsOak, N, Cherniack, AD, R Mashl, J, Hirsch, FR, Ding, L, Beroukhim, R, Gümüş, ZH, Plon, SE, Huang, K-L
Corporate AuthorsTCGA Analysis Network
JournalGenome Med
Date Published2020 May 29
KeywordsAtaxia Telangiectasia Mutated Proteins, BRCA2 Protein, Fanconi Anemia Complementation Group Proteins, Female, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Male, Neoplasms, Risk Factors, RNA Helicases, Succinate Dehydrogenase, Von Hippel-Lindau Tumor Suppressor Protein

BACKGROUND: Distinct prevalence of inherited genetic predisposition may partially explain the difference of cancer risks across ancestries. Ancestry-specific analyses of germline genomes are required to inform cancer genetic risk and prognosis of diverse populations.

METHODS: We conducted analyses using germline and somatic sequencing data generated by The Cancer Genome Atlas. Collapsing pathogenic and likely pathogenic variants to cancer predisposition genes (CPG), we analyzed the association between CPGs and cancer types within ancestral groups. We also identified the predisposition-associated two-hit events and gene expression effects in tumors.

RESULTS: Genetic ancestry analysis classified the cohort of 9899 cancer cases into individuals of primarily European (N = 8184, 82.7%), African (N = 966, 9.8%), East Asian (N = 649, 6.6%), South Asian (N = 48, 0.5%), Native/Latin American (N = 41, 0.4%), and admixed (N = 11, 0.1%) ancestries. In the African ancestry, we discovered a potentially novel association of BRCA2 in lung squamous cell carcinoma (OR = 41.4 [95% CI, 6.1-275.6]; FDR = 0.002) previously identified in Europeans, along with a known association of BRCA2 in ovarian serous cystadenocarcinoma (OR = 8.5 [95% CI, 1.5-47.4]; FDR = 0.045). In the East Asian ancestry, we discovered one previously known association of BRIP1 in stomach adenocarcinoma (OR = 12.8 [95% CI, 1.8-90.8]; FDR = 0.038). Rare variant burden analysis further identified 7 suggestive associations in African ancestry individuals previously described in European ancestry, including SDHB in pheochromocytoma and paraganglioma, ATM in prostate adenocarcinoma, VHL in kidney renal clear cell carcinoma, FH in kidney renal papillary cell carcinoma, and PTEN in uterine corpus endometrial carcinoma. Most predisposing variants were found exclusively in one ancestry in the TCGA and gnomAD datasets. Loss of heterozygosity was identified for 7 out of the 15 African ancestry carriers of predisposing variants. Further, tumors from the SDHB or BRCA2 carriers showed simultaneous allelic-specific expression and low gene expression of their respective affected genes, and FH splice-site variant carriers showed mis-splicing of FH.

CONCLUSIONS: While several CPGs are shared across patients, many pathogenic variants are found to be ancestry-specific and trigger somatic effects. Studies using larger cohorts of diverse ancestries are required to pinpoint ancestry-specific genetic predisposition and inform genetic screening strategies.

Alternate JournalGenome Med
PubMed ID32471518
PubMed Central IDPMC7260738
Grant ListR01 CA188228 / CA / NCI NIH HHS / United States
U24 CA210978 / CA / NCI NIH HHS / United States
P30 CA016672 / CA / NCI NIH HHS / United States
U41HG009649 / HG / NHGRI NIH HHS / United States
U41 HG009649 / HG / NHGRI NIH HHS / United States
R01 CA219943 / CA / NCI NIH HHS / United States

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