TY - JOUR
T1 - Ancestry-specific predisposing germline variants in cancer
AU - Oak, Ninad
AU - Cherniack, Andrew D.
AU - Mashl, R. Jay
AU - Carrot-Zhang, Jian
AU - Chambwe, Nyasha
AU - Damrauer, Jeffrey S.
AU - Knijnenburg, Theo A.
AU - Robertson, A. Gordon
AU - Yau, Christina
AU - Zhou, Wanding
AU - Berger, Ashton C.
AU - Newberg, Justin
AU - Romanel, Alessandro
AU - Sayaman, Rosalyn W.
AU - Demichelis, Francesca
AU - Felau, Ina
AU - Frampton, Garret
AU - Han, Seunghun
AU - Hoadley, Katherine A.
AU - Kemal, Anab
AU - Laird, Peter W.
AU - Lazar, Alexander J.
AU - Le, Xiuning
AU - Shen, Hui
AU - Wong, Christopher K.
AU - Zenklusen, Jean C.
AU - Ziv, Elad
AU - Aguet, Francois
AU - Demchok, John A.
AU - Mensah, Michael K.A.
AU - Tarnuzzer, Roy
AU - Wang, Zhining
AU - Yang, Liming
AU - Alfoldi, Jessica
AU - Karczewski, Konrad J.
AU - MacArthur, Daniel G.
AU - Frampton, Garret M.
AU - Benz, Christopher
AU - Stuart, Joshua M.
AU - Hirsch, Fred R.
AU - Ding, Li
AU - Beroukhim, Rameen
AU - Gümüş, Zeynep H.
AU - Plon, Sharon E.
AU - Huang, Kuan Lin
N1 - Publisher Copyright:
© 2020 The Author(s).
PY - 2020/5/29
Y1 - 2020/5/29
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85085701416&partnerID=8YFLogxK
U2 - 10.1186/s13073-020-00744-3
DO - 10.1186/s13073-020-00744-3
M3 - Article
C2 - 32471518
AN - SCOPUS:85085701416
SN - 1756-994X
VL - 12
JO - Genome medicine
JF - Genome medicine
IS - 1
M1 - 51
ER -