TY - JOUR
T1 - Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes from a dataset of 3,552 Japanese whole genomes (3.5KJPNv2)
AU - Tokunaga, Hideki
AU - Iida, Keita
AU - Hozawa, Atsushi
AU - Ogishima, Soichi
AU - Watanabe, Yoh
AU - Shigeta, Shogo
AU - Shimada, Muneaki
AU - Yamaguchi-Kabata, Yumi
AU - Tadaka, Shu
AU - Katsuoka, Fumiki
AU - Ito, Shin
AU - Kumada, Kazuki
AU - Hamanaka, Yohei
AU - Fuse, Nobuo
AU - Kinoshita, Kengo
AU - Yamamoto, Masayuki
AU - Yaegashi, Nobuo
AU - Yasuda, Jun
N1 - Funding Information:
Funding:ThisworkwassupportedbyJSPS KAKENHI(GrantNumberJP17K07193, JP19H03795,andJP17K11265)forJY,NY,and MS,respectively.ThisworkwassupportedbyThe NationalCancerCenterResearchandDevelopment Fund(29-A-3)andAMED(GrantNumber JP19ck0106319)forNYandHT,respectively.This workwassupportedinpartbytheTohokuMedical MegabankProjectthroughtheMinistryof Education,Culture,Sports,Scienceand Technology(MEXT),JapanforMY;the ReconstructionAgency,MEXT,JapanforMY;by theJapanAgencyforMedicalResearchand development(AMED;Grantnumbers JP17km0105001andJP17km0105002)awarded toMY;andAMEDGRIFINproject(grantnumbers JP17km0405203andJP18km0405203)awarded toMY.Allcomputationalresourceswereprovided bytheToMMosupercomputersystem(http://sc. megabank.tohoku.ac.jp/en),whichissupportedby
Funding Information:
This work was supported by JSPS KAKENHI (Grant Number JP17K07193, JP19H03795, and JP17K11265) for JY, NY, and MS, respectively. This work was supported by The National Cancer Center Research and Development Fund (29-A-3) and AMED (Grant Number JP19ck0106319) for NY and HT, respectively. This work was supported in part by the Tohoku Medical Megabank Project through the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan for MY; the Reconstruction Agency, MEXT, Japan for MY; by the Japan Agency for Medical Research and development (AMED; Grant numbers JP17km0105001 and JP17km0105002) awarded to MY; and AMED GRIFIN project (grant numbers JP17km0405203 and JP18km0405203) awarded to MY. All computational resources were provided by the ToMMo supercomputer system (http://sc. megabank.tohoku.ac.jp/en), which is supported by the Facilitation of R&D Platform for AMED Genome Medicine Support conducted by AMED (Grant number JP17km0405001) awarded to MY. We thank all past and present members of Tohoku Medical Megabank Organization at Tohoku University (present members are listed at https://www.megabank.tohoku.ac.jp/english/a191201/). We also thank Edanz Group (https://en-author-services.edanzgroup.com/ ac) for editing the English text of a draft of this manuscript.
Publisher Copyright:
© 2021 Tokunaga et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2021/1
Y1 - 2021/1
N2 - Identification of the population frequencies of definitely pathogenic germline variants in two major hereditary breast and ovarian cancer syndrome (HBOC) genes, BRCA1/2, is essential to estimate the number of HBOC patients. In addition, the identification of moderately penetrant HBOC gene variants that contribute to increasing the risk of breast and ovarian cancers in a population is critical to establish personalized health care. A prospective cohort subjected to genome analysis can provide both sets of information. Computational scoring and prospective cohort studies may help to identify such likely pathogenic variants in the general population. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of a prospective cohorts with genome data in the Tohoku Medical Megabank Project (TMM) with InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAFs) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar were used for filtration criteria. Familial predispositions to cancers among the 35,000 TMM genome cohort participants were analyzed to verify the identified pathogenicity. Seven potentially pathogenic variants were newly identified. The sisters of carriers of these moderately deleterious variants and definite P and LP variants among members of the TMM prospective cohort showed a statistically significant preponderance for cancer onset, from the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potentially pathogenic variants in BRCA genes in the Japanese population. These results should help to follow up the carriers of variants of uncertain significance in the HBOC genes in the longitudinal prospective cohort study.
AB - Identification of the population frequencies of definitely pathogenic germline variants in two major hereditary breast and ovarian cancer syndrome (HBOC) genes, BRCA1/2, is essential to estimate the number of HBOC patients. In addition, the identification of moderately penetrant HBOC gene variants that contribute to increasing the risk of breast and ovarian cancers in a population is critical to establish personalized health care. A prospective cohort subjected to genome analysis can provide both sets of information. Computational scoring and prospective cohort studies may help to identify such likely pathogenic variants in the general population. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of a prospective cohorts with genome data in the Tohoku Medical Megabank Project (TMM) with InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAFs) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar were used for filtration criteria. Familial predispositions to cancers among the 35,000 TMM genome cohort participants were analyzed to verify the identified pathogenicity. Seven potentially pathogenic variants were newly identified. The sisters of carriers of these moderately deleterious variants and definite P and LP variants among members of the TMM prospective cohort showed a statistically significant preponderance for cancer onset, from the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potentially pathogenic variants in BRCA genes in the Japanese population. These results should help to follow up the carriers of variants of uncertain significance in the HBOC genes in the longitudinal prospective cohort study.
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U2 - 10.1371/journal.pone.0236907
DO - 10.1371/journal.pone.0236907
M3 - Article
C2 - 33428613
AN - SCOPUS:85099889820
SN - 1932-6203
VL - 16
JO - PLoS One
JF - PLoS One
IS - 1 January
M1 - e0236907
ER -