Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry.

Tytuł:: Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry.
Autorzy:: Eygelaar D; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa.; Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa.; Genomics Research Institute, University of Pretoria, Pretoria, 0001, South Africa.
van Rensburg EJ; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa.; Genomics Research Institute, University of Pretoria, Pretoria, 0001, South Africa.; Genetics Division, University of Pretoria, Pretoria, 0001, South Africa.
Joubert F; Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa. .; Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa. .; Genomics Research Institute, University of Pretoria, Pretoria, 0001, South Africa. .
Źródło:: Scientific reports [Sci Rep] 2022 Jan 17; Vol. 12 (1), pp. 802. Date of Electronic Publication: 2022 Jan 17.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Original Publication: London : Nature Publishing Group, copyright 2011-
MeSH Terms:: Genetic Association Studies*
Breast Neoplasms/*genetics
Genetic Predisposition to Disease/*genetics
Germ-Line Mutation/*genetics
Adult ; Age Distribution ; BRCA2 Protein/genetics ; Black People/genetics ; Cohort Studies ; Female ; Humans ; Middle Aged ; Risk ; South Africa ; Ubiquitin-Protein Ligases/genetics ; Young Adult
References:: Rebbeck, T. R. Cancer in sub-Saharan Africa. Science 367, 27–28 (2020). (PMID: 3189670610.1126/science.aay4743)
Anyigba, C. A., Awandare, G. A. & Paemka, L. Breast cancer in sub-Saharan Africa: The current state and uncertain future. Exp. Biol. Med. 246, 1–11 (2021). (PMID: 10.1177/15353702211006047)
Ferlay, J. et al. Global Cancer Observatory: Cancer Tomorrow (International Agency for Research on Cancer, 2020).
Miki, Y. et al. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266, 66–71 (1994). (PMID: 754595410.1126/science.7545954)
Wooster, R. et al. Identification of the breast cancer susceptibility gene BRCA2. Nature 378, 789–792 (1995). (PMID: 852441410.1038/378789a0)
Haffty, B. et al. Breast cancer in young women (YBC): Prevalence of BRCA1/2 mutations and risk of secondary malignancies across diverse racial groups. Ann. Oncol. 20, 1653–1659 (2009). (PMID: 1949128410.1093/annonc/mdp051)
Couch, F. J. et al. Associations between cancer predisposition testing panel genes and breast cancer. JAMA Oncol. 3, 1190–1196 (2017). (PMID: 28418444559932310.1001/jamaoncol.2017.0424)
Samadder, N. J., Giridhar, K. V., Baffy, N., Riegert-Johnson, D. & Couch, F. J. Hereditary cancer syndromes a primer on diagnosis and management: Part 1: Breast-ovarian cancer syndromes. Mayo Clin. Proc. 94, 1084–1098 (2019). (PMID: 3117111910.1016/j.mayocp.2019.02.017)
Easton, D. F. et al. Gene-panel sequencing and the prediction of breast-cancer risk. N. Engl. J. Med. 372, 2243–2257 (2015). (PMID: 26014596461013910.1056/NEJMsr1501341)
Castéra, L. et al. Landscape of pathogenic variations in a panel of 34 genes and cancer risk estimation from 5131 HBOC families. Genet. Med. 20, 1677–1686 (2018). (PMID: 2998807710.1038/s41436-018-0005-9)
Baharian, S. et al. The great migration and African-American genomic diversity. PLoS Genet. 12(5), e1006059 (2016). (PMID: 27232753488379910.1371/journal.pgen.1006059)
Abbad, A. et al. Genetics of breast cancer in African populations: A literature review. Glob. Health Epidemiol. Genomics 3, e8 (2018). (PMID: 10.1017/gheg.2018.8)
Zengh, Y. et al. Inherited breast cancer in Nigerian women. J. Clin. Oncol. 36, 2820–2825 (2018). (PMID: 10.1200/JCO.2018.78.3977)
Adedokun, B. et al. Prevalence of inherited mutations in breast cancer predisposition genes among women in Uganda and Cameroon. Cancer Epidemiol. Biomark. Prev. 29, 359–367 (2020). (PMID: 10.1158/1055-9965.EPI-19-0506)
Jedy-Agba, E., McCormack, V., Adebamowo, C. & Dos-Santos-Silva, I. Stage at diagnosis of breast cancer in sub-Saharan Africa: A systematic review and meta-analysis. Lancet Glob. Health 4, e923–e935 (2016). (PMID: 27855871570854110.1016/S2214-109X(16)30259-5)
Renwick, A. et al. ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat. Genet. 38(8), 873–875 (2006). (PMID: 1683235710.1038/ng1837)
Marabelli, M., Cheng, S.-C. & Parmigiani, G. Penetrance of ATM Gene mutations in breast cancer: A meta-analysis of different measures of risk. Genet. Epidemiol. 40, 425–431 (2016). (PMID: 27112364737695210.1002/gepi.21971)
Toss, A. et al. Clinicopathologic profile of breast cancer in germline ATM and CHEK2 mutation carriers. Genes 12, 616 (2021). (PMID: 33919281814327910.3390/genes12050616)
Gatti, R. A., Tward, A. & Concannon, P. Cancer risk in ATM heterozygotes: A model of phenotypic and mechanistic differences between missense and truncating mutations. Mol. Genet. Metab. 68(4), 419–423 (1999). (PMID: 1060747110.1006/mgme.1999.2942)
Tavtigian, S. V. et al. Rare, evolutionarily unlikely missense substitutions in ATM confer increased risk of breast cancer. Am. J. Hum. Genet. 85, 427–446 (2009). (PMID: 19781682275655510.1016/j.ajhg.2009.08.018)
Goldgar, D. E. et al. Rare variants in the ATM gene and risk of breast cancer. Breast Cancer Res. 13, R73 (2011). (PMID: 21787400323633710.1186/bcr2919)
Breast Cancer Association Consortium et al. Breast cancer risk genes—Association analysis in more than 113,000 women. N. Engl. J. Med. 384, 428–439 (2021). (PMID: 10.1056/NEJMoa1913948)
Loman, N. et al. Family history of breast and ovarian cancers and BRCA1 and BRCA2 mutations in a population-based series of early-onset breast cancer. J. Natl. Cancer Inst. 93, 1215–1223 (2001). (PMID: 1150476710.1093/jnci/93.16.1215)
Laitman, Y. et al. Germline mutations in BRCA1 and BRCA2 genes in ethnically diverse high risk families in Israel. Breast Cancer Res. Treat. 127, 489–495 (2011). (PMID: 2096022810.1007/s10549-010-1217-0)
Walsh, T. et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc. Natl. Acad. Sci. U.S.A. 108, 18032–18037 (2011). (PMID: 22006311320765810.1073/pnas.1115052108)
Kang, E. et al. The prevalence and spectrum of BRCA1 and BRCA2 mutations in Korean population: Recent update of the Korean Hereditary Breast Cancer (KOHBRA) study. Breast Cancer Res. Treat. 151, 157–168 (2015). (PMID: 2586347710.1007/s10549-015-3377-4)
Lynce, F. et al. Deleterious BRCA1/2 mutations in an urban population of Black women. Breast Cancer Res. Treat. 153(1), 201–209 (2015). (PMID: 26250392596369810.1007/s10549-015-3527-8)
Bu, R. et al. Identification of novel BRCA founder mutations in Middle Eastern breast cancer patients using capture and Sanger sequencing analysis. Int. J. Cancer 139, 1091–1097 (2016). (PMID: 27082205511178310.1002/ijc.30143)
Plaskocinska, I. et al. New paradigms for BRCA1/BRCA2 testing in women with ovarian cancer: Results of the genetic testing in epithelial ovarian cancer (GTEOC) study. J. Med. Genet. 53(10), 655–661 (2016). (PMID: 2720820610.1136/jmedgenet-2016-103902)
Briceño-Balcázar, I. et al. Mutational spectrum in breast cancer associated BRCA1 and BRCA2 genes in Colombia. Colomb. Med. 48(2), 58–63 (2017). (PMID: 10.25100/cm.v48i2.1867)
Spurdle, A. B. et al. BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk. J. Med. Genet. 49, 525–532 (2012). (PMID: 2288985510.1136/jmedgenet-2012-101037)
Moghadasi, S. et al. The BRCA1 c.5096G>A p.Arg1699Gln (R1699Q) intermediate risk variant: breast and ovarian cancer risk estimation and recommendations for clinical management from the ENIGMA consortium. J. Med. Genet. 55(1), 15–20 (2018). (PMID: 2849061310.1136/jmedgenet-2017-104560)
Petitalot, A. et al. Combining homologous recombination and phosphopeptide-binding data to predict the impact of BRCA1 BRCT variants on cancer risk. Mol. Cancer Res. 17(1), 54–69 (2019). (PMID: 3025799110.1158/1541-7786.MCR-17-0357)
Breast Cancer Information Core (BIC). https://research.nhgri.nih.gov/bic/ (Accessed 9 June 2021).
Van der Merwe, N. C. et al. A founder BRCA2 mutation in non-Afrikaner breast cancer patients of the Western Cape of South Africa. Clin. Genet. 81(2), 179–184 (2012). (PMID: 2120479910.1111/j.1399-0004.2010.01617.x)
Chrisanthar, R. et al. CHEK2 mutations affecting kinase activity together with mutations in TP53 indicate a functional pathway associated with resistance to Epirubicin in primary breast cancer. PLoS ONE 3(8), e3062 (2008). (PMID: 18725978251811610.1371/journal.pone.0003062)
Knappskog, S. et al. Prevalence of the CHEK2 R95* germline mutation. Hered. Cancer Clin. Pract. 14, 19 (2016). (PMID: 27708748503991510.1186/s13053-016-0059-0)
Stolarova, L. et al. CHEK2 germline variants in cancer predisposition: Stalemate rather than checkmate. Cells 9, 2675 (2020). (PMID: 776366310.3390/cells9122675)
Kurian, A. W. et al. Genetic testing and results in a population-based cohort of breast cancer patients and ovarian cancer patients. J. Clin. Oncol. 37, 1305–1315 (2019). (PMID: 30964716652498810.1200/JCO.18.01854)
Tischkowitz, M. et al. Rare germline mutations in PALB2 and breast cancer risk: A population-based study. Hum. Mutat. 33(4), 674–680 (2012). (PMID: 22241545376775710.1002/humu.22022)
Antoniou, A. C. et al. Breast-cancer risk in families with mutations in PALB2. N. Engl. J. Med. 371(6), 497–506 (2014). (PMID: 25099575415759910.1056/NEJMoa1400382)
Norquist, B. M. et al. Inherited mutations in women with ovarian carcinoma. JAMA Oncol. 2(4), 482–490 (2016). (PMID: 26720728484593910.1001/jamaoncol.2015.5495)
Eliade, M. et al. The transfer of multigene panel testing for hereditary breast and ovarian cancer to healthcare: What are the implications for the management of patients and families? Oncotarget 8(2), 1957–1971 (2017). (PMID: 2777911010.18632/oncotarget.12699)
Casadei, S. et al. Characterization of splice-altering mutations in inherited predisposition to cancer. Proc. Natl. Acad. Sci. U.S.A. 116(52), 26798–26807 (2019). (PMID: 693655410.1073/pnas.1915608116)
Xia, B. et al. Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol. Cell 22, 719–729 (2006). (PMID: 1679354210.1016/j.molcel.2006.05.022)
Oliver, A. W., Swift, S., Lord, C. J., Ashworth, A. & Pearl, L. H. Structural basis for recruitment of BRCA2 by PALB2. EMBO Rep. 10, 990–996 (2009). (PMID: 19609323275005210.1038/embor.2009.126)
Mosse, Y. P. et al. Identification of ALK as a major familial neuroblastoma predisposition gene. Nature 455, 930–935 (2008). (PMID: 18724359267204310.1038/nature07261)
Janoueix-Lerosey, I. et al. Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature 455, 967–970 (2008). (PMID: 1892352310.1038/nature07398)
Hanks, S. et al. Constitutional aneuploidy and cancer predisposition caused by biallelic mutations in BUB1B. Nat. Genet. 36, 1159–1161 (2004). (PMID: 1547595510.1038/ng1449)
Morgan, N. V. et al. A common Fanconi anemia mutation in black populations of sub-Saharan Africa. Blood 105(9), 3542–3544 (2005). (PMID: 1565717510.1182/blood-2004-10-3968)
Lee, W.-H. et al. Human retinoblastoma susceptibility gene: Cloning, identification, and sequence. Science 235, 1394–1399 (1987). (PMID: 382388910.1126/science.3823889)
Sarasin, A., Munier, P. & Cartault, F. How history and geography may explain the distribution in the Comorian archipelago of a novel mutation in DNA repair-deficient xeroderma pigmentosum patients. Genet. Mol. Biol. 43, e20190046 (2020). (PMID: 10.1590/1678-4685-gmb-2019-0046)
Shen, Y. et al. BMN 673, a novel and highly potent PARP1/2 inhibitor for the treatment of human cancers with DNA repair deficiency. Clin. Cancer Res. 19, 5003–5015 (2013). (PMID: 23881923648544910.1158/1078-0432.CCR-13-1391)
Smith, M. A. et al. Initial testing (stage 1) of the PARP inhibitor BMN 673 by the pediatric preclinical testing program: PALB2 mutation predicts exceptional in vivo response to BMN 673. Pediatr. Blood Cancer 62, 91–98 (2015). (PMID: 2526353910.1002/pbc.25201)
Rodrigue, A. et al. A global functional analysis of missense mutations reveals two major hotspots in the PALB2 tumor suppressor. Nucleic Acids Res. 47, 10662–10677 (2019). (PMID: 31586400684779910.1093/nar/gkz780)
Boonen, R. A. C. M., Vreeswijk, M. P. G. & van Attikum, H. Functional characterization of PALB2 variants of uncertain significance: Toward cancer risk and therapy response prediction. Front. Mol. Biosci. 7, 169 (2020). (PMID: 33195396752536310.3389/fmolb.2020.00169)
Johns, M. B. & Paulus-Thomas, J. E. Purification of human genomic DNA from whole blood using sodium perchlorate in place of phenol. Anal. Biochem. 180(2), 276–278 (1989). (PMID: 255475410.1016/0003-2697(89)90430-2)
Andrews, S. FastQC (2018). https://www.bioinformatics.babraham.ac.uk/projects/fastqc .
Hannon, G. The FastX Toolkit (2018). http://hannonlab.cshl.edu/fastx_toolkit/ .
Van der Auwera, G. A. et al. From FastQ data to high confidence variant calls: The genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinform. 43, 1–33 (2013). (PMID: 10.1002/0471250953.bi1110s43)
Chapman, B. bcbio: Blue Collar Bioinformatics (2018). https://github.com/bcbio/bcbio-nextgen .
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754–1760 (2009). (PMID: 19451168270523410.1093/bioinformatics/btp324)
McLaren, W. et al. The ensembl variant effect predictor. Genome Biol. 17(1), 122 (2016). (PMID: 27268795489382510.1186/s13059-016-0974-4)
Chun, S. & Fay, J. C. Identification of deleterious mutations within three human genomes. Genome Res. 19, 1553–1561 (2009). (PMID: 19602639275213710.1101/gr.092619.109)
Schwarz, J. M. et al. MutationTaster2: Mutation prediction for the deep-sequencing age. Nat. Methods 11(4), 361–362 (2014). (PMID: 2468172110.1038/nmeth.2890)
Choi, Y. & Chan, A. P. PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31(16), 2745–2747 (2015). (PMID: 25851949452862710.1093/bioinformatics/btv195)
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46(3), 310–315 (2014). (PMID: 24487276399297510.1038/ng.2892)
Shihab, H. A. et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum. Mutat. 34(1), 57–65 (2013). (PMID: 2303331610.1002/humu.22225)
Karolchik, D. et al. The UCSC table browser data retrieval tool. Nucleic Acids Res. 32, D493–D496 (2004). (PMID: 1468146530883710.1093/nar/gkh103)
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet. Med. 17(5), 405–424 (2015). (PMID: 25741868454475310.1038/gim.2015.30)
den Dunnen, J. T. et al. HGVS recommendations for the description of sequence variants: 2016 update. Hum. Mutat. 37, 564–569 (2016). (PMID: 10.1002/humu.22981)
Grant Information:: IFR160218158695 South African National Research Foundation; BFG14081491267 South African National Research Foundation; CPRR13091237847 South African National Research Foundation; the Rated Researcher Incentive Grant author FJ South African National Research Foundation
Substance Nomenclature:: 0 (BRCA2 Protein)
0 (BRCA2 protein, human)
EC 2.3.2.27 (BRAP protein, human)
EC 2.3.2.27 (Ubiquitin-Protein Ligases)
Entry Date(s):: Date Created: 20220118 Date Completed: 20220303 Latest Revision: 20221207
Update Code:: 20240105
PubMed Central ID:: PMC8763903
DOI:: 10.1038/s41598-022-04791-1
PMID:: 35039564
: Czasopismo naukowe

Pełny tekst

Since the discovery of the breast cancer susceptibility genes, BRCA1 and BRCA2, various other genes conferring an increased risk for breast cancer have been identified. Studies to evaluate sequence variants in cancer predisposition genes among women of African ancestry are limited and mostly focused on BRCA1 and BRCA2. To characterize germline sequence variants in cancer susceptibility genes, we analysed a cohort of 165 South African women of self-identified African ancestry diagnosed with breast cancer, who were unselected for family history of cancer. With the exception of four cases, all others were previously investigated for BRCA1 and BRCA2 deleterious variants, and were negative for pathogenic variants. We utilized the Illumina TruSight cancer panel for targeted sequencing of 94 cancer susceptibility genes. A total of 3.6% of patients carried a pathogenic/likely pathogenic variant in a known breast cancer susceptibility gene: 1.2% in BRCA1, 0.6% in each of BRCA2, ATM, CHEK2 and PALB, none of whom had any family history of breast cancer. The mean age of patients who carried deleterious variant in BRCA1/BRCA2 was 39 years and 8 months compared to 47 years and 3 months among women who carried a deleterious variant in other breast cancer susceptibility genes.
(© 2022. The Author(s).)

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