Background: In breast tumors, somatic mutation frequencies in TP53 and PIK3CA vary by tumor subtype and ancestry. HER2 positive and triple negative breast cancers (TNBC) have a higher frequency of TP53 somatic mutations than other subtypes. PIK3CA mutations are more frequently observed in hormone receptor positive tumors. Emerging data suggest tumor mutation status is associated with germline variants and genetic ancestry. We aimed to identify germline variants that are associated with somatic TP53 or PIK3CA mutation status in breast tumors. Methods: A genome-wide association study was conducted using breast cancer mutation status of TP53 and PIK3CA and functional mutation categories including TP53 gain of function (GOF) and loss of function mutations and PIK3CA activating/hotspot mutations. The discovery analysis consisted of 2850 European ancestry women from three datasets. Germline variants showing evidence of association with somatic mutations were selected for validation analyses based on predicted function, allele frequency, and proximity to known cancer genes or risk loci. Candidate variants were assessed for association with mutation status in a multi-ancestry validation study, a Malaysian study, and a study of African American/Black women with TNBC. Results: The discovery Germline x Mutation (GxM) association study found five variants associated with one or more TP53 phenotypes with P values <1x10-6, 33 variants associated with one or more TP53 phenotypes with P values <1x10-5, and 44 variants associated with one or more PIK3CA phenotypes with P values <1x10-5. In the multi-ancestry and Malaysian validation studies, germline ESR1 locus variant, rs9383938, was associated with the presence of TP53 mutations overall (P values 6.8x10-5 and 9.8x10-8, respectively) and TP53 GOF mutations (P value 8.4x10-6). Multiple variants showed suggestive evidence of association with PIK3CA mutation status in the validation studies, but none were significant after correction for multiple comparisons. Conclusions: We found evidence that germline variants were associated with TP53and PIK3CA mutation status in breast cancers. Variants near the estrogen receptor alpha gene, ESR1, were significantly associated with overall TP53 mutations and GOF mutations. Larger multi-ancestry studies are needed to confirm these findings and determine if these variants contribute to ancestry-specific differences in mutation frequency.

HH is on the scientific advisory board for Invitae Genetics, Promega, and Genome Medical and has stock/stock options in Genome Medical and GI OnDemand. None of these are direct conflicts with this study.

This work was supported in part by National Cancer Institutes (NCI) R01 CA215151-01 (AET). Johnny Ramroop was supported by a Pelotonia Postdoctoral Fellowship, Nijole Pollock was supported by a Pelotonia Graduate Research Fellowship and Tanish Gandhi was supported by a Pelotonia Undergraduate Research Fellowship. Monica Paredes was supported by an OSU CCC CREATES Program Fellowship. The OSU CCC GSR and Total Cancer Care were funded in part by NCI grant P30 CA016058. The Spielman Breast Bank was funded in part by the Stefanie Spielman Fund for Breast Cancer Research. For the COH Latina Breast Cancer study, the work was funded by the NCI (R01CA184585, K24CA169004), the National Institute on Minority Health and Health Disparities (NIMHD) Division of Intramural Research, and the California Initiative to Advance Precision Medicine (OPR18111). Research reported in this publication included work performed in the COH Integrative Genomics Core and the Pathology Core supported by the NCI of the National Institutes of Health (NIH) under grant number P30CA033572. SLN and this research were partially funded by the Morris and Horowitz Families Professorship. Sample collection and data were collected under support from NIH R01CA184585 (SLN and EZ). The Nigerian Breast Cancer study was funded in part by NCI grant R01CA228198 and NIMHD grant R01 MD013452 (DH). MyBrCa was funded by the Newton-Ungku Omar Fund (grant no: MR/P012930/1), Wellcome Trust (grant no: v203477/Z/16/Z), Scientex Foundation, Estee Lauder Companies, Yayasan PETRONAS, and Yayasan Sime Darby. The B-CAUSE study was supported in part by NCI R01 CA228156 (Yao, Palmer, Zheng, Carpten), NCI R01 CA255242 (Wei), NCI U24 CA232979, and NCI U24 CA274159 (Liu). The genome-wide genotype was supported in part by NIH grant R01 CA202981 (Zheng) Sample preparation and genotyping assays at Vanderbilt University Medical Center were conducted at the Survey and Biospecimen Shared Resources and Vanderbilt Technologies for Advanced Genomics, which are supported in part by the Vanderbilt-Ingram Cancer Center NCI grant (P30CA068485). The content of this study is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

This study was approved by the Ohio State University Cancer Institutional Review Board (IRB) (protocol number 2005C0082). All data and samples were from de-identified individuals who had undergone informed consent for participation in research studies. Nigerian Study: The VOH IRB and the University of Chicago IRB approved study for participants enrolled at their respective sites. COH Latina Study: One hundred and twenty Latina breast-cancer patients seen at City of Hope (COH) in Duarte, California were included in this study. All participants signed a written informed consent approved by the COH Institutional Review Board. MyBrCa was approved by the Independent Ethics Committee, Ramsay Sime Darby Health Care (reference no: 201208.1), and the Medical Ethics Committee, University Malaya Medical Centre (reference no: 842.9).

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

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I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

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I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

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The majority of data generated or analyzed during this study are included in this published article (Supplementary Tables S2-S35), in TCGA, dbGAP and/or the following data repositories as listed below. TCGA tumor mutation data and SNV genotyping data are available in dbGAP under accession numbers phs001687.v1.p1, phs000178.v11.p8, and phs002387.v1.p1. METABRIC sequencing data of tumors and SNV genotyping data are available on the European Genome-Phenome archive using accession numbers EGAD0001000164, EGAS00000000083, EGAD00010000158, EGAD00010000266, EGAS00001004518 and EGAD00001006399. The Welcome Trust Sanger Institute data are available in the European Genome-Phenome archive using accessing number EGAS00001001178 and EGAD0010000915. Sequencing data and processed genomic data from the Nigerian breast cancer cases are in dbGAP under study accession number phs001687.v1.p1. Tumor/normal WES and RNAseq data and accompanying phenotypic and clinical/histologic data for the COH Latina Breast Cancer Study are deposited in dbGAP (dbGaP Study Accession: phs003218)[71]. MyBrCa WES and sWGS files are available on the European Genome-phenome Archive under the study accession number EGAS00001004518. Access to controlled patient data will require the approval of the MyBrCa Tumour Genomics Data Access Committee upon request to genetics@cancerresearch.my. Sequence and genotyping data for the Banerji et al. study [72] are available in dbGAP under accession number phs000369.v1.p1. Summary-level statistics genotyping data for the AABCG study are available at GWAS Catalog (accession number: GCST90296719, GCST90296720, GCST90296721, and GCST90296722). B-CAUSE TNBC sequencing data is in the process being deposited into dbGaP with accession number pending.