ArticleNature communications2026
Multi-ancestry transcriptome-wide association studies uncover insights into breast cancer genetics and biology.
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Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed.
- Cell-type aware transcriptome-wide association study of mammographic density phenotypes.medRxiv : the preprint server for health sciences · 2025Article
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Authors and funding
68 authors.
Jie PingDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Guochong JiaDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-8455-1832
Qiuyin CaiDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-9384-5648
Xingyi GuoDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0001-5269-1294
Jifeng WangDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0003-0649-3494
Ran TaoDepartment of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-1106-2923
Bingshan LiDepartment of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.ORCID http://orcid.org/0000-0003-2129-168X
Joshua A BauerDepartment of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-8019-900X
Yuhan XieDepartment of Biostatistics, Yale School of Public Health, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-1738-0885
Stefan AmbsLaboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0001-7651-9309
Mollie E BarnardSlone Epidemiology Center, Boston University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-4843-4655
Yu ChenDepartment of Population Health, Division of Epidemiology, NYU Grossman School of Medicine, New York, NY, USA.
Ji-Yeob ChoiDepartment of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.ORCID http://orcid.org/0000-0001-5365-8189
Yu-Tang GaoState Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Montserrat Garcia-ClosasDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
Jian GuDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.ORCID http://orcid.org/0000-0003-3499-0973
Jennifer J HuDepartment of Public Health Sciences, University of Miami School of Medicine, Miami, FL, USA.ORCID http://orcid.org/0000-0002-0021-5699
Motoki IwasakiDivision of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan.
Esther M JohnDepartments of Epidemiology & Population Health and of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
Sun-Seog KweonDepartment of Preventive Medicine, Chonnam National University Medical School, Hwasun, Republic of Korea.
Christopher I LiDivision of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Koichi MatsudaLaboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0001-7292-2686
Keitaro MatsuoDivision of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan.ORCID http://orcid.org/0000-0003-1761-6314
Katherine L NathansonDepartment of Medicine, Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-6740-0901
Barbara NemesureDepartment of Family, Population and Preventive Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
Olufunmilayo I OlopadeDepartment of Medicine, Center for Clinical Cancer Genetics and Global Health, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-9936-1599
Tuya PalDepartment of Medicine, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Sue K ParkDepartment of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.ORCID http://orcid.org/0000-0001-5002-9707
Boyoung ParkDepartment of Preventive Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea.ORCID http://orcid.org/0000-0003-1902-3184
Michael F PressDepartment of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0003-3400-6614
Maureen SandersonDepartment of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA.
Dale P SandlerEpidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, USA.ORCID http://orcid.org/0000-0002-6776-0018
Song YaoDepartment of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.ORCID http://orcid.org/0000-0001-9442-1313
Ying ZhengShanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
Thomas AhearnDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-0771-7752
Abenaa M BrewsterDepartment of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Adeyinka FalusiGenetic and Bioethics Research Unit, Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria.
Anselm J M HennisDepartment of Family, Population and Preventive Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
Hidemi ItoDivision of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, Japan.ORCID http://orcid.org/0000-0002-8023-4581
Michiaki KuboRIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
Eun-Sook LeeNational Cancer Center Graduate School of Cancer Science and Policy, Goyang, Republic of Korea.ORCID http://orcid.org/0000-0003-1122-8230
Timothy MakumbiDepartment of Surgery, Mulago Hospital, Kampala, Uganda.
Berthe S E MapokoYaounde Central Hospital, Yaounde, Cameroon.
Dong-Young NohCollege of Medicine, Cancer Research Institute, Seoul National University, Seoul, Republic of Korea.
Katie M O'BrienEpidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, USA.ORCID http://orcid.org/0000-0002-1931-1349
Oladosu OjengbedeCenter for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria.
Andrew F OlshanDepartment of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Min-Ho ParkDepartment of Surgery, Chonnam National University Medical School, Gwangju, Republic of Korea.ORCID http://orcid.org/0000-0003-1504-3815
Sonya ReidDivision of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Taiki YamajiDivision of Epidemiology, National Cancer Center Institute for Cancer Control, Tokyo, Japan.
Gary ZirpoliSlone Epidemiology Center, Boston University, Boston, MA, USA.ORCID http://orcid.org/0000-0003-1417-5349
Ebonee N ButlerDepartment of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID http://orcid.org/0000-0002-4638-1190
Maosheng HuangDepartment of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
Siew-Kee LowRIKEN Center for Integrative Medical Sciences, Yokohama, Japan.ORCID http://orcid.org/0000-0003-2386-0698
John ObafunwaDepartment of Pathology and Forensic Medicine, Lagos State University Teaching Hospital, Lagos, Nigeria.
Clarice R WeinbergBiostatistics and Computational Biology Branch, National Institutes of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.
Haoyu ZhangDivision of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.ORCID http://orcid.org/0000-0001-6423-0444
Hongyu ZhaoDepartment of Biostatistics, Yale School of Public Health, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-1195-9607
Christine B AmbrosoneDepartment of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.ORCID http://orcid.org/0000-0003-1717-9943
Michelle L CoteFairbanks School of Public Health, Indiana University, Indianapolis, IN, USA.
Dezheng HuoDepartment of Public Health Sciences, The University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-4041-1678
Christopher A HaimanDepartment of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-0097-9971
Daehee KangDepartment of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
Julie R PalmerSlone Epidemiology Center, Boston University, Boston, MA, USA.
Melissa A TroesterDepartment of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.ORCID http://orcid.org/0000-0001-9506-6624
Xiao-Ou ShuDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
Jirong LongDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.ORCID http://orcid.org/0000-0002-7433-9766
Wei ZhengDepartment of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA. wei.zheng@vanderbilt.edu.ORCID http://orcid.org/0000-0003-1226-070X
Funding
Breast Cancer genetic study in African-ancestry populationsR01CA202981 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI Wei Zheng · 2016 to 2026
$14.1MIntegrating genomic and transcriptomic data to identify breast cancer susceptibility genesR01CA235553 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI LONG, JIRONG, ZHENG, WEI · 2019 to 2024
$3.3MConsortium Study to Identify Breast Cancer Susceptibility LociR01CA148667 · NCI · VANDERBILT UNIVERSITY MEDICAL CENTER · PI LONG, JIRONG, ZHENG, WEI · 2011 to 2015
$3.3MGenetic Factors for Breast Cancer- A genome Wide StudyR01CA124558 · NCI · VANDERBILT UNIVERSITY · PI ZHENG, WEI · 2008 to 2012
$3.1MCancer Pharmacologist and HTS ScientistR50CA211206 · NCI · VANDERBILT UNIVERSITY · PI Joshua A. Bauer · 2016 to 2026
$1.8MIntegrated ImageXpress Micro Confocal High Content Screening SystemS10OD028719 · OD · VANDERBILT UNIVERSITY · PI BAUER, JOSHUA A. · 2021 to 2021
$799kNCI NIH HHS R01 CA124558NCI NIH HHS R01 CA148667NCI NIH HHS R01 CA202981NCI NIH HHS R01 CA235553NCI NIH HHS R50 CA211206NIH HHS S10 OD028719U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA124558U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA148667U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA202981U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01CA235553
Abstract
Genome-wide association studies (GWAS) have identified over 200 genetic risk loci for breast cancer, yet their target genes remain largely unknown. We conduct multi-ancestry transcriptome-wide association studies (TWAS) to discover potential breast cancer susceptibility genes. We develop ancestry-specific genetic models to predict levels of gene expression, alternative splicing, and 3' UTR alternative polyadenylation using genomic and transcriptomic data from 652 normal female tissue samples and apply these models to GWAS data of 178,534 cases and 248,300 controls for association analyses. We identify 290 genes associated with breast cancer risk, including 103 previously unreported and 46 not located at known GWAS loci, and 39 genes show distinct associations with breast cancer risk by estrogen-receptor status. Single-cell RNA sequencing and in vitro experiment data provide additional functional evidence for 169 genes. These genes are enriched in pathways implicated in breast carcinogenesis. Our study uncovers insights into breast cancer genetics and biology.
Indexed as
Breast NeoplasmsGenetic Predisposition to DiseaseGenome-Wide Association StudyTranscriptome3' Untranslated RegionsAlternative SplicingFemaleGene Expression ProfilingGene Expression Regulation, NeoplasticHumansPolymorphism, Single Nucleotide3' Untranslated Regions
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