Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
In: ISSN: 1756-994X ; Genome Medicine ; https://hal.science/hal-04069286 ; Genome Medicine, 2023, 15 (1), ⟨10.1186/s13073-022-01152-5⟩, 2023
Online
academicJournal
Zugriff:
International audience ; Background: Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. Methods: We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes’ coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. Results: In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10−6) and AC058822.1 (P = 1.47 × 10−4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C. Conclusions: Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10−5), demonstrating the importance of diversifying study cohorts.
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Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
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| Autor/in / Beteiligte Person: | Mueller, Stefanie H. ; Lai, Alvina G. ; Valkovskaya, Maria ; Michailidou, Kyriaki ; Bolla, Manjeet K. ; Wang, Qin ; Dennis, Joe ; Lush, Michael J. ; Abu-Ful, Zomoroda ; Ahearn, Thomas U. ; Andrulis, Irene L. ; Anton-Culver, Hoda ; Antonenkova, Natalia Nikolaevna ; Arndt, Volker R. ; Aronson, Kristan J. ; Augustinsson, Annelie ; Baert, Thaïs ; Freeman, Laura E. ; Beckmann, Matthias Wilhelm ; Behrens, Sabine ; Benitez, Javier J. ; Bermisheva, Marina A. ; Blomqvist, Carl ; Bogdanova, Natalia Valerijevna ; Bojesen, Stig Egil ; Bonanni, Bernardo ; Brenner, Hermann ; Brucker, Sara Yvonne ; Buys, Saundra S. ; Castelao, Jose Esteban ; Chan, Tsun Leung ; Chang-Claude, Jenny C. ; Chanock, Stephen J. ; Choi, Ji-Yeob ; Chung, Wendy K. ; Sahlberg, Kristine Kleivi ; Børresen-Dale, Anne Lise ; Ottestad, Lars O. ; Kåresen, Rolf ; Schlichting, Ellen ; Holmen, Marit Muri ; Sauer, Toril ; Haakensen, Vilde Drageset ; Engebråten, Olav ; Naume, Björn ; Fosså, Alexander ; Kiserud, Cecile E. ; Reinertsen, Kristin Valborg ; Helland, Åslaug ; Riis, Margit L.H. ; Geisler, Jürgen ; Grenaker Alnaes, Grethe Irene ; Colonna, Sarah V. ; Cornelissen, Sten ; Couch, Fergus J. ; Czene, Kamila ; Daly, Mary B. ; Devilee, Peter ; Dörk, Thilo ; Dossus, Laure ; Dwek, Miriam Victoria ; Eccles, Diana M. ; Ekici, Arif Bülent ; Eliassen, A. Heather ; Engel, Christoph ; Evans, D. Gareth R. ; Fasching, Peter Andreas ; Fletcher, Olivia ; Flyger, Henrik Lavlund ; Gago-Dominguez, Manuela ; Gao, Yutang ; García-Closas, Montserrat ; García-Sáenz, José Ángel ; Genkinger, Jeanine M. ; Gentry-Maharaj, Aleksandra ; Grassmann, Felix ; Guénel, Pascal ; Gündert, Melanie ; Haeberle, Lothar ; Hahnen, Eric T. ; Haiman, Christopher A. ; Håkansson, Niclas N. ; Hall, Per ; Harkness, Elaine F. ; Harrington, Patricia A. ; Hartikainen, Jaana M. ; Hartman, Mikael ; Hein, Alexander ; Ho, Weang Kee ; Hooning, Maartje Joanneke ; Hoppe, Reiner ; Hopper, John Llewelyn ; Houlston, Richard S. ; Howell, Anthony ; Hunter, David J. ; Huo, Dezheng ; Marsh, Deborah ; Scott, Rodney ; Baxter, Robert ; Yip, Desmond ; Carpenter, Jane E. ; Davis, Alison J. ; Pathmanathan, Nirmala ; Simpson, Peter Thomas ; Graham, Dinny ; Sachchithananthan, Mythily ; Ito, Hidemi ; Iwasaki, Motoki ; Jakubowska, Anna ; Janni, Wolfgang J. ; John, Esther M. ; Jones, Michael E. ; Jung, Audrey Y. ; Kaaks, Rudolf J. ; Kang, Daehee ; Khusnutdinova, Elza K. ; Kim, Sung-Won ; Kitahara, Cari Meinhold ; Koutros, Stella ; Kraft, Peter P. ; Kristensen, Vessela N. ; Kubelka-Sabit, Katerina B. ; Kurian, Allison W. ; Kwong, Ava ; Lacey, James V. ; Lambrechts, Diether ; Le Marchand, Loïc ; Li, Jingmei ; Linet, Martha S. ; Lo, Wing Yee ; Long, Jirong ; Lophatananon, Artitaya ; Mannermaa, Arto Msci ; Manoochehri, Mehdi ; Margolin, Sara J. ; Matsuo, Keitaro ; Mavroudis, Dimitris A. ; Menon, Usha ; Muir, Kenneth R. ; Murphy, Rachel A. ; Nevanlinna, Heli ; Newman, William G. ; Niederacher, Dieter ; O’brien, Katie M. ; Obi, Nadia ; Offit, Kenneth ; Olopade, Olufunmilayo I. ; Olshan, Andrew F. ; Olsson, Håkan ; Park, Sue K. ; Patel, Alpa V. ; Patel, Achal P. ; Perou, Charles M. ; Peto, Julian ; Pharoah, Paul D.P. ; Plaseska-Karanfilska, Dijana A. ; Presneau, Nadège ; Rack, Brigitte K. ; Radice, Paolo ; Ramachandran, Dhanya ; Rashid, Muhammad Usman ; Rennert, Gad ; Romero, Atocha ; Ruddy, Kathryn Jean ; Ruebner, Matthias ; Saloustros, Emmanouil ; Sandler, Dale P. ; Sawyer, Elinor J. ; Schmidt, Marjanka K. ; Schmutzler, Rita K. ; Schneider, Michael Oliver ; Scott, Christopher G. ; Shah, Mitul N. ; Sharma, Priyanka ; Shen, Chenyang ; Shu, Xiaoou ; Simard, Jacques ; Surowy, Harald M. ; Tamimi, Rulla M. ; Tapper, William J. ; Taylor, Jack A. ; Teo, Soo Hwang ; Teras, Lauren R. ; Toland, Amanda Ewart ; Tollenaar, Rob A.E.M. ; Torres, Diana ; Torres-Mejía, Gabriela ; Troester, Melissa A. ; Truong, Thérèse ; Vachon, Celine M. ; Vijai, Joseph ; Weinberg, Clarice Ring ; Wendt, Camilla ; Winqvist, Robert ; Wolk, Alicja ; Wu, Alan H.B. ; Yamaji, Taiki ; Yang, Xiaohong Rose ; Yu, Jyhcherng ; Zheng, Wei ; Ziogas, Argyrios ; Ziv, Elad ; Dunning, Alison M. ; Easton, Douglas F. ; Hemingway, Harry ; Hamann, Ute ; Kuchenbaecker, Karoline B. ; Centre international de Recherche sur le Cancer (CIRC) ; Centre de recherche en épidémiologie et santé des populations (CESP) ; Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay ; Ministère de l’Économie et de l'Innovation du Québec ; National Institutes of Health, NIH ; National Cancer Institute, NCI ; Genome Canada, GC ; Horizon 2020 Framework Programme, H2020, (633,784, 634935) ; Génome Québec, GQ ; Fondation du cancer du sein du Québec, FCSQ ; Government of Canada ; Canadian Institutes of Health Research, IRSC ; European Research Council, ERC, (948561) |
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| Zeitschrift: | ISSN: 1756-994X ; Genome Medicine ; https://hal.science/hal-04069286 ; Genome Medicine, 2023, 15 (1), ⟨10.1186/s13073-022-01152-5⟩, 2023 |
| Veröffentlichung: | HAL CCSD ; BioMed Central, 2023 |
| Medientyp: | academicJournal |
| DOI: | 10.1186/s13073-022-01152-5 |
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