Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry Journal Article
| Authors: | Mueller, S. H.; Lai, A. G.; Valkovskaya, M.; Michailidou, K.; Bolla, M. K.; Wang, Q.; Dennis, J.; Lush, M.; Abu-Ful, Z.; Ahearn, T. U.; Andrulis, I. L.; Anton-Culver, H.; Antonenkova, N. N.; Arndt, V.; Aronson, K. J.; Augustinsson, A.; Baert, T.; Freeman, L. E. B.; Beckmann, M. W.; Behrens, S.; Benitez, J.; Bermisheva, M.; Blomqvist, C.; Bogdanova, N. V.; Bojesen, S. E.; Bonanni, B.; Brenner, H.; Brucker, S. Y.; Buys, S. S.; Castelao, J. E.; Chan, T. L.; Chang-Claude, J.; Chanock, S. J.; Choi, J. Y.; Chung, W. K.; NBCS Collaborators; Colonna, S. V.; CTS Consortium; Cornelissen, S.; Couch, F. J.; Czene, K.; Daly, M. B.; Devilee, P.; Dörk, T.; Dossus, L.; Dwek, M.; Eccles, D. M.; Ekici, A. B.; Eliassen, A. H.; Engel, C.; Evans, D. G.; Fasching, P. A.; Fletcher, O.; Flyger, H.; Gago-Dominguez, M.; Gao, Y. T.; García-Closas, M.; García-Sáenz, J. A.; Genkinger, J.; Gentry-Maharaj, A.; Grassmann, F.; Guénel, P.; Gündert, M.; Haeberle, L.; Hahnen, E.; Haiman, C. A.; Håkansson, N.; Hall, P.; Harkness, E. F.; Harrington, P. A.; Hartikainen, J. M.; Hartman, M.; Hein, A.; Ho, W. K.; Hooning, M. J.; Hoppe, R.; Hopper, J. L.; Houlston, R. S.; Howell, A.; Hunter, D. J.; Huo, D.; ABCTB Investigators; Ito, H.; Iwasaki, M.; Jakubowska, A.; Janni, W.; John, E. M.; Jones, M. E.; Jung, A.; Kaaks, R.; Kang, D.; Khusnutdinova, E. K.; Kim, S. W.; Kitahara, C. M.; Koutros, S.; Kraft, P.; Kristensen, V. N.; Kubelka-Sabit, K.; Kurian, A. W.; Kwong, A.; Lacey, J. V.; Lambrechts, D.; Le Marchand, L.; Li, J.; Linet, M.; Lo, W. Y.; Long, J.; Lophatananon, A.; Mannermaa, A.; Manoochehri, M.; Margolin, S.; Matsuo, K.; Mavroudis, D.; Menon, U.; Muir, K.; Murphy, R. A.; Nevanlinna, H.; Newman, W. G.; Niederacher, D.; O’Brien, K. M.; Obi, N.; Offit, K.; Olopade, O. I.; Olshan, A. F.; Olsson, H.; Park, S. K.; Patel, A. V.; Patel, A.; Perou, C. M.; Peto, J.; Pharoah, P. D. P.; Plaseska-Karanfilska, D.; Presneau, N.; Rack, B.; Radice, P.; Ramachandran, D.; Rashid, M. U.; Rennert, G.; Romero, A.; Ruddy, K. J.; Ruebner, M.; Saloustros, E.; Sandler, D. P.; Sawyer, E. J.; Schmidt, M. K.; Schmutzler, R. K.; Schneider, M. O.; Scott, C.; Shah, M.; Sharma, P.; Shen, C. Y.; Shu, X. O.; Simard, J.; Surowy, H.; Tamimi, R. M.; Tapper, W. J.; Taylor, J. A.; Teo, S. H.; Teras, L. R.; Toland, A. E.; Tollenaar, R. A. E. M.; Torres, D.; Torres-Mejía, G.; Troester, M. A.; Truong, T.; Vachon, C. M.; Vijai, J.; Weinberg, C. R.; Wendt, C.; Winqvist, R.; Wolk, A.; Wu, A. H.; Yamaji, T.; Yang, X. R.; Yu, J. C.; Zheng, W.; Ziogas, A.; Ziv, E.; Dunning, A. M.; Easton, D. F.; Hemingway, H.; Hamann, U.; Kuchenbaecker, K. B. |
| Article Title: | Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry |
| Abstract: | 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. © 2023, The Author(s). |
| Keywords: | controlled study; human tissue; human cell; major clinical study; single nucleotide polymorphism; genetics; polymorphism, single nucleotide; genetic predisposition to disease; breast cancer; cohort analysis; genetic association; genetic variability; genome-wide association study; breast neoplasms; statistical significance; breast tumor; genetic predisposition; genetic screening; genetic code; meta analysis; south and central america; genetic testing; gene structure; hispanic; african; asian; meta analysis (topic); gene regulation; gene expression level; rare variants; procedures; european; ancestry group; cancer prognosis; breast cancer susceptibility; humans; human; female; article; black person; genetic association study; fgfr2 gene; map3k1 gene; esr1 gene; tumor-related gene; formins; black people; diverse ancestry; boredom susceptibility; cblb gene; fmnl3 gene; gene base aggregation; lsp1 gene; srgap2c gene; fmnl3 protein, human; methenamine |
| Journal Title: | Genome Medicine |
| Volume: | 15 |
| Issue: | 1 |
| ISSN: | 1756-994X |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2023-01-26 |
| Start Page: | 7 |
| Language: | English |
| DOI: | 10.1186/s13073-022-01152-5 |
| PUBMED: | 36703164 |
| PROVIDER: | scopus |
| PMCID: | PMC9878779 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 March 2023 -- Source: Scopus |
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