Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry
Authors: Mueller Stefanie H. , Lai Alvina G. , Valkovskaya Maria , Michailidou Kyriaki , Bolla Manjeet K. , Wang Qin , Dennis Joe , Lush Michael , Abu-Ful Zomoruda , Ahearn Thomas U. , Andrulis Irene L. , Anton-Culver Hoda , Antonenkova Natalia N. , Arndt Volker , Aronson Kristan J. , Augustinsson Annelie , Baert Thais , Freeman Laura E. Beane , Beckmann Matthias W. , Behrens Sabine , Benitez Javier , Bermisheva Marina , Blomqvist Carl , Bogdanova Natalia V. , Bojesen Stig E. , Bonanni Bernardo , Brenner Hermann , Brucker Sara Y. , Buys Saundra S. , Castelao Jose E. , Chan Tsun L. , Chang-Claude Jenny , Chanock Stephen J. , Choi Ji-Yeob , Chung Wendy K. ,   NBCS Collaborators, Sahlberg Kristine K. , Børresen-Dale Anne-Lise , Ottestad Lars , Kåresen Rolf , Schlichting Ellen , Holmen Marit Muri , Sauer Toril , Haakensen Vilde , Engebråten Olav , Naume Bjørn , Fosså Alexander , Kiserud Cecile E. , Reinertsen Kristin V. , Helland Åslaug , Riis Margit , Geisler Jürgen ,   OSBREAC, Grenaker Alnaes Grethe I. , Colonna Sarah V. ,   CTS Consortium, Cornelissen Sten , Couch Fergus J. , Czene Kamila , Daly Mary B. , Devilee Peter , Dörk Thilo , Dossus Laure , Dwek Miriam , Eccles Diana M. , Ekici Arif B. , Eliassen A. Heather , Engel Christoph , Evans D. Gareth , Fasching Peter A. , Fletcher Olivia , Flyger Henrik , Gago-Dominguez Manuela , Gao Yu-Tang , García-Closas Montserrat , García-Sáenz José A. , Genkinger Jeanine , Gentry-Maharaj Aleksandra , Grassmann Felix , Guénel Pascal , Gündert Melanie , Haeberle Lothar , Hahnen Eric , Haiman Christopher A. , Håkansson Niclas , Hall Per , Harkness Elaine F. , Harrington Patricia A. , Hartikainen Jaana M. , Hartman Mikael , Hein Alexander , Ho Weang-Kee , Hooning Maartje J. , Hoppe Reiner , Hopper John L. , Houlston Richard S. , Howell Anthony , Hunter David J. , Huo Dezheng ,   ABCTB Investigators, Marsh Deborah , Scott Rodney , Baxter Robert , Yip Desmond , Carpenter Jane , Davis Alison , Pathmanathan Nirmala , Simpson Peter , Graham Dinny , Sachchithananthan Mythily , Ito Hidemi , Iwasaki Motoki , Jakubowska Anna , Janni Wolfgang , John Esther M. , Jones Michael E. , Jung Audrey , Kaaks Rudolf , Kang Daehee , Khusnutdinova Elza K. , Kim Sung-Won , Kitahara Cari M. , Koutros Stella , Kraft Peter , Kristensen Vessela N. , Kubelka-Sabit Katerina , Kurian Allison W. , Kwong Ava , Lacey James V. , Lambrechts Diether , Le Marchand Loic , Li Jingmei , Linet Martha , Lo Wing-Yee , Long Jirong , Lophatananon Artitaya , Mannermaa Arto , Manoochehri Mehdi , Margolin Sara , Matsuo Keitaro , Mavroudis Dimitrios , Menon Usha , Muir Kenneth , 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 , Perou Charles M. , Peto Julian , Pharoah Paul D. P. , Plaseska-Karanfilska Dijana , Presneau Nadege , Rack Brigitte , Radice Paolo , Ramachandran Dhanya , Rashid Muhammad U. , Rennert Gad , Romero Atocha , Ruddy Kathryn J. , Ruebner Matthias , Saloustros Emmanouil , Sandler Dale P. , Sawyer Elinor J. , Schmidt Marjanka K. , Schmutzler Rita K. , Schneider Michael O. , Scott Christopher , Shah Mitul , Sharma Priyanka , Shen Chen-Yang , Shu Xiao-Ou , Simard Jacques , Surowy Harald , Tamimi Rulla M. , Tapper William J. , Taylor Jack A. , Teo Soo Hwang , Teras Lauren R. , Toland Amanda E. , Tollenaar Rob A. E. M. , Torres Diana , Torres-Mejía Gabriela , Troester Melissa A. , Truong Thérèse , Vachon Celine M. , Vijai Joseph , Weinberg Clarice R. , Wendt Camilla , Winqvist Robert , Wolk Alicja , Wu Anna H. , Yamaji Taiki , Yang Xiaohong R. , Yu Jyh-Cherng , Zheng Wei , Ziogas Argyrios , Ziv Elad , Dunning Alison M. , Easton Douglas F. , Hemingway Harry , Hamann Ute , Kuchenbaecker Karoline B. 
Published: January 2023

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.