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Table S3 from ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk

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posted on 2023-07-14, 13:40 authored by Lenka Stolarova, Petra Kleiblova, Petra Zemankova, Barbora Stastna, Marketa Janatova, Jana Soukupova, Maria Isabel Achatz, Christine Ambrosone, Paraskevi Apostolou, Banu K. Arun, Paul Auer, Mollie Barnard, Birgitte Bertelsen, Koichi Matsuda, Yoichiro Kamatani, Takayuki Morisaki, Akiko Nagai, Kaori Muto, Yoshinori Murakami, Yoichi Furukawa, Yuji Yamanashi, Yusuke Nakamura, Taisei Mushiroda, Yukihide Momozawa, Toshihiro Tanaka, Yozo Ohnishi, Michiaki Kubo, Shinichi Higashiue, Shuzo Kobayashi, Shiro Minami, Hiroki Yamaguhci, Hajime Arai, Ken Yamaji, Yasushi Okazaki, Satoshi Asai, Yasuo Takahashi, Tomoaki Fujioka, Wataru Obara, Seijiro Mori, Shigeo Murayama, Satoshi Nagayama, Yoshio Miki, Akihide Masumoto, Akira Yamada, Yasuko Nishizawa, Masahiko Higashiyama, Hiromu Kutsumi, Yukihiro Koretsune, Takashi Yoshiyama, Marinus J. Blok, Nicholas Boddicker, Joan Brunet, Elizabeth S. Burnside, Mariarosaria Calvello, Ian Campbell, Sock Hoai Chan, Fei Chen, Jian Bang Chiang, Anna Coppa, Laura Cortesi, Ana Crujeiras-González, Marianna Borecka, Marta Cerna, Milena Hovhannisyan, Sandra Jelinkova, Petr Nehasil, Lenka Foretova, Eva Machackova, Vera Krutilkova, Spiros Tavandzis, Leona Cerna, Stepan Chvojka, Monika Koudova, Alena Puchmajerova, Ondrej Havranek, Jan Novotny, Kamila Vesela, Michal Vocka, Lucie Hruskova, Renata Michalovska, Denisa Schwetzova, Zdenka Vlckova, Monika Cerna, Marketa Hejnalova, Nikol Jedlickova, Ivan Subrt, Tomas Zavoral, Marcela Kosarova, Gabriela Vacinova, Maria Janikova, Romana Kratochvilova, Vaclava Curtisova, Radek Vrtel, Ondrej Scheinost, Petra Duskova, Viktor Stranecky, Kim De Leeneer, Robin De Putter, Allison DePersia, Lisa Devereux, Susan Domchek, Anna Efremidis, Christoph Engel, Corinna Ernst, D. Gareth R. Evans, Lidia Feliubadaló, Florentia Fostira, Olivia Fuentes-Ríos, Encarna B. Gómez-García, Sara González, Christopher Haiman, Thomas van Overeem Hansen, Jan Hauke, James Hodge, Chunling Hu, Hongyan Huang, Nur Diana Binte Ishak, Yusuke Iwasaki, Irene Konstantopoulou, Peter Kraft, James Lacey, Conxi Lázaro, Na Li, Weng Khong Lim, Sara Lindstrom, Adriana Lori, Elana Martinez, Alexandra Martins, Koichi Matsuda, Giuseppe Matullo, Simone McInerny, Kyriaki Michailidou, Marco Montagna, Alvaro N.A. Monteiro, Luigi Mori, Katherine Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Janet E. Olson, Julie Palmer, Barbara Pasini, Alpa Patel, Maria Piane, Bruce Poppe, Paolo Radice, Alessandra Renieri, Nicoletta Resta, Marcy E. Richardson, Toon Rosseel, Kathryn J. Ruddy, Marta Santamariña, Elizabeth Santana Dos Santos, Lauren Teras, Amanda E. Toland, Amy Trentham-Dietz, Celine M. Vachon, Alexander E. Volk, Nana Weber-Lassalle, Jeffrey N. Weitzel, Lisa Wiesmuller, Stacey Winham, Siddhartha Yadav, Drakoulis Yannoukakos, Song Yao, Valentina Zampiga, Magnus Zethoven, Ze Wen Zhang, Tomas Zima, Amanda B. Spurdle, Ana Vega, Maria Rossing, Jesús Del Valle, Arcangela De Nicolo, Eric Hahnen, Kathleen B.M. Claes, Joanne Ngeow, Yukihide Momozawa, Paul A. James, Fergus J. Couch, Libor Macurek, Zdenek Kleibl

Frequencies of all reported germline CHEK2 variant carriers and carriers of variants concordantly categorized by functional our kinase assays in breast cancer patients and controls in 12 analyzed population datasets.

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ARTICLE ABSTRACT

Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT). We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1–CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case–control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls. A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)–like (N = 226). We then examined their association with breast cancer risk in the case–control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35–3.41), 1.57 (95% CI, 1.41–1.75), and 1.19 (95% CI, 1.08–1.31), respectively. The meta-analysis of population-specific datasets showed similar results. We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.

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