ENIGMA <i>CHEK2</i> gether Project: A Comprehensive Study Identifies Functionally Impaired <i>CHEK2</i> Germline Missense Variants Associated with Increased Breast Cancer Risk
Lenka Stolařová, Petra Kleiblová, Petra Zemánková, Barbora Šťastná, Markéta Janatová, Jana Soukupová, Maria Isabel Achatz, Christine B. Ambrosone, Paraskevi Apostolou, Banu Arun, Paul L. Auer, Mollie E. Barnard, Birgitte Bertelsen, Biobank Japan, 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, Jianbang Chiang, Anna Coppa, Laura Cortesi, Ana Crujeiras-González, Marianna Borecká, Marta Černá, Milena Hovhannisyan, Sandra Jelínková, Petr Nehasil, Lenka Foretová, Eva Macháčková, Vera Krutilkova, Spiros Tavandzis, Leona Cerna, Štěpán Chvojka, Monika Koudová, Alena Puchmajerová, Ondřej Havránek, Jan Novotný, Kamila Veselá, Michal Vočka, Lucie Hrušková, Renata Michalovska, Denisa Schwetzova, Zdeňka Vlčková, Monika Černá, Markéta Hejnalová, Nikol Jedlickova, Ivan Šubrt, Tomas Zavoral, Marcela Kosařová, Gabriela Vacínová, Mária Janíková, Romana Kratochvílová, Václava Curtisová, Radek Vrtěl, Ondřej Scheinost, Petra Duskova, Viktor Stránecký, Kim De Leeneer, Robin De Putter, Allison DePersia
Abstract
PURPOSE: 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). EXPERIMENTAL DESIGN: 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. RESULTS: 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. CONCLUSIONS: 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.