Data from ENIGMA <i>CHEK2</i>gether Project: A Comprehensive Study Identifies Functionally Impaired <i>CHEK2</i> Germline Missense Variants Associated with Increased Breast Cancer Risk
Authors: Stolarova Lenka , Kleiblova Petra , Zemankova Petra , Stastna Barbora , Janatova Marketa , Soukupova Jana , Achatz Maria Isabel , Ambrosone Christine , Apostolou Paraskevi , Arun Banu K. , Auer Paul , Barnard Mollie , Bertelsen Birgitte , Matsuda Koichi , Kamatani Yoichiro , Morisaki Takayuki , Nagai Akiko , Muto Kaori , Murakami Yoshinori , Furukawa Yoichi , Yamanashi Yuji , Nakamura Yusuke , Mushiroda Taisei , Momozawa Yukihide , Tanaka Toshihiro , Ohnishi Yozo , Kubo Michiaki , Higashiue Shinichi , Kobayashi Shuzo , Minami Shiro , Yamaguhci Hiroki , Arai Hajime , Yamaji Ken , Okazaki Yasushi , Asai Satoshi , Takahashi Yasuo , Fujioka Tomoaki , Obara Wataru , Mori Seijiro , Murayama Shigeo , Nagayama Satoshi , Miki Yoshio , Masumoto Akihide , Yamada Akira , Nishizawa Yasuko , Higashiyama Masahiko , Kutsumi Hiromu , Koretsune Yukihiro , Yoshiyama Takashi , Blok Marinus J. , Boddicker Nicholas , Brunet Joan , Burnside Elizabeth S. , Calvello Mariarosaria , Campbell Ian , Chan Sock Hoai , Chen Fei , Chiang Jian Bang , Coppa Anna , Cortesi Laura , Crujeiras-González Ana , Borecka Marianna , Cerna Marta , Hovhannisyan Milena , Jelinkova Sandra , Nehasil Petr , Foretova Lenka , Machackova Eva , Krutilkova Vera , Tavandzis Spiros , Cerna Leona , Chvojka Stepan , Koudova Monika , Puchmajerova Alena , Havranek Ondrej , Novotny Jan , Vesela Kamila , Vocka Michal , Hruskova Lucie , Michalovska Renata , Schwetzova Denisa , Vlckova Zdenka , Cerna Monika , Hejnalova Marketa , Jedlickova Nikol , Subrt Ivan , Zavoral Tomas , Kosarova Marcela , Vacinova Gabriela , Janikova Maria , Kratochvilova Romana , Curtisova Vaclava , Vrtel Radek , Scheinost Ondrej , Duskova Petra , Stranecky Viktor , De Leeneer Kim , De Putter Robin , DePersia Allison , Devereux Lisa , Domchek Susan , Efremidis Anna , Engel Christoph , Ernst Corinna , Evans D. Gareth R. , Feliubadaló Lidia , Fostira Florentia , Fuentes-Ríos Olivia , Gómez-García Encarna B. , González Sara , Haiman Christopher , Hansen Thomas van Overeem , Hauke Jan , Hodge James , Hu Chunling , Huang Hongyan , Ishak Nur Diana Binte , Iwasaki Yusuke , Konstantopoulou Irene , Kraft Peter , Lacey James , Lázaro Conxi , Li Na , Lim Weng Khong , Lindstrom Sara , Lori Adriana , Martinez Elana , Martins Alexandra , Matsuda Koichi , Matullo Giuseppe , McInerny Simone , Michailidou Kyriaki , Montagna Marco , Monteiro Alvaro N.A. , Mori Luigi , Nathanson Katherine , Neuhausen Susan L. , Nevanlinna Heli , Olson Janet E. , Palmer Julie , Pasini Barbara , Patel Alpa , Piane Maria , Poppe Bruce , Radice Paolo , Renieri Alessandra , Resta Nicoletta , Richardson Marcy E. , Rosseel Toon , Ruddy Kathryn J. , Santamariña Marta , Dos Santos Elizabeth Santana , Teras Lauren , Toland Amanda E. , Trentham-Dietz Amy , Vachon Celine M. , Volk Alexander E. , Weber-Lassalle Nana , Weitzel Jeffrey N. , Wiesmuller Lisa , Winham Stacey , Yadav Siddhartha , Yannoukakos Drakoulis , Yao Song , Zampiga Valentina , Zethoven Magnus , Zhang Ze Wen , Zima Tomas , Spurdle Amanda B. , Vega Ana , Rossing Maria , Del Valle Jesús , De Nicolo Arcangela , Hahnen Eric , Claes Kathleen B.M. , Ngeow Joanne , Momozawa Yukihide , James Paul A. , Couch Fergus J. , Macurek Libor , Kleibl Zdenek 
Published: July 2023

<div>AbstractPurpose:<p>Germline pathogenic variants in <i>CHEK2</i> confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense <i>CHEK2</i> variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT).</p>Experimental Design:<p>We collected 460 <i>CHEK2</i> missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using <i>CHEK2</i>-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1–<i>CHEK2</i>-knockout cells. Concordant results in both functional assays were used to categorize <i>CHEK2</i> VUS from 12 ENIGMA case–control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls.</p>Results:<p>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 (<i>N</i> = 102), functionally intermediate (<i>N</i> = 12), or functionally wild-type (WT)–like (<i>N</i> = 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.</p>Conclusions:<p>We determined the functional consequences for the majority of <i>CHEK2</i> 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 <i>CHEK2</i> 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.</p></div>