A molecular inversion probe-based next-generation sequencing panel to detect germline mutations in Chinese early-onset colorectal cancer patients

// Junxiao Zhang 1 , Xiaoyan Wang 2 , Richarda M. de Voer 1 , Jayne Y. Hehir-Kwa 1 , Eveline J. Kamping 1 , Robbert D.A. Weren 1 , Marcel Nelen 1 , Alexander Hoischen 1 , Marjolijn J.L. Ligtenberg 1, 3 , Nicoline Hoogerbrugge 1 , Xiangling Yang 2 , Zihuan Yang 2 , Xinjuan Fan 4 , Lei Wang 2 , Huanliang Liu 2, 5 , Jianping Wang 2, * , Roland P. Kuiper 1, 6, * , Ad Geurts van Kessel 1, * 1 Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands 2 Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology and the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China 3 Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands 4 Department of Pathology, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China 5 Department of Clinical Laboratory, the Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China 6 Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands * These authors contributed equally to this work Correspondence to: Roland P. Kuiper, email: r.kuiper@prinsesmaximacentrum.nl Jianping Wang, email: wangjpgz@126.com Keywords: molecular inversion probes, early-onset colorectal cancer, Mendelian colorectal cancer predisposition syndromes, next-generation sequencing Received: June 17, 2016 Accepted: February 12, 2017 Published: February 21, 2017 ABSTRACT The currently known Mendelian colorectal cancer (CRC) predisposition syndromes account for ~5–10% of all CRC cases, and are caused by inherited germline mutations in single CRC predisposing genes. Using molecular inversion probes (MIPs), we designed a targeted next-generation sequencing panel to identify mutations in seven CRC predisposing genes: APC, MLH1, MSH2, MSH6, PMS2, MUTYH and NTHL1 . From a consecutive series of 2,371 Chinese CRC patients, 140 familial and non-familial cases were selected that were diagnosed with CRC at or below the age of 35 years. Through MIP-based sequencing we identified pathogenic variants in six genes in 16 out of the 140 (11.4%) patients selected. In 10 patients, known pathogenic mutations in APC (five patients), MLH1 (three patients), or MSH2 (two patients) were identified. Three additional patients were found to carry novel, likely pathogenic truncating ( n = 2) and missense ( n = 1) mutations in the MSH2 gene and a concomitant loss of expression of both the MSH2 and MSH6 proteins in their respective tumor tissues. From our data, we conclude that targeted MIP-based sequencing is a reliable and cost-efficient approach to identify patients with a Mendelian CRC syndrome.