Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
Tianyun Wang, Kendra Hoekzema, Davide Vecchio, Huidan Wu, Arvis Sulovari, Bradley P. Coe, Madelyn A. Gillentine, Amy B. Wilfert, Luis A. Pérez‐Jurado, Malin Kvarnung, Yoeri Sleyp, Rachel K. Earl, Jill A. Rosenfeld, Madeleine R. Geisheker, Lin Han, Bing Du, Chris Barnett, E. A. Thompson, Marie Shaw, Renée Carroll, Kathryn Friend, Rachael Catford, Elizabeth E. Palmer, Xiaobing Zou, Jianjun Ou, Honghui Li, Hui Guo, Jennifer Gerdts, Emanuela Avola, Giuseppe Calabrese, Maurizio Elia, Donatella Greco, Anna Lindstrand, Ann Nordgren, Britt‐Marie Anderlid, Geert Vandeweyer, Anke Van Dijck, Nathalie Van der Aa, Brooke G. McKenna, Miroslava Hančárová, Šárka Bendová, Markéta Havlovicová, Giovanni Malerba, Bernardo Dalla Bernardina, Pierandrea Muglia, Arie van Haeringen, Mariëtte J.V. Hoffer, Barbara Franke, Gerarda Cappuccio, Martin B. Delatycki, Paul J. Lockhart, Melanie A. Manning, Pengfei Liu, Ingrid E. Scheffer, Nicola Brunetti‐Pierri, Nanda Rommelse, David G. Amaral, Gijs W.E. Santen, Elisabetta Trabetti, Zdeněk Sedláček, Jacob J. Michaelson, Karen Pierce, Eric Courchesne, R. Frank Kooy, John Acampado, Andrea J. Ace, Alpha Amatya, Irina Astrovskaya, Asif Bashar, Elizabeth Brooks, Martin E. Butler, Lindsey A. Cartner, Wubin Chin, Wendy K. Chung, Amy M. Daniels, Pamela Feliciano, Chris Fleisch, Swami Ganesan, William B. Jensen, Alex Lash, Richard P. Marini, Vincent J. Myers, Eirene O’Connor, Chris Rigby, B. E. Robertson, Neelay Shah, Swapnil Shah, Emily Singer, LeeAnne Green Snyder, Alexandra N. Stephens, Jennifer Tjernagel, Brianna M. Vernoia, Natalia Volfovsky, L. Casey White, Alexander Hsieh, Yufeng Shen, Xueya Zhou, Tychele N. Turner, Ethan Bahl, Taylor Thomas
Abstract
Most genes associated with neurodevelopmental disorders (NDDs) were identified with an excess of de novo mutations (DNMs) but the significance in case-control mutation burden analysis is unestablished. Here, we sequence 63 genes in 16,294 NDD cases and an additional 62 genes in 6,211 NDD cases. By combining these with published data, we assess a total of 125 genes in over 16,000 NDD cases and compare the mutation burden to nonpsychiatric controls from ExAC. We identify 48 genes (25 newly reported) showing significant burden of ultra-rare (MAF < 0.01%) gene-disruptive mutations (FDR 5%), six of which reach family-wise error rate (FWER) significance (p < 1.25E-06). Among these 125 targeted genes, we also reevaluate DNM excess in 17,426 NDD trios with 6,499 new autism trios. We identify 90 genes enriched for DNMs (FDR 5%; e.g., GABRG2 and UIMC1); of which, 61 reach FWER significance (p < 3.64E-07; e.g., CASZ1). In addition to doubling the number of patients for many NDD risk genes, we present phenotype-genotype correlations for seven risk genes (CTCF, HNRNPU, KCNQ3, ZBTB18, TCF12, SPEN, and LEO1) based on this large-scale targeted sequencing effort.