Matthew Jensen, Corrine Smolen, Anastasia Tyryshkina, Lucilla Pizzo, Jiawan Sun, Serena Noss, Deepro Banerjee, Matthew T. Oetjens, Hermela Shimelis, Cora Taylor, Vijay Kumar Pounraja, Hyebin Song, Laura Rohan, Emily Huber, Laïla El Khattabi, Ingrid M.B.H. van de Laar, Rafik Tadros, Connie R. Bezzina, Marjon van Slegtenhorst, Janneke A.E. Kammeraad, Paolo Prontera, Jean-Hubert Caberg, Harry Fraser, Siddharth Banka, Anke Van Dijck, Charles E. Schwartz, Els Voorhoeve, Patrick Callier, Anne‐Laure Mosca‐Boidron, Nathalie Marle, Mathilde Lefebvre, Kate Pope, Penny Snell, Amber Boys, Paul J. Lockhart, Myla Ashfaq, M. Elizabeth McCready, Margaret Nowacyzk, Lucia Castiglia, Ornella Galesi, Emanuela Avola, Teresa Mattina, Marco Fichera, Maria Grazia Bruccheri, Giuseppa Maria Luana Mandarà, Francesca Mari, Flavia Privitera, Ilaria Longo, Aurora Currò, Alessandra Renieri, Boris Keren, Perrine Charles, Silvestre Cuinat, Mathilde Nizon, Olivier Pichon, Claire Bénéteau, Radka Stoeva, Dominique Martin‐Coignard, S. Blesson, Cédric Le Caignec, Sandra Mercier, Marie Vincent, Christa Lese Martin, Katrin Männik, Alexandre Reymond, Laurence Faivre, Erik A. Sistermans, R. Frank Kooy, David J. Amor, Corrado Romano, Joris Andrieux, Santhosh Girirajan
Variable expressivity of disease-associated variants implies a role for secondary variants that modify clinical features. We assessed the effects of modifier variants on the clinical outcomes of 2,455 individuals with primary variants. Among 124 families with the 16p12.1 deletion, distinct rare and common variant classes conferred risks for specific developmental features, including short tandem repeats for neurological defects. Network analysis suggested distinct mechanisms involving 16p12.1 genes and secondary variants specific to each proband. Within disease and population cohorts of 976 individuals with the 16p12.1 deletion, we found opposing effects of secondary variants on clinical features across ascertainments. Additional analysis of 1,479 probands with other primary variants, such as the 16p11.2 deletion and CHD8 variants, and 1,528 probands without primary variants showed that phenotypic associations differed by primary variant context and were influenced by synergistic interactions between primary and secondary variants. Our study provides a paradigm to dissect the personalized genomic architecture of complex disorders.