Genetic modifiers and ascertainment drive variable expressivity of complex disorders
Matthew Jensen 1 2, Corrine Smolen 1 2, Anastasia Tyryshkina 1, Lucilla Pizzo 1, Deepro Banerjee 1, Matthew Oetjens 3, Hermela Shimelis 3, Cora M Taylor 3, Vijay Kumar Pounraja 1 2, Hyebin Song 4, Laura Rohan 1, Emily Huber 1, Laila El Khattabi 5, Ingrid van de Laar 6, Rafik Tadros 6, Connie Bezzina 6, Marjon van Slegtenhorst 6, Janneke Kammeraad 6, Paolo Prontera 7, Jean-Hubert Caberg 8, Harry Fraser 9, Siddhartha Banka 9 10, Anke Van Dijck 11, Charles Schwartz 12, Els Voorhoeve 13, Patrick Callier 14, Anne-Laure Mosca-Boidron 14, Nathalie Marle 14, Mathilde Lefebvre 15, Kate Pope 16, Penny Snell 16, Amber Boys 16, Paul J Lockhart 16 17, Myla Ashfaq 18, Elizabeth McCready 19, Margaret Nowacyzk 19, Lucia Castiglia 20, Ornella Galesi 20, Emanuela Avola 20, Teresa Mattina 20, Marco Fichera 20 21, Maria Grazia Bruccheri 20, Giuseppa Maria Luana Mandarà 22, Francesca Mari 23, Flavia Privitera 23, Ilaria Longo 23, Aurora Curró 23, Alessandra Renieri 23, Boris Keren 24, Perrine Charles 24, Silvestre Cuinat 25, Mathilde Nizon 25, Olivier Pichon 25, Claire Bénéteau 25, Radka Stoeva 25, Dominique Martin-Coignard 26, Sophia Blesson 27, Cedric Le Caignec 28 29, Sandra Mercier 27, Marie Vincent 27, Christa Martin 3, Katrin Mannik 30 31, Alexandre Reymond 32, Laurence Faivre 14 15, Erik Sistermans 13, R Frank Kooy 11, David J Amor 13, Corrado Romano 20 21, Joris Andrieux 33, Santhosh Girirajan 1 2 34
[Preprint]. 2024 Aug 28:2024.08.27.24312158.
doi: 10.1101/2024.08.27.24312158.
Abstract
Variable expressivity of disease-associated variants implies a role for secondary variants that modify clinical features. We assessed the effects of modifier variants towards clinical outcomes of 2,252 individuals with primary variants. Among 132 families with the 16p12.1 deletion, distinct rare and common variant classes conferred risk for specific developmental features, including short tandem repeats for neurological defects and SNVs for microcephaly, while additional disease-associated variants conferred multiple genetic diagnoses. Within disease and population cohorts of 773 individuals with the 16p12.1 deletion, we found opposing effects of secondary variants towards clinical features across ascertainments. Additional analysis of 1,479 probands with other primary variants, such as 16p11.2 deletion and CHD8 variants, and 1,084 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 genomic architecture of complex disorders towards personalized treatment.