Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy
Robert Lesurf, Abdelrahman Said, Oyediran Akinrinade, Jeroen Breckpot, Kathleen Delfosse, Ting Liu, Roderick Yao, Gabrielle Persad, Fintan McKenna, Ramil R. Noche, Winona Oliveros, Kaia Mattioli, Shreya Shah, Anastasia Miron, Qian Yang, Guoliang Meng, Michelle Chan‐Seng‐Yue, Wilson W. L. Sung, Bhooma Thiruvahindrapuram, Jane Lougheed, Erwin Oechslin, Tapas Mondal, Lynn Bergin, John Smythe, Shashank Jayappa, Vinay J. Rao, Jayaprakash Shenthar, Perundurai S. Dhandapany, Christopher Semsarian, Robert G. Weintraub, Richard D. Bagnall, Jodie Ingles, John C. Ambrose, Paramasivam Arumugam, E. L. Baple, Marta Bleda, F. Boardman-Pretty, J. M. Boissiere, C. R. Boustred, Helen Brittain, Mark J. Caulfield, G. C. Chan, C. E. H. Craig, Louise C. Daugherty, Anna de Burca, A. Devereau, Greg Elgar, Rebecca E. Foulger, Tom Fowler, Pedro Furió‐Tarí, Adam Giess, J.M. Hackett, Dina Halai, Angela Hamblin, Shirley Henderson, John E. Holman, Tim Hubbard, Kristina Ibáñez, R. Jackson, J. Louise Jones, Dalia Kasperavičiūtė, Melis Kayikci, Athanasios Kousathanas, L. Lahnstein, Katy L. Lawson, S. E. A. Leigh, I. U. S. Leong, Fabrice Lopez, F. Maleady-Crowe, Joanne Mason, Ellen M. McDonagh, Loukas Moutsianas, Michael Mueller, Nirupa Murugaesu, Anna C. Need, Christopher A. Odhams, Andrea Orioli, Christine Patch, D. Perez-Gil, Mariana Buongermino Pereira, Dimitris Polychronopoulos, J. Pullinger, T. Rahim, Augusto Rendon, Pablo Riesgo-Ferreiro, T. Rogers, Mina Ryten, K. Savage, K. Sawant, Richard H. Scott, Afshan Siddiq, A. Sieghart, Damian Smedley, K. R. Smith, Samuel C. Smith, Alona Sosinsky, Will Spooner, Hallam Stevens, A. Stuckey, R. Sultana
Abstract
Abstract Cardiomyopathy (CMP) is a heritable disorder. Over 50% of cases are gene-elusive on clinical gene panel testing. The contribution of variants in non-coding DNA elements that result in cryptic splicing and regulate gene expression has not been explored. We analyzed whole-genome sequencing (WGS) data in a discovery cohort of 209 pediatric CMP patients and 1953 independent replication genomes and exomes. We searched for protein-coding variants, and non-coding variants predicted to affect the function or expression of genes. Thirty-nine percent of cases harbored pathogenic coding variants in known CMP genes, and 5% harbored high-risk loss-of-function (LoF) variants in additional candidate CMP genes. Fifteen percent harbored high-risk regulatory variants in promoters and enhancers of CMP genes (odds ratio 2.25, p = 6.70 × 10 −7 versus controls). Genes involved in α-dystroglycan glycosylation ( FKTN , DTNA ) and desmosomal signaling ( DSC2 , DSG2 ) were most highly enriched for regulatory variants (odds ratio 6.7–58.1). Functional effects were confirmed in patient myocardium and reporter assays in human cardiomyocytes, and in zebrafish CRISPR knockouts. We provide strong evidence for the genomic contribution of functionally active variants in new genes and in regulatory elements of known CMP genes to early onset CMP.