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Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

2016; Nature Portfolio; Volume: 1; Issue: 1 Linguagem: Inglês

10.1038/npjgenmed.2015.12

2056-7944

Dimitri J. Stavropoulos, Daniele Merico, Rebekah Jobling, Sarah Bowdin, Nasim Monfared, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Ryan K. C. Yuen, Michael J. Szego, Robin Z. Hayeems, Randi Zlotnik Shaul, Michael Brudno, Marta Gîrdea, Brendan J. Frey, Babak Alipanahi, Sohnee Ahmed, Riyana Babul‐Hirji, Ramses Badilla Porras, Melissa T. Carter, Lauren Chad, Ayeshah Chaudhry, David Chitayat, Soghra Jougheh Doust, Cheryl Cytrynbaum, Lucie Dupuis, Resham Ejaz, Leona Fishman, Andrea Guerin, Bita Hashemi, Mayada Helal, Stacy Hewson, Michal Inbar‐Feigenberg, Pekka Kannus, Natalya Karp, Raymond H. Kim, Jonathan B. Kronick, Eriskay Liston, H. Robson MacDonald, Saadet Mercimek‐Mahmutoglu, Roberto Mendoza‐Londono, Enas Nasr, Graeme Nimmo, Nicole Parkinson, Nada Quercia, Julian Raiman, Maian Roifman, Andreas Schulze, Andrea Shugar, Cheryl Shuman, Pierre Sinajon, Komudi Siriwardena, Rosanna Weksberg, Grace Yoon, Chris Carew, Raith Erickson, Richard A. Leach, Robert J. Klein, Peter N. Ray, M. Stephen Meyn, Stephen W. Scherer, Ronald D. Cohn, Christian R. Marshall,

Congenital heart defects research

Abstract The standard of care for first-tier clinical investigation of the aetiology of congenital malformations and neurodevelopmental disorders is chromosome microarray analysis (CMA) for copy-number variations (CNVs), often followed by gene(s)-specific sequencing searching for smaller insertion–deletions (indels) and single-nucleotide variant (SNV) mutations. Whole-genome sequencing (WGS) has the potential to capture all classes of genetic variation in one experiment; however, the diagnostic yield for mutation detection of WGS compared to CMA, and other tests, needs to be established. In a prospective study we utilised WGS and comprehensive medical annotation to assess 100 patients referred to a paediatric genetics service and compared the diagnostic yield versus standard genetic testing. WGS identified genetic variants meeting clinical diagnostic criteria in 34% of cases, representing a fourfold increase in diagnostic rate over CMA (8% ; P value=1.42E−05) alone and more than twofold increase in CMA plus targeted gene sequencing (13%; P value=0.0009). WGS identified all rare clinically significant CNVs that were detected by CMA. In 26 patients, WGS revealed indel and missense mutations presenting in a dominant (63%) or a recessive (37%) manner. We found four subjects with mutations in at least two genes associated with distinct genetic disorders, including two cases harbouring a pathogenic CNV and SNV. When considering medically actionable secondary findings in addition to primary WGS findings, 38% of patients would benefit from genetic counselling. Clinical implementation of WGS as a primary test will provide a higher diagnostic yield than conventional genetic testing and potentially reduce the time required to reach a genetic diagnosis.