Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases
Alistair T. Pagnamenta, Carlos Camps, Edoardo Giacopuzzi, John Taylor, Mona Hashim, Eduardo Calpena, Pamela J. Kaisaki, Akiko Hashimoto, Jing Yu, Edward Sanders, Ron Schweßinger, Jim R. Hughes, Gerton Lunter, Hélène Dreau, Matteo P. Ferla, Lukas Lange, Yeşim Kesim, Vassilis Ragoussis, Dimitrios V. Vavoulis, Holger Allroggen, Olaf Ansorge, Christian Babbs, Siddharth Banka, Benito Baños-Piñero, David Beeson, Tal Ben‐Ami, David Bennett, Celeste Bento, Edward Blair, Charlotte Brasch‐Andersen, Katherine R. Bull, Holger Cario, Deirdre Cilliers, Valerio Conti, E. Graham Davies, Fatima Dhalla, Beatriz Diez Dacal, Dong Yin, James E. Dunford, Renzo Guerrini, Adrian L. Harris, Jane Hartley, Georg A. Holländer, M K Javaid, Maureen A. Kane, Déirdre Kelly, Dominic F. Kelly, Samantha J.L. Knight, Alexandra Y. Kreins, Erika Kvikstad, Craig B. Langman, Tracy Lester, Kate E Lines, Simon Lord, Xin Lü, Sahar Mansour, Adnan Manzur, Reza Maroofian, Brian D. Marsden, Joanne Mason, Simon J. McGowan, Davide Mei, Hana Mlčochová, Yoshiko Murakami, Andrea H. Németh, Steven Okoli, Elizabeth Ormondroyd, Lilian Bomme Ousager, Jacqueline Palace, Smita Y. Patel, Melissa M. Pentony, Christopher W. Pugh, Abolfazl Rad, Archana Ramesh, Simone G. Riva, Irene Roberts, Noémi Roy, Outi Salminen, Kyleen D. Schilling, Caroline Scott, Arjune Sen, Conrad Smith, Mark Stevenson, Rajesh V. Thakker, Stephen R.F. Twigg, Holm H. Uhlig, Richard van Wijk, Barbara Vona, Steven A. Wall, Jing Wang, Hugh Watkins, Jaroslav Žák, Anna Schuh, Usha Kini, Andrew O.M. Wilkie, Niko Popitsch, Jenny C. Taylor
Abstract
BACKGROUND: Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS: We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS: Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS: Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.