Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases

Alistair T Pagnamenta, Carme Camps, Edoardo Giacopuzzi, Mona Hashim, Eduardo Calpena, Pamela J Kaisaki, Akiko Hashimoto, Edward Sanders, Ron Schwessinger, Jim R Hughes, Gerton Lunter, Helene Dreau, Matteo Ferla, Lukas Lange, Yesim Kesim, Vassilis Ragoussis, Dimitrios V Vavoulis, Holger Allroggen, Olaf Ansorge, Christian BabbsSiddharth Banka, Benito Baños-Piñero, David Beeson, Tal Ben-Ami, Celeste Bento, Edward Blair, Charlotte Brasch-Andersen, Katherine R Bull, Holger Cario, Deirdre Cilliers, Valerio Conti, E Graham Davies, Fatima Dhalla, Beatriz Diez Dacal, Yin Dong, James E Dunford, Renzo Guerrini, Adrian L Harris, Jane Hartley, Georg Hollander, Kassim Javaid, Maureen Kane, Deirdre Kelly, Samantha J L Knight, Alexandra Y Kreins, Erika M Kvikstad, Craig B Langman, Tracy Lester, Kate E Lines, Simon R Lord, Xin Lu, Sahar Mansour, Adnan Manzur, Reza Maroofian, Brian Marsden, Joanne Mason, Simon J McGowan, Davide Mei, Hana Mlcochova, Yoshiko Murakami, Steven Okoli, Elizabeth Ormondroyd, Lilian Bomme Ousager, Jacqueline Palace, Smita Y Patel, Melissa M Pentony, Chris Pugh, Aboulfazl 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 Wall, Hugh Watkins, Jaroslav Zak, Anna H Schuh, Usha Kini, Andrew O M Wilkie, Niko Popitsch, Jenny C Taylor

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article number94
JournalGenome Medicine
Issue number1
Publication statusPublished - 9 Nov 2023


  • Bioinformatics pipeline development
  • Clinical impact
  • Diagnostic yield
  • Genome sequencing
  • Non-coding
  • Pipeline optimisation
  • Rare diseases
  • Splice site variant
  • Structural variant


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