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Comprehensive rare variant analysis via whole-genome sequencing to determine the molecular pathology of inherited retinal disease

Carss, Keren J., Arno, Gavin, Erwood, Marie, Stephens, Jonathan, Sanchis-Juan, Alba, Hull, Sarah, Megy, Karyn, Grozeva, Detelina, Dewhurst, Eleanor, Malka, Samantha, Plagnol, Vincent, Penkett, Christopher, Stirrups, Kathleen, Rizzo, Roberta, Wright, Genevieve, Josifova, Dragana, Bitner-Glindzicz, Maria, Scott, Richard H., Clement, Emma, Allen, Louise, Armstrong, Ruth, Brady, Angela F., Carmichael, Jenny, Chitre, Manali, Henderson, Robert H. H., Hurst, Jane, MacLaren, Robert E., Murphy, Elaine, Paterson, Joan, Rosser, Elisabeth, Thompson, Dorothy A., Wakeling, Emma, Ouwehand, Willem H., Michaelides, Michel, Moore, Anthony T., Webster, Andrew R. and Raymond, F. Lucy 2017. Comprehensive rare variant analysis via whole-genome sequencing to determine the molecular pathology of inherited retinal disease. American Journal of Human Genetics 100 (1) , pp. 75-90. 10.1016/j.ajhg.2016.12.003

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Abstract

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in CHM in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Medicine
Publisher: Elsevier
ISSN: 0002-9297
Date of Acceptance: 29 November 2016
Last Modified: 12 Jul 2019 13:26
URI: http://orca-mwe.cf.ac.uk/id/eprint/110389

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