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DECIPHER: Supporting the interpretation and sharing of rare disease phenotype-linked variant data to advance diagnosis and research
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  • Julia Foreman,
  • Simon Brent,
  • Daniel Perrett,
  • Andrew Bevan,
  • Sarah Hunt,
  • Fiona Cunningham,
  • Matthew Hurles,
  • Helen Firth
Julia Foreman
Wellcome Sanger Institute

Corresponding Author:jf11@sanger.ac.uk

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Simon Brent
Wellcome Sanger Institute
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Daniel Perrett
Wellcome Sanger Institute
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Andrew Bevan
Wellcome Sanger Institute
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Sarah Hunt
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Fiona Cunningham
European Bioinformatics Institute
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Matthew Hurles
Wellcome Sanger Institute
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Helen Firth
Cambridge University Hospitals NHS Foundation Trust
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DECIPHER (https://www.deciphergenomics.org) is a free web platform for sharing anonymised phenotype-linked variant data from rare disease patients. Its dynamic interpretation interfaces contextualise genomic and phenotypic data to enable more informed variant interpretation, incorporating international standards for variant classification. DECIPHER supports almost all types of germline and mosaic variation in the nuclear and mitochondrial genome: sequence variants, short tandem repeats, copy-number variants and large structural variants. Patient phenotypes are deposited using Human Phenotype Ontology (HPO) terms, supplemented by quantitative data, which is aggregated to derive gene-specific phenotypic summaries. It hosts data from >250 projects from ~40 countries, openly sharing ~40,000 patient records containing >51,000 variants and >172,000 phenotype terms. The rich phenotype-linked variant data in DECIPHER drives rare disease research and diagnosis by enabling patient matching within DECIPHER and with other resources, and has been cited in >2,600 publications. In this paper, we describe the types of data deposited to DECIPHER, the variant interpretation tools, and patient matching interfaces which make DECIPHER an invaluable rare disease resource.
30 Sep 2021Submitted to Human Mutation
04 Oct 2021Submission Checks Completed
04 Oct 2021Assigned to Editor
10 Oct 2021Reviewer(s) Assigned
26 Oct 2021Review(s) Completed, Editorial Evaluation Pending
12 Nov 2021Editorial Decision: Revise Minor
17 Jan 20221st Revision Received
18 Jan 2022Submission Checks Completed
18 Jan 2022Assigned to Editor
27 Jan 2022Review(s) Completed, Editorial Evaluation Pending
07 Feb 2022Editorial Decision: Accept
21 Feb 2022Published in Human Mutation. 10.1002/humu.24340