CAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants.

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TitleCAGI4 SickKids clinical genomes challenge: A pipeline for identifying pathogenic variants.
Publication TypeJournal Article
Year of Publication2017
AuthorsPal, LR, Kundu, K, Yin, Y, Moult, J
JournalHum Mutat
Date Published2017 May 16
ISSN1098-1004
Abstract

Compared with earlier more restricted sequencing technologies, identification of rare disease variants using whole genome sequence has the possibility of finding all causative variants, but issues of data quality and an overwhelming level of background variants complicate the analysis. The CAGI4 SickKids clinical genome challenge provided an opportunity to assess the landscape of variants found in a difficult set of 25 unsolved rare disease cases. To address the challenge, we developed a three-stage pipeline, first carefully analyzing data quality, then classifying high quality gene specific variants into seven categories, and finally examining each candidate variant for compatibility with the often complex phenotypes of these patients for final prioritization. Variants consistent with the phenotypes were found in 24 out of the 25 cases, and in a number of these, there are prioritized variants in multiple genes. Data quality analysis suggests that some of the selected variants are likely incorrect calls, complicating interpretation. The data providers followed up on three suggested variants with Sanger sequencing, and in one case a prioritized variant was confirmed as likely causative by the referring physician, providing a diagnosis in a previously intractable case. This article is protected by copyright. All rights reserved.

DOI10.1002/humu.23257
Alternate JournalHum. Mutat.
PubMed ID28512736