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

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

SUBMITTER: Pal LR 

PROVIDER: S-EPMC5577808 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature