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A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

Abstract

The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Overall, Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease.

Type Journal
ISBN 1537-6605 (Electronic) 0002-9297 (Linking)
Authors Smedley, D.; Schubach, M.; Jacobsen, J. O.; Kohler, S.; Zemojtel, T.; Spielmann, M.; Jager, M.; Hochheiser, H.; Washington, N. L.; McMurry, J. A.; Haendel, M. A.; Mungall, C. J.; Lewis, S. E.; Groza, T.; Valentini, G.; Robinson, P. N.;
Garvan Authors Dr Tudor Groza
Publisher Name AM J HUM GENET
Published Date 2016-01-01 00:00:00
Published Volume 99
Published Issue 3
Published Pages 595-606
URL http://www.ncbi.nlm.nih.gov/pubmed/27569544
Status Published In-print