A new analysis framework called Genomiser combines a pathogenicity score to assess Mendelian non-coding variation with other measures — such as predicted regulatory regions, allele frequency or the phenotypic relevance of associated genes — to improve the identification of regulatory variants from whole-genome sequences. Genomiser takes as input a variant call format (VCF) file obtained from whole-genome sequencing, a list of human phenotype ontology (HPO) terms matching the clinical signs and symptoms observed in the individual under investigation, and optional user parameters. Focusing on small (<25 nucleotides) non-coding mutations, the authors report that Genomiser was able to identify the causative regulatory Mendelian mutation as the top candidate in 77% of simulated whole genomes.
References
Smedley, D. et al. A whole-genome analysis framework for effective identification of pathogenic regulatory variants in Mendelian disease. Am. J. Hum. Genet. 3, 595–606 (2016)
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Koch, L. Pathogenic non-coding variant identification. Nat Rev Genet 17, 583 (2016). https://doi.org/10.1038/nrg.2016.124
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DOI: https://doi.org/10.1038/nrg.2016.124