TY - JOUR
T1 - A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease
AU - Smedley, Damian
AU - Schubach, Max
AU - Jacobsen, Julius O O.B.
AU - Köhler, Sebastian
AU - Zemojtel, Tomasz
AU - Spielmann, Malte
AU - Jäger, Marten
AU - Hochheiser, Harry
AU - Washington, Nicole L L.
AU - McMurry, Julie A A.
AU - Haendel, Melissa A A.
AU - Mungall, Christopher J J.
AU - Lewis, Suzanna E E.
AU - Groza, Tudor
AU - Valentini, Giorgio
AU - Robinson, Peter N N.
N1 - Funding Information:
This work was supported by grants from the European Union Seventh Framework Programme (FP7/2007-2013) (“SYBIL” grant No. 602300), NIH (1 U54 HG006370-01), the NIH Office of the Director (#5R24OD011883), the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy (Contract No. DE-AC02-05CH11231), the Bundesministerium für Bildung und Forschung (BMBF project numbers 0313911 and 01EC1402B), the Deutsche Forschungsgemeinschaft (DFG SP1532/2-1), and the DAAD Funding programme Research Stays for University Academics and Scientists (ID 57210259).
Publisher Copyright:
© 2016 American Society of Human Genetics
PY - 2016/9/1
Y1 - 2016/9/1
N2 - 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.
AB - 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.
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U2 - 10.1016/j.ajhg.2016.07.005
DO - 10.1016/j.ajhg.2016.07.005
M3 - Article
C2 - 27569544
AN - SCOPUS:85002624508
SN - 0002-9297
VL - 99
SP - 595
EP - 606
JO - American Journal of Human Genetics
JF - American Journal of Human Genetics
IS - 3
ER -