OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

Imene Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

An increasing number of disorders have been identified for which two or more distinct alleles in two or more genes are required to either cause the disease or to significantly modify its onset, severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of alleles underlying digenic and oligogenic diseases in individual whole exome or whole genome sequences. Information that links patient phenotypes to databases of gene–phenotype associations observed in clinical or non-human model organism research can provide useful information and improve variant prioritization for genetic diseases. Additional background knowledge about interactions between genes can be utilized to identify sets of variants in different genes in the same individual which may then contribute to the overall disease phenotype. We have developed OligoPVP, an algorithm that can be used to prioritize causative combinations of variants in digenic and oligogenic diseases, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods in the case of digenic diseases. Our results show that OligoPVP can efficiently prioritize sets of variants in digenic diseases using a phenotype-driven approach and identify etiologically important variants in whole genomes. OligoPVP naturally extends to oligogenic disease involving interactions between variants in two or more genes. It can be applied to the identification of multiple interacting candidate variants contributing to phenotype, where the action of modifier genes is suspected from pedigree analysis or failure of traditional causative variant identification.
Original languageEnglish (US)
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Oct 2 2018

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): URF/1/3454-01-01, FCC/1/1976-08-01, FCS/1/3657-02-01
Acknowledgements: The authors thank Dr. Nadia Schoenmakers and Professor Eamonn Maher for helpful comments on our manuscript. This work was supported by funding from King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/3454-01-01, FCC/1/1976-08-01, and FCS/1/3657-02-01. GVG acknowledges support from H2020-EINFRA (731075) and the National Science Foundation (IOS:1340112) as well as support from the NIHR Birmingham ECMC, NIHR Birmingham SRMRC and the NIHR Birmingham Biomedical Research Centre and the MRC HDR UK. The views expressed in this publication are those of the authors and not necessarily those of the NHS, the National Institute for Health Research, the Medical Research Council or the Department of Health.

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