Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.

TitleInferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Publication TypeJournal Article
Year of Publication2014
AuteursBureau, A, Younkin, SG, Parker, MM, Bailey-Wilson, JE, Marazita, ML, Murray, JC, Mangold, E, Albacha-Hejazi, H, Beaty, TH, Ruczinski, I
JournalBioinformatics
Volume30
Issue15
Pagination2189-96
Date Published2014 Aug 01
ISSN1367-4811
KeywordsCase-Control Studies, Exome, Female, Genetic Linkage, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Genomics, Humans, Male, Monte Carlo Method, Pedigree, Probability, Rare Diseases
Abstract

MOTIVATION: Family-based designs are regaining popularity for genomic sequencing studies because they provide a way to test cosegregation with disease of variants that are too rare in the population to be tested individually in a conventional case-control study.RESULTS: Where only a few affected subjects per family are sequenced, the probability that any variant would be shared by all affected relatives-given it occurred in any one family member-provides evidence against the null hypothesis of a complete absence of linkage and association. A P-value can be obtained as the sum of the probabilities of sharing events as (or more) extreme in one or more families. We generalize an existing closed-form expression for exact sharing probabilities to more than two relatives per family. When pedigree founders are related, we show that an approximation of sharing probabilities based on empirical estimates of kinship among founders obtained from genome-wide marker data is accurate for low levels of kinship. We also propose a more generally applicable approach based on Monte Carlo simulations. We applied this method to a study of 55 multiplex families with apparent non-syndromic forms of oral clefts from four distinct populations, with whole exome sequences available for two or three affected members per family. The rare single nucleotide variant rs149253049 in ADAMTS9 shared by affected relatives in three Indian families achieved significance after correcting for multiple comparisons ([Formula: see text]).AVAILABILITY AND IMPLEMENTATION: Source code and binaries of the R package RVsharing are freely available for download at http://cran.r-project.org/web/packages/RVsharing/index.html.CONTACT: alexandre.bureau@msp.ulaval.ca or ingo@jhu.eduSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btu198
Alternate JournalBioinformatics
PubMed ID24740360
PubMed Central IDPMC4103601
Grant ListR01-DE016148 / DE / NIDCR NIH HHS / United States
R37 DE008559 / DE / NIDCR NIH HHS / United States
R10-DE-014581 / DE / NIDCR NIH HHS / United States
X01-HG006177 / HG / NHGRI NIH HHS / United States
U01 DE018993 / DE / NIDCR NIH HHS / United States
R37-DE008559 / DE / NIDCR NIH HHS / United States
R01 GM083084 / GM / NIGMS NIH HHS / United States
R01 DE014581 / DE / NIDCR NIH HHS / United States
R01 DE016148 / DE / NIDCR NIH HHS / United States
U01 DE020073 / DE / NIDCR NIH HHS / United States
R01 DE009886 / DE / NIDCR NIH HHS / United States
R01-DE009886 / DE / NIDCR NIH HHS / United States
U01 DE020057 / DE / NIDCR NIH HHS / United States