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Bioinformatics. 2018 Nov 30. doi: 10.1093/bioinformatics/bty976. [Epub ahead of print]

Detection of rare disease variants in extended pedigrees using RVS.

Author information

1
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA.
2
Department of Oncology, Johns Hopkins School of Medicine, Baltimore MD, USA.
3
Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada.

Abstract

Summary:

Family-based sequencing studies enable researchers to identify highly penetrant genetic variants too rare to be tested in conventional case-control studies, by studying co-segregation of variant and disease phenotype. When multiple affected subjects in a family are sequenced, the probability that a variant or a set of variants is shared identical-by-descent by some or all affected relatives provides evidence against the null hypothesis of complete absence of linkage and association. The Rare Variant Sharing software package RVS implements a suite of tools to assess association and linkage between rare genetic variants and a dichotomous disease indicator in family pedigrees.

Availability and Implementation:

RVS is available as open source software from the Bioconductor webpage at https://bioconductor.org/packages/release/bioc/html/RVS.html.

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