GENLIB: new function to simulate haplotype transmission in large complex genealogies

Mohan Rakesh; Hélène Vézina; Catherine Laprise; Ellen E Freeman; Kelly M Burkett; Marie-Hélène Roy-Gagnon

doi:10.1093/bioinformatics/btad136

GENLIB: new function to simulate haplotype transmission in large complex genealogies

Bioinformatics. 2023 Mar 1;39(3):btad136. doi: 10.1093/bioinformatics/btad136.

Authors

Mohan Rakesh¹, Hélène Vézina^{2

3

4}, Catherine Laprise^{4

5}, Ellen E Freeman^{1

6}, Kelly M Burkett⁷, Marie-Hélène Roy-Gagnon¹

Affiliations

¹ School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada.
² Projet BALSAC, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
³ Département des sciences humaines et sociales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
⁴ Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
⁵ Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada.
⁶ Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada.
⁷ Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.

Abstract

Summary: Founder populations with deep genealogical data are well suited for investigating genetic variants contributing to diseases. Here, we present a major update of the genealogical analysis R package GENLIB, centered around a new function which can simulate the transmission of haplotypes from founders to probands along very large and complex user-specified genealogies.

Availability and implementation: The latest update of the GENLIB package (v1.1.9) contains the new gen.simuHaplo() function and is available on the CRAN repository and from https://github.com/R-GENLIB/GENLIB. Examples can be accessed at https://github.com/R-GENLIB/simuhaplo_functions.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Haplotypes
Humans
Population Groups*
Software*

Grants and funding

MOP 133560/CIHR/Canada