GENLIB: new function to simulate haplotype transmission in large complex genealogies-Reference-Cited by-同舟云学术

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

Published:2023-03-01 Issue:3 Volume:39 Page:
ISSN:1367-4811
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Rakesh Mohan¹,Vézina Hélène²³⁴,Laprise Catherine⁴⁵,Freeman Ellen E¹⁶,Burkett Kelly M⁷,Roy-Gagnon Marie-Hélène¹^ORCID

Affiliation:

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

AbstractSummaryFounder 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 implementationThe 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.

Funder

Natural Sciences and Engineering Research Council of Canada

Canada Foundation for Innovation

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad136/49552234/btad136.pdf

Reference28 articles.

1. Complex trait mapping in isolated populations: are specific statistical methods required?;Bourgain;Eur J Hum Genet,2005

2. Characterization of human crossover interference;Broman;Am J Hum Genet,2000

3. Correspondence between genomic- and genealogical/coalescent-based inference of homozygosity by descent in large French-Canadian genealogies;Burkett;Front Genet,2022

4. Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives;Caballero;PLoS Genet,2019

5. Ashkenazi Jewish genetic disorders;Charrow;Fam Cancer,2004