GENLIB: an R package for the analysis of genealogical data

BMC Bioinformatics

Héloïse Gauvin³  Jean-François Lefebvre³  Claudia Moreau³  Eve-Marie Lavoie²  Damian Labuda⁴  Hélène Vézina²  Marie-Hélène Roy-Gagnon¹ 

[1] School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, 600 Peter Morand Cres, Room 101E, Ottawa K1G 5Z3, ON, Canada

[2] BALSAC Project, Université du Québec à Chicoutimi, Chicoutimi, Québec, Canada

[3] Centre de recherche, Centre hospitalier universitaire Sainte-Justine, Montréal, Québec, Canada

[4] Département de pédiatrie, Université de Montréal, Montréal, Québec, Canada

关键词: Gene-dropping simulations;    Genetics;    Inbreeding;    Kinship;    Historical demography;    Software;    Founder populations;    Genealogical data;   

Others  :  1232567
DOI  :  10.1186/s12859-015-0581-5

 received in 2014-12-19, accepted in 2015-04-22,  发布年份 2015

【 摘 要 】

Background

Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for researchers in evolutionary and population genetics, demography and genetic epidemiology. However, analyzing large genealogical datasets requires specialized methods and software. The GENLIB software was developed to study the large genealogies of the French Canadian population of Quebec, Canada. These genealogies are accessible through the BALSAC database, which contains over 3 million records covering the whole province of Quebec over four centuries. Using this resource, extended pedigrees of up to 17 generations can be constructed from a sample of present-day individuals.

Results

We have extended and implemented GENLIB as a package in the R environment for statistical computing and graphics, thus allowing optimal flexibility for users. The GENLIB package includes basic functions to manage genealogical data allowing, for example, extraction of a part of a genealogy or selection of specific individuals. There are also many functions providing information to describe the size and complexity of genealogies as well as functions to compute standard measures such as kinship, inbreeding and genetic contribution. GENLIB also includes functions for gene-dropping simulations.

The goal of this paper is to present the full functionalities of GENLIB. We used a sample of 140 individuals from the province of Quebec (Canada) to demonstrate GENLIB’s functions. Ascending genealogies for these individuals were reconstructed using BALSAC, yielding a large pedigree of 41,523 individuals. Using GENLIB’s functions, we provide a detailed description of these genealogical data in terms of completeness, genetic contribution of founders, relatedness, inbreeding and the overall complexity of the genealogical tree. We also present gene-dropping simulations based on the whole genealogy to investigate identical-by-descent sharing of alleles and chromosomal segments of different lengths and estimate probabilities of identical-by-descent sharing.

Conclusions

The R package GENLIB provides a user friendly and flexible environment to analyze extensive genealogical data, allowing an efficient and easy integration of different types of data, analytical methods and additional developments and making this tool ideal for genealogical analysis.

【 授权许可】

   
2015 Gauvin et al.; licensee BioMed Central.

【 图 表 】

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