Abstract
With the highly dense genomic data available nowadays, ignoring linkage between genes would result in a huge loss of information. One way to prevent such a loss is to focus on the blocks of chromosomes shared identical by descent (IBD) in populations. The development of the theoretical framework modelling IBD processes is essential to support the advent of new tools such as haplotype phasing, imputation, inferring population structure and demographic history, mapping loci or detecting signatures of selection. This article aims to present the relevant models used in this context, and specify the underlying definitions of identity by descent that are yet to be gathered at one place. In light of this, we derived a general expression for the expected IBD block length, for any population model at any generation after founding.
Highlights
Two alleles are said to be identical by descent (IBD) if they are inherited copies of the same ancestral allele
Paraphrasing some articles of the literature on IBD studies [8,9,10,11], we suggest in this article that n homologous tracts of chromosomes are IBD if they are inherited copies of the same ancestral homologous tract of a chromosome
Martin & Hospital [20] studied the distribution of the length of IBD blocks depending on their positions on a semi-infinite chromosome, and showed that the successive blocks are almost independent and that the block at the origin of the chromosome was larger than the others
Summary
Two alleles are said to be identical by descent (IBD) if they are inherited copies of the same ancestral allele. The idea is to take full account of the high number of available marker loci, and of their high density per genome length (in Morgan). In such analyses, linkage and linkage disequilibrium can no longer be ignored as was the case in the past with scarcer maps. Blocks of chromosomes identical by descent in a population will present some of the relevant models used to study IBD blocks in a population. Practical applications of these models were thoroughly reviewed in Browning’s article [1]
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