6
Identity by Descent in the Mapping of Genetic
Traits
Elizabeth A. Thompson
Abstract
This chapter shows how the descent of genome from an ancestor to currently
observed descendants results in identity by descent (IBD) in current individuals
and hence similarities in their DNA at genetic marker loci. Conversely, data on
the marker genotypes of individuals provides inferences of shared descent of
genome in current individuals, not just genome-wide but in specific genome
regions. Regions where shared genome accords with phenotypic similarities
for a trait provide evidence of causal DNA at some location in the region.
The chapter considers both data observed on defined pedigree structures, and
data on population members whose pedigree relationships may be remote and
are unknown. We take a model-based approach, deriving probabilities of IBD
and likelihoods of mapping parameters, given observed genetic data. We first
consider probabilities of gene IBD among individuals and across a chromosome,
using either a known pedigree or a population-based model. We then consider
probabilities of genotypic and phenotypic data on individuals, conditional on
latent IBD. Thence IBD may be inferred from marker genotypes, combining
information from multiple SNP markers. Finally, we show how location-specific
realizations of IBD can be used to address questions of gene mapping. By
focusing on IBD, we unify pedigree and population-based approaches.
E. A. Thompson ()
Department of Statistics, University of Washington, Seattle, WA, USA
e-mail: eathomp@uw.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_6
123
Identity by Descent in the Mapping of Genetic
Traits
Elizabeth A. Thompson
Abstract
This chapter shows how the descent of genome from an ancestor to currently
observed descendants results in identity by descent (IBD) in current individuals
and hence similarities in their DNA at genetic marker loci. Conversely, data on
the marker genotypes of individuals provides inferences of shared descent of
genome in current individuals, not just genome-wide but in specific genome
regions. Regions where shared genome accords with phenotypic similarities
for a trait provide evidence of causal DNA at some location in the region.
The chapter considers both data observed on defined pedigree structures, and
data on population members whose pedigree relationships may be remote and
are unknown. We take a model-based approach, deriving probabilities of IBD
and likelihoods of mapping parameters, given observed genetic data. We first
consider probabilities of gene IBD among individuals and across a chromosome,
using either a known pedigree or a population-based model. We then consider
probabilities of genotypic and phenotypic data on individuals, conditional on
latent IBD. Thence IBD may be inferred from marker genotypes, combining
information from multiple SNP markers. Finally, we show how location-specific
realizations of IBD can be used to address questions of gene mapping. By
focusing on IBD, we unify pedigree and population-based approaches.
E. A. Thompson ()
Department of Statistics, University of Washington, Seattle, WA, USA
e-mail: eathomp@uw.edu
© The Author(s), under exclusive license to Springer Nature Switzerland AG 2021
K. E. Lohmueller, R. Nielsen (eds.), Human Population Genomics,
https://doi.org/10.1007/978-3-030-61646-5_6
123