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Reconciling the analysis of IBD and IBS in complex trait studies


Identity by descent (IBD) is a fundamental concept in genetics and refers to alleles that are descended from a common ancestor in a base population. Identity by state (IBS) simply refers to alleles that are the same, irrespective of whether they are inherited from a recent ancestor. In modern applications, IBD relationships are estimated from genetic markers in individuals without any known relationship. This can lead to erroneous inference because a consistent base population is not used. We argue that the purpose of most IBD calculations is to predict IBS at unobserved loci. Recognizing this aim leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression.

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We acknowledge funding from the Australian National Health and Medical Research Council (grants 389892, 613672 and 613601) and the Australian Research Council (grants DP0770096 and DP1093900). We thank M. Keller for discussions and advice on simulation.

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Corresponding authors

Correspondence to Joseph E. Powell or Peter M. Visscher.

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The authors declare no competing financial interests.

Supplementary information

Supplementary information S1 (box)

Simulation of genotypic data and estimation of relatedness coefficients (PDF 297 kb)

Supplementary information S2 (box)

Probability that a hidden SNP within a ROH is homozygous (PDF 295 kb)

Supplementary information S3 (box)

Estimating heritability using relatedness coefficients (PDF 288 kb)

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Genetic Epidemiology, Molecular Epidemiology and Queensland Statistical Genetics Laboratories Brisbane, Australia

Nature Reviews Genetics series on Study Designs


Coalescence theory

A population genetics model of inheritance relationships among alleles at a given locus. The coalescence of two alleles is the most recent point (going back in time) at which they shared a common ancestor.

Cryptic relatedness

The presence of close relatives in a sample of ostensibly unrelated individuals. It is characterized by a recent common ancestry that can be revealed from marker-based relatedness coefficients.

Genome-wide association study

Analysis of the entire genome using association models to identify regions of the genome that contribute to genetic variation in a phenotype. These studies typically analyse data from high-density SNP arrays.


The proportion of phenotypic variation in a population that is attributable to genetic variation among individuals. Statistical methods are used to estimate the relative contributions of differences in genetic and non-genetic factors to the total phenotypic variation in a population.

Identity by descent

(IBD). Two or more alleles are IBD if they are identical copies of the same ancestral allele in a base population. IBD can be estimated for alleles at single loci in a diploid individual or between individuals.

Identity by state

(IBS). Refers to two or more alleles that 'look' the same. For example, if two individuals both carry a 'G' allele at a specific locus.


A population of individuals in which the mating records for multiple generations are known. Pedigree information is typically available for livestock populations, in which controlled breeding has been implemented to maximize the response to genetic selection.

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Powell, J., Visscher, P. & Goddard, M. Reconciling the analysis of IBD and IBS in complex trait studies. Nat Rev Genet 11, 800–805 (2010).

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