Genetic relatedness analysis: modern data and new challenges

Weir, B. S.; Anderson, Amy D.; Hepler, Amanda B.

doi:10.1038/nrg1960

Cited by 308 publications

(291 citation statements)

References 32 publications

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“…Molecular marker data have been used to infer the degree of relatedness between two individuals in a variety of contexts (Weir et al 2006). The primary interest is often in the relatedness estimates themselves.…”

Section: Introductionmentioning

confidence: 99%

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

et al. 2008

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Several estimators have been proposed that use molecular marker data to infer the degree of relatedness for pairs of individuals. The objective of this study was to evaluate the performance of seven estimators when applied to marker data of a set of 33 key individuals from a large complex apple pedigree. The evaluation considered different scenarios of allele frequencies and different numbers of marker loci. The method of moments estimators were Similarity, Queller-Goodknight, Lynch-Ritland and Wang. The maximum likelihood estimators were Thompson, Anderson-Weir and Jacquard. The pedigree-based coancestry coefficients were taken as the point of reference in calculating correlations and root mean square error (RMSE). The marker data comprised 86 multi-allelic SSR markers on 17 linkage groups, covering 11 Morgans. Additionally, we simulated 10 datasets conditional on the real pedigree to support the results on the real dataset. None of the estimators outperformed the others. Knowledge of allele frequencies appeared to be the most influential, i.e., the highest correlations and lowest RMSE were found when frequencies from the founder population were available. When equal allele frequencies were used, all estimators resulted in very similar, but on average lower, correlations. The use of allele frequencies estimated from the set of 33 individuals gave, on average, the poorest results. The maximum likelihood estimators and the Lynch-Ritland estimator were the most sensitive to allele frequencies. The results from the simulation study fully supported the trends in results of the real dataset. This study indicated that high correlations (up to 0.90) and small RMSE (below 0.03), may be obtained when population allelic frequencies are available. In this scenario, the performances of the various estimators were similar, but seemed to favor the maximum likelihood estimators. In the absence of reliable allele frequencies the method of moments estimators were shown to be more robust. The number of marker loci influenced the average performance of the estimators; however, the ranking was not affected. Correlations up to 0.80 were obtained when two markers per chromosome and appropriate allele frequencies were available. Adding more markers to the current dataset may lead to marginal improvements.

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Section: Introductionmentioning

confidence: 99%

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

et al. 2008

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“…Table 2 shows the values of the Cotterman coefficients for some standard relationships. Cotterman’s coefficients can be estimated by the maximum likelihood method (Milligan, 2003; Weir, 2006). The maximum likelihood estimates reveal the most likely relationship for a pair given the observed genotype data.…”

Section: Ibd Studiesmentioning

confidence: 99%

Graphics for relatedness research

Galván-Femenía

Graffelman

Barcelo-i-Vidal

2017

Molecular Ecology Resources

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Studies of relatedness have been crucial in molecular ecology over the last decades. Good evidence of this is the fact that studies of population structure, evolution of social behaviours, genetic diversity and quantitative genetics all involve relatedness research. The main aim of this article is to review the most common graphical methods used in allele sharing studies for detecting and identifying family relationships. Both IBS and IBD based allele sharing studies are considered. Furthermore, we propose two additional graphical methods from the field of compositional data analysis: the ternary diagram and scatterplots of isometric log-ratios of IBS and IBD probabilities. We illustrate all graphical tools with genetic data from the HGDP-CEPH diversity panel, using mainly 377 microsatellites genotyped for 25 individuals from the Maya population of this panel. We enhance all graphics with convex hulls obtained by simulation and use these to confirm the documented relationships. The proposed compositional graphics are shown to be useful in relatedness research, as they also single out the most prominent related pairs. The ternary diagram is advocated for its ability to display all three allele sharing probabilities simultaneously. The log-ratio plots are advocated as an attempt to overcome the problems with the Euclidean distance interpretation in the classical graphics.

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“…There is an extensive literature on this general problem for unlinked markers and a recent review is provided in [1]. There are some distinguishing features of the problems we address and the solutions we propose.…”

Section: Introductionmentioning

confidence: 99%

On identification problems requiring linked autosomal markers

Egeland

Sheehan

2008

Forensic Science International: Genetics

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This paper considers identification problems based on DNA marker data. The topics we discuss are general, but we will exemplify them in a simple context. There is DNA available from two persons. There is uncertainty about the relationship between the two individuals and a number of hypotheses describing the possible relationship is available.The task is to determine the most likely pedigree. This problem is fairly standard. However, there are some problems that cannot be solved using DNA from independently segregating loci. More generally, the above problems can be solved using linked autosomal markers. To study the problem in detail and understand how linkage works in this regard, we derive an explicit formula for a pair of linked markers. The formula extends to independent pairs of linked markers. While this approach adds to the understanding of the problem, more markers are required to obtain satisfactory results and then the Lander-Green algorithm is needed. Simulation experiments are presented based on a range of scenarios and we conclude that useful results can be obtained using available freeware (MERLIN and R).The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed based on existing technology and freeware.

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Genetic relatedness analysis: modern data and new challenges

Cited by 308 publications

References 32 publications

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population

Graphics for relatedness research

On identification problems requiring linked autosomal markers

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