On identification problems requiring linked autosomal markers

Egeland, Thore; Sheehan, Nuala A.

doi:10.1016/j.fsigen.2008.02.006

Cited by 39 publications

(27 citation statements)

References 17 publications

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“…SNPs have the advantages of having negligible mutation rates, being very numerous and are more reliably typed on degraded DNA which can yield incomplete STR profiles. Moreover, some problems can never be resolved by any number of unlinked markers [17,19,55].…”

Section: Introductionmentioning

confidence: 99%

On the use of dense SNP marker data for the identification of distant relative pairs

Sun

Jobling

Taliun

et al. 2016

Theoretical Population Biology

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There has been recent interest in the exploitation of readily available dense genome scan marker data for the identification of relatives. However, there are conflicting findings on how informative these data are in practical situations and, in particular, sets of thinned markers are often used with no concrete justification for the chosen spacing. We explore the potential usefulness of dense single nucleotide polymorphism (SNP) arrays for this application with a focus on inferring distant relative pairs. We distinguish between relationship estimation, as defined by a pedigree connecting the two individuals of interest, and estimation of general relatedness as would be provided by a kinship coefficient or a coefficient of relatedness. Since our primary interest is in the former case, we adopt a pedigree likelihood approach. We consider the effect of additional SNPs and data on an additional typed relative, together with choice of that relative, on relationship inference. We also consider the effect of linkage disequilibrium. When overall relatedness, rather than the specific relationship, would suffice, * Theoretical Population Biology. In Press. http://dx.doi.org/10.1016/j.tpb.2015.10 † Corresponding author. E-mail address: Nuala.Sheehan@leicester.ac.uk 1 we propose an approximate approach that is easy to implement and appears to compete well with a popular moment-based estimator and a recent maximum likelihood approach based on chromosomal sharing. We conclude that denser marker data are more informative for distant relatives. However, linkage disequilibrium cannot be ignored and will be the main limiting factor for applications to real data.

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Section: Introductionmentioning

confidence: 99%

On the use of dense SNP marker data for the identification of distant relative pairs

Sun

Jobling

Taliun

et al. 2016

Theoretical Population Biology

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“…The example of the set of pedigrees avuncular, grandparent-grandchild and half-sibling, involving two non-inbred individuals, is most frequently referred to. See, for example, the paper by Egeland and Sheehan [10] , where the particular case of this set is addressed to promote the use of linked autosomal markers in forensics because for those markers, the pedigrees referred to have different algebraic expressions. In this paper, discussing unlinked autosomal markers, we develop a theoretical framework that supports the description of pedigrees with the same IBD partitions, along with the achievement of those probabilities, based on a simple counting rule.…”

Section: Discussionmentioning

confidence: 99%

“…An early discussion on linked autosomal markers is provided by Thompson [8]. Thompson and Meagher revisited and extended the discussion on this issue [9] , and it is additionally debated by Egeland and Sheehan [10] . A theoretical framework for X-chromosomal markers is given by Pinto et al [11] .…”

Section: Introductionmentioning

confidence: 99%

General Derivation of the Sets of Pedigrees with the Same Kinship Coefficients

Pinto

Amorim²

2010

Hum Hered

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Quantification of kinships between two individuals using unlinked autosomal markers rests upon the identity-by-descent (IBD) probabilities among their four alleles at a locus because they determine the algebraic expressions of the joint genotypic probabilities. Nevertheless, some pedigrees share the same IBD probabilities and are therefore indistinguishable using those markers. Examples of these pedigrees were previously described, such as the case of half-siblings, grandparent-grandchild and avuncular, but a general analysis has not been attempted. The aim of this study is to present a systematic and mathematically supported framework where considering unlinked autosomal markers complete sets of indistinguishable pedigrees linking two non-inbred individuals are generally derived. In our work, complete sets of pedigrees with the same IBD partitions are formally established and mathematically treated, considering kinships linking any pair of non-inbred individuals, whether they are related just maternally or paternally, or both. Moreover, general expressions for IBD partitions, and consequently for joint genotypic probabilities, are derived considering a simple counting rule based on two ‘atom’ pedigrees: parent-child and full-siblings. Besides the theoretical formalization of the problem, the developed framework has potential applications in forensics as well as in breeding strategies design and in conservation studies.

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“…The kit genotypes the 21 autosomal STRs (including the 15 ID loci), Amelogenin, DYS391 and Y-Indel loci. In general, increasing the number of tested loci improves the ability of the kit to determine whether or not a relationship exists [4,5].…”

Section: Introductionmentioning

confidence: 99%