Familial searching on DNA mixtures with dropout

Slooten, Klaas

doi:10.1016/j.fsigen.2016.02.002

Cited by 11 publications

(5 citation statements)

References 14 publications

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“…The CSYseq panel enables to find both distant paternal relatives through approximately 81 slow mutating Y-STRs (<10 −3 mpg) and distinguish closely related individuals through 26 RM Y-STRs (≥10 −2 mpg), which significantly increases the level of discrimination useful in forensic human identification processes [ 7 ]. This combination of Y-STRs is especially useful for familial searching, where the donor of an unknown trace has to be identified by searching for a male relative in a chrY database or through a large-scale voluntary DNA mass-screening [ 2 , 67 ]. Additionally, around 32 private Y-SNPs are typed which originated more recently, which makes it possible to link them to a specific population or even a single family [ 6 ].…”

Section: Discussionmentioning

confidence: 99%

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

et al. 2021

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Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.

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Section: Discussionmentioning

confidence: 99%

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

et al. 2021

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“…We start by recalling the characteristics of the semi-continuous model that we use in this article. This description is a summary of the one given in [15] and we refer the reader to that paper for further details. Suppose that a mixture has n contributors.…”

Section: Semi-continuous Modelmentioning

confidence: 99%

“…Note that, when c = 0, we see from this formula that an allele is recorded unless it drops out for all the contributors that have that allele. In [4,15] we have used the approximation e Àcpa % 1 À cp a for c ( 1. To compute the probability that the observed mixture M is equal to the set of alleles M, one simply uses (2.1) to obtain…”

Section: Semi-continuous Modelmentioning

confidence: 99%

Accurate assessment of the weight of evidence for DNA mixtures by integrating the likelihood ratio

Slooten

2017

Forensic Science International: Genetics

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“…In terms of using mixtures as court evidence, there are various methods to estimate the evidential weight of a DNA sample [82][83][84][85][86]. Extending such analyses further, studies have examined the viability of using mixtures for familial searching [87][88][89] indicating feasibility even with common forensic STRs.…”

Section: The Use Of Dna Mixturesmentioning

confidence: 99%

Investigative genetic genealogy: Current methods, knowledge and practice

Kling

Phillips

Kennett

et al. 2021

Forensic Science International: Genetics

101

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Investigative genetic genealogy (IGG) has emerged as a new, rapidly growing field of forensic science. We describe the process whereby dense SNP data, commonly comprising more than half a million markers, are employed to infer distant relationships. By distant we refer to degrees of relatedness exceeding that of first cousins. We review how methods of relationship matching and SNP analysis on an enlarged scale are used in a forensic setting to identify a suspect in a criminal investigation or a missing person. There is currently a strong need in forensic genetics not only to understand the underlying models to infer relatedness but also to fully explore the DNA technologies and data used in IGG. This review brings together many of the topics and examines their effectiveness and operational limits, while suggesting future directions for their forensic validation. We further investigated the methods used by the major direct-to-consumer (DTC) genetic ancestry testing companies as well as submitting a questionnaire where providers of forensic genetic genealogy summarized their operation/ services. Although most of the DTC market, and genetic genealogy in general, has undisclosed, proprietary algorithms we review the current knowledge where information has been discussed and published more openly.

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Familial searching on DNA mixtures with dropout

Cited by 11 publications

References 14 publications

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics

Accurate assessment of the weight of evidence for DNA mixtures by integrating the likelihood ratio

Investigative genetic genealogy: Current methods, knowledge and practice

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