Fast and accurate kinship estimation using sparse SNPs in relatively large database searches

Snedecor, June; Fennell, Tim; Stadick, Seth; Homer, Nils; Antunes, Joana; Stephens, K; Holt, Cydne

doi:10.1016/j.fsigen.2022.102769

Cited by 27 publications

(22 citation statements)

References 20 publications

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“…Snedecor et al demonstrated that the windowed kinship algorithm used by GEDmatch PRO is relatively robust to diminished numbers of SNPs called and loss of heterozygosity, but the impact depends on the degree of relationship. 16 As is often the case with challenging case samples, stochastic drop-out is expected causing decreased call rate and loss of heterozygosity to be compounded. Thus, call rate and heterozygosity should be considered in conjunction with the degree of relation that is detected to help provide guidance on the quality of the match.…”

Section: Discussionmentioning

confidence: 99%

“…3,[13][14][15] To address some of these limitations, Verogen developed the ForenSeq® Kintelligence kit that targets 10,230 SNPs spanning the genome, maintaining compatibility with direct-to-consumer kits that largely populate the publicly available databases, while excluding medically relevant SNPs. 16 The targeted sequencing method is well-suited for low quantity samples, and the total input can reach high quantities even for samples with low concentration due to the ability to add up to 25 µL of extract. Further, the kit is designed for degraded samples with an average amplicon size of <150 bp.…”

Section: Introductionmentioning

confidence: 99%

“…1 In contrast, kinship matching with profiles generated by the Kintelligence kit uses the One-to-Many Kinship tool within GEDmatch PRO™ due to the reduced number of SNPs. The One-to-Many Kinship tool uses a windowed kinship algorithm 16 that modifies the principal component analysis approaches of PC-Relate 17 and PC-AiR 18 to estimate genetic relatedness. While distant kinship matching (out to 4 th degree) has high sensitivity and specificity with this method, reduced call rates and loss of heterozygosity will diminish this performance.…”

Section: Introductionmentioning

confidence: 99%

“…While distant kinship matching (out to 4 th degree) has high sensitivity and specificity with this method, reduced call rates and loss of heterozygosity will diminish this performance. 16…”

Section: Introductionmentioning

confidence: 99%

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Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Peck

Koeppel

Gorden

et al. 2022

Preprint

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Forensic Genetic Genealogy (FGG) requires high density single nucleotide polymorphism (SNP) profiles to infer distant relationships. The ForenSeq Kintelligence kit is a recently developed method targeting approximately 10,000 SNPs that were selected to be compatible with genetic genealogy databases, while avoiding medically relevant SNPs. The targeted PCR method is ideal for low input and degraded samples, which are particularly challenging for microarray analysis. We made modifications to library preparation and sample pooling to further enhance the performance of low input samples. To align this FGG method with forensic laboratory standards, we performed an internal validation study in accordance with the Scientific Working Group on DNA Analysis Methods Validation Guidelines for DNA Analysis Methods. The sensitivity and precision and accuracy studies produced accurate and reliable profiles down to 0.05 ng of DNA. The mixture and contamination studies demonstrated that the method could detect the presence of a minor contributor down to 0.02 ng, while system wide contamination was negligible. Nonprobative bone, fired shell casing, and adhesive tape samples performed well with inputs ranging from 0.05 to 1.0 ng of DNA. A bone with a high degradation index and tested at 0.1 ng DNA input resulted in a call rate of 92.9% and a heterozygosity rate of 0.387. We demonstrated the importance of both call rate and heterozygosity rate to assess profile performance. Validating FGG methods is critical to ensuring the reliability and utility of SNP profiles that will be uploaded to genetic genealogy databases for the purpose of generating investigative leads.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…While distant kinship matching (out to 4 th degree) has high sensitivity and specificity with this method, reduced call rates and loss of heterozygosity will diminish this performance. 16…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Peck

Koeppel

Gorden

et al. 2022

Preprint

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show abstract

“…The Kintelligence kit provides genotypes on 10,230 SNPs, of which 9,867 are kinship-informative SNPs used for SNP-based kinship analysis across populations, while the remaining 363 are used to inform biogeographical ancestry, identity, hair and eye color, and biological sex (Snedecor et al 2022). The Kintelligence kit integrates data analysis in a browser-based application, and also produces Excel and text file outputs containing genotype data in a custom format.…”

Section: Introductionmentioning

confidence: 99%

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

Turner

Peck

2022

Preprint

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The ForenSeq Kintelligence kit developed by Verogen is a targeted Illumina sequencing assay that genotypes 10,230 single nucleotide polymorphisms designed for forensic genetic genealogy, forensic DNA phenotyping, and ancestry inference. We developed k2v, a containerized workflow for creating standard specification-compliant variant call format (VCF) files from the custom output data produced by the Kintelligence Universal Analysis Software. VCF files produced with k2v enable the use of many pre-existing, widely used, community-developed tools for manipulating and analyzing genetic data in the standard VCF format. Here we describe the k2v implementation, demonstrate its usage, and use the VCF produced by k2v to demonstrate downstream analyses that can easily be performed with pre-existing tools using VCF data as input: concordance analysis, ancestry inference, and relationship estimation. k2v is distributed as a Docker container available on Docker Hub. Documentation and source code for k2v is freely available under the GNU Public License (GPL-3.0) at https://github.com/signaturescience/k2v.

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Detailed kinship estimation for detecting bias among breeding families in a reintroduced population of the endangered bagrid catfish Tachysurus ichikawai

Mizuno,

Nakayama,

Akita

et al. 2024

Population Ecology

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In the context of initiatives focused on captive breeding and reintroduction of endangered animal species, it is crucial to minimize any bias in reproductive success during the reintroduction phase in order to preserve genetic diversity. One population of Tachysurus ichikawai, a critically endangered bagrid catfish endemic to Japan, faces a threat from the construction of a dam. To address this, a captive breeding program followed by translocation is being implemented. Multiple breeding families are involved in this process; however, if there is a bias in reproductive success among them after release, it will result in a decline in genetic diversity. To ascertain potential biases of reproductive success among released individuals, we attempted to identify the familial lineage of individuals born at the release site. Due to the unavailability of samples from the released individuals themselves, we reconstructed the pedigree of three generations using distant kinship relationships, such as grandparent–grandchild and uncle–aunt–nephew–niece relationships, with data of 2230–5674 single‐nucleotide polymorphisms obtained from whole genome re‐sequence, and three different software. Our findings indicate no bias between lineages in the first year after reintroduction, but a significant bias in the second year, emphasizing the need for continuous management and monitoring of reintroduced populations. This study demonstrates that monitoring kinship after reintroduction can correct lineage bias, which is critical for the prompt restoration of genetic diversity.

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Fast and accurate kinship estimation using sparse SNPs in relatively large database searches

Cited by 27 publications

References 20 publications

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

Detailed kinship estimation for detecting bias among breeding families in a reintroduced population of the endangered bagrid catfish Tachysurus ichikawai

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