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Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples

Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic gen...

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Autores principales: Turner, Stephen D., Nagraj, V.P., Scholz, Matthew, Jessa, Shakeel, Acevedo, Carlos, Ge, Jianye, Woerner, August E., Budowle, Bruce
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282869/
https://www.ncbi.nlm.nih.gov/pubmed/35846115
http://dx.doi.org/10.3389/fgene.2022.882268
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author Turner, Stephen D.
Nagraj, V.P.
Scholz, Matthew
Jessa, Shakeel
Acevedo, Carlos
Ge, Jianye
Woerner, August E.
Budowle, Bruce
author_facet Turner, Stephen D.
Nagraj, V.P.
Scholz, Matthew
Jessa, Shakeel
Acevedo, Carlos
Ge, Jianye
Woerner, August E.
Budowle, Bruce
author_sort Turner, Stephen D.
collection PubMed
description Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA. In this study, the accuracy of genome-wide relatedness methods and identity by descent (IBD) segment approaches was evaluated in the presence of challenges commonly encountered with forensic data: missing data and genotyping error. Pedigree whole-genome simulations were used to estimate the genotypes of thousands of individuals with known relationships using multiple populations with different biogeographic ancestral origins. Simulations were also performed with varying error rates and types. Using these data, the performance of different methods for quantifying relatedness was benchmarked across these scenarios. When the genotyping error was low (<1%), IBD segment methods outperformed genome-wide relatedness methods for close relationships and are more accurate at distant relationship inference. However, with an increasing genotyping error (1–5%), methods that do not rely on IBD segment detection are more robust and outperform IBD segment methods. The reduced call rate had little impact on either class of methods. These results have implications for the use of dense SNP data in forensic genomics for distant kinship analysis and FGG, especially when the sample quality is low.
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spelling pubmed-92828692022-07-15 Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples Turner, Stephen D. Nagraj, V.P. Scholz, Matthew Jessa, Shakeel Acevedo, Carlos Ge, Jianye Woerner, August E. Budowle, Bruce Front Genet Genetics Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA. In this study, the accuracy of genome-wide relatedness methods and identity by descent (IBD) segment approaches was evaluated in the presence of challenges commonly encountered with forensic data: missing data and genotyping error. Pedigree whole-genome simulations were used to estimate the genotypes of thousands of individuals with known relationships using multiple populations with different biogeographic ancestral origins. Simulations were also performed with varying error rates and types. Using these data, the performance of different methods for quantifying relatedness was benchmarked across these scenarios. When the genotyping error was low (<1%), IBD segment methods outperformed genome-wide relatedness methods for close relationships and are more accurate at distant relationship inference. However, with an increasing genotyping error (1–5%), methods that do not rely on IBD segment detection are more robust and outperform IBD segment methods. The reduced call rate had little impact on either class of methods. These results have implications for the use of dense SNP data in forensic genomics for distant kinship analysis and FGG, especially when the sample quality is low. Frontiers Media S.A. 2022-06-30 /pmc/articles/PMC9282869/ /pubmed/35846115 http://dx.doi.org/10.3389/fgene.2022.882268 Text en Copyright © 2022 Turner, Nagraj, Scholz, Jessa, Acevedo, Ge, Woerner and Budowle. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Turner, Stephen D.
Nagraj, V.P.
Scholz, Matthew
Jessa, Shakeel
Acevedo, Carlos
Ge, Jianye
Woerner, August E.
Budowle, Bruce
Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title_full Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title_fullStr Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title_full_unstemmed Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title_short Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples
title_sort evaluating the impact of dropout and genotyping error on snp-based kinship analysis with forensic samples
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282869/
https://www.ncbi.nlm.nih.gov/pubmed/35846115
http://dx.doi.org/10.3389/fgene.2022.882268
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