Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) mul...
| Autores: | , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Universidad de Santiago de Compostela (USC) |
| Repositorio: | Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela |
| Idioma: | inglés |
| OAI Identifier: | oai:minerva.usc.gal:10347/45901 |
| Acceso en línea: | https://hdl.handle.net/10347/45901 |
| Access Level: | acceso abierto |
| Palabra clave: | 1000 Genomes Human Origins SNP array SNPs Ancestry informative markers Bio-geographical ancestry Massively parallel sequencing 3203 Medicina forense |
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Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic ToolPuente Vila, María del Carmen de laRuiz Ramírez, JorgeAmbroa Conde, AdriánÁlvarez Dios, José AntonioFreire Aradas, Ana MaríaMosquera Miguel, AnaCarracedo Álvarez, ÁngelLareu Huidobro, María VictoriaPhillips, Christopher Paul1000 GenomesHuman Origins SNP arraySNPsAncestry informative markersBio-geographical ancestryMassively parallel sequencing3203 Medicina forenseWe detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.MDPIUniversidade de Santiago de Compostela. Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía e Obstetricia, e PediatríaUniversidade de Santiago de Compostela. Instituto de Ciencias Forenses "Luís Concheiro" (INCIFOR)20212021-08-2220212021-08-22journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10347/45901reponame:Minerva. Repositorio Institucional de la Universidad de Santiago de Compostelainstname:Universidad de Santiago de Compostela (USC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2© 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:minerva.usc.gal:10347/459012026-06-15T12:47:27Z |
| dc.title.none.fl_str_mv |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| title |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| spellingShingle |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool Puente Vila, María del Carmen de la 1000 Genomes Human Origins SNP array SNPs Ancestry informative markers Bio-geographical ancestry Massively parallel sequencing 3203 Medicina forense |
| title_short |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| title_full |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| title_fullStr |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| title_full_unstemmed |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| title_sort |
Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool |
| dc.creator.none.fl_str_mv |
Puente Vila, María del Carmen de la Ruiz Ramírez, Jorge Ambroa Conde, Adrián Álvarez Dios, José Antonio Freire Aradas, Ana María Mosquera Miguel, Ana Carracedo Álvarez, Ángel Lareu Huidobro, María Victoria Phillips, Christopher Paul |
| author |
Puente Vila, María del Carmen de la |
| author_facet |
Puente Vila, María del Carmen de la Ruiz Ramírez, Jorge Ambroa Conde, Adrián Álvarez Dios, José Antonio Freire Aradas, Ana María Mosquera Miguel, Ana Carracedo Álvarez, Ángel Lareu Huidobro, María Victoria Phillips, Christopher Paul |
| author_role |
author |
| author2 |
Ruiz Ramírez, Jorge Ambroa Conde, Adrián Álvarez Dios, José Antonio Freire Aradas, Ana María Mosquera Miguel, Ana Carracedo Álvarez, Ángel Lareu Huidobro, María Victoria Phillips, Christopher Paul |
| author2_role |
author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Universidade de Santiago de Compostela. Departamento de Ciencias Forenses, Anatomía Patolóxica, Xinecoloxía e Obstetricia, e Pediatría Universidade de Santiago de Compostela. Instituto de Ciencias Forenses "Luís Concheiro" (INCIFOR) |
| dc.subject.none.fl_str_mv |
1000 Genomes Human Origins SNP array SNPs Ancestry informative markers Bio-geographical ancestry Massively parallel sequencing 3203 Medicina forense |
| topic |
1000 Genomes Human Origins SNP array SNPs Ancestry informative markers Bio-geographical ancestry Massively parallel sequencing 3203 Medicina forense |
| description |
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the Snipper online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The Snipper analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects. |
| publishDate |
2021 |
| dc.date.none.fl_str_mv |
2021 2021-08-22 2021 2021-08-22 |
| dc.type.none.fl_str_mv |
journal article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85 |
| dc.type.openaire.fl_str_mv |
info:eu-repo/semantics/article |
| format |
article |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10347/45901 |
| url |
https://hdl.handle.net/10347/45901 |
| dc.language.none.fl_str_mv |
Inglés eng |
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Inglés |
| language |
eng |
| dc.rights.none.fl_str_mv |
open access http://purl.org/coar/access_right/c_abf2 http://creativecommons.org/licenses/by/4.0/ |
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info:eu-repo/semantics/openAccess |
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open access http://purl.org/coar/access_right/c_abf2 http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf |
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MDPI |
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MDPI |
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reponame:Minerva. Repositorio Institucional de la Universidad de Santiago de Compostela instname:Universidad de Santiago de Compostela (USC) |
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