Development and evaluation of the ancestry informative marker panel of the visage basic tool

María de la Puente; Jorge Ruiz-Ramírez; the VISAGE Consortium; Adrián Ambroa-Conde; Catarina Xavier; Jacobo Pardo-Seco; Jose Álvarez-Dios; Ana Freire-Aradas; Ana Mosquera-Miguel; Theresa E. Gross; Elaine Y.Y. Cheung; Wojciech Branicki; Michael Nothnagel; Walther Parson; Peter M. Schneider; Manfred Kayser; Ángel Carracedo; Maria Victoria Lareu; Christopher Phillips

doi:10.3390/genes12081284

Development and evaluation of the ancestry informative marker panel of the visage basic tool

María de la Puente, Jorge Ruiz-Ramírez, the VISAGE Consortium, Adrián Ambroa-Conde, Catarina Xavier, Jacobo Pardo-Seco, Jose Álvarez-Dios, Ana Freire-Aradas, Ana Mosquera-Miguel, Theresa E. Gross, Elaine Y.Y. Cheung, Wojciech Branicki, Michael Nothnagel, Walther Parson, Peter M. Schneider, Manfred Kayser, Ángel Carracedo, Maria Victoria Lareu, Christopher Phillips^*

^*Corresponding author for this work

Genetic Identification

Research output: Contribution to journal › Article › Academic › peer-review

22 Citations (Scopus)

Abstract

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.

Original language	English
Article number	1284
Journal	Genes
Volume	12
Issue number	8
DOIs	https://doi.org/10.3390/genes12081284
Publication status	Published - 22 Aug 2021

Bibliographical note

Funding Information:
Funding: The study was supported by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the “Programa de axudas á etapa predoutoral” funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039).

Funding Information:
The study was supported by the European Union?s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the ?Programa de axudas ? etapa predoutoral? funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039).STRUCTURE and ADMIXTURE runs were performed by the FinisTerrae II super-computer at the Centro de Supercomputaci?n de Galicia, Santiago de Compostela (CESGA), Spain.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

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de la Puente, M., Ruiz-Ramírez, J., the VISAGE Consortium, Ambroa-Conde, A., Xavier, C., Pardo-Seco, J., Álvarez-Dios, J., Freire-Aradas, A., Mosquera-Miguel, A., Gross, T. E., Cheung, E. Y. Y., Branicki, W., Nothnagel, M., Parson, W., Schneider, P. M., Kayser, M., Carracedo, Á., Lareu, M. V., & Phillips, C. (2021). Development and evaluation of the ancestry informative marker panel of the visage basic tool. Genes, 12(8), Article 1284. https://doi.org/10.3390/genes12081284

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title = "Development and evaluation of the ancestry informative marker panel of the visage basic tool",

abstract = "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.",

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note = "Funding Information: Funding: The study was supported by the European Union{\textquoteright}s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Conseller{\'i}a de Cultura, Educaci{\'o}n e Ordenaci{\'o}n Universitaria e da Conseller{\'i}a de Econom{\'i}a, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the “Programa de axudas {\'a} etapa predoutoral” funded by the Conseller{\'i}a de Cultura, Educaci{\'o}n e Ordenaci{\'o}n Universitaria e da Conseller{\'i}a de Econom{\'i}a, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039). Funding Information: The study was supported by the European Union?s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the ?Programa de axudas ? etapa predoutoral? funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039).STRUCTURE and ADMIXTURE runs were performed by the FinisTerrae II super-computer at the Centro de Supercomputaci?n de Galicia, Santiago de Compostela (CESGA), Spain. Publisher Copyright: {\textcopyright} 2021 by the authors. Licensee MDPI, Basel, Switzerland.",

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month = aug,

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doi = "10.3390/genes12081284",

language = "English",

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journal = "Genes",

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de la Puente, M, Ruiz-Ramírez, J, the VISAGE Consortium, Ambroa-Conde, A, Xavier, C, Pardo-Seco, J, Álvarez-Dios, J, Freire-Aradas, A, Mosquera-Miguel, A, Gross, TE, Cheung, EYY, Branicki, W, Nothnagel, M, Parson, W, Schneider, PM, Kayser, M, Carracedo, Á, Lareu, MV & Phillips, C 2021, 'Development and evaluation of the ancestry informative marker panel of the visage basic tool', Genes, vol. 12, no. 8, 1284. https://doi.org/10.3390/genes12081284

TY - JOUR

T1 - Development and evaluation of the ancestry informative marker panel of the visage basic tool

AU - de la Puente, María

AU - Ruiz-Ramírez, Jorge

AU - the VISAGE Consortium

AU - Ambroa-Conde, Adrián

AU - Xavier, Catarina

AU - Pardo-Seco, Jacobo

AU - Álvarez-Dios, Jose

AU - Freire-Aradas, Ana

AU - Mosquera-Miguel, Ana

AU - Gross, Theresa E.

AU - Cheung, Elaine Y.Y.

AU - Branicki, Wojciech

AU - Nothnagel, Michael

AU - Parson, Walther

AU - Schneider, Peter M.

AU - Kayser, Manfred

AU - Carracedo, Ángel

AU - Lareu, Maria Victoria

AU - Phillips, Christopher

N1 - Funding Information: Funding: The study was supported by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the “Programa de axudas á etapa predoutoral” funded by the Consellería de Cultura, Educación e Ordenación Universitaria e da Consellería de Economía, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039). Funding Information: The study was supported by the European Union?s Horizon 2020 Research and Innovation Programme under grant agreement No. 740580 within the framework of the VISible Attributes through GEnomics (VISAGE) Project and Consortium. MdlP is supported by a post-doctorate grant funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481D-2021-008). J.R. is supported by the ?Programa de axudas ? etapa predoutoral? funded by the Conseller?a de Cultura, Educaci?n e Ordenaci?n Universitaria e da Conseller?a de Econom?a, Emprego e Industria from Xunta de Galicia, Spain (ED481A-2020/039).STRUCTURE and ADMIXTURE runs were performed by the FinisTerrae II super-computer at the Centro de Supercomputaci?n de Galicia, Santiago de Compostela (CESGA), Spain. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/8/22

Y1 - 2021/8/22

N2 - 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.

AB - 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.

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DO - 10.3390/genes12081284

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VL - 12

JO - Genes

JF - Genes

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M1 - 1284

ER -

Development and evaluation of the ancestry informative marker panel of the visage basic tool

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