Cargando…

Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data

The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms...

Descripción completa

Detalles Bibliográficos
Autores principales: de la Puente, María, Ruiz-Ramírez, Jorge, Ambroa-Conde, Adrián, Xavier, Catarina, Amigo, Jorge, Casares de Cal, María Ángeles, Gómez-Tato, Antonio, Carracedo, Ángel, Parson, Walther, Phillips, Christopher, Lareu, María Victoria
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606911/
https://www.ncbi.nlm.nih.gov/pubmed/33193704
http://dx.doi.org/10.3389/fgene.2020.581041
_version_ 1783604532151844864
author de la Puente, María
Ruiz-Ramírez, Jorge
Ambroa-Conde, Adrián
Xavier, Catarina
Amigo, Jorge
Casares de Cal, María Ángeles
Gómez-Tato, Antonio
Carracedo, Ángel
Parson, Walther
Phillips, Christopher
Lareu, María Victoria
author_facet de la Puente, María
Ruiz-Ramírez, Jorge
Ambroa-Conde, Adrián
Xavier, Catarina
Amigo, Jorge
Casares de Cal, María Ángeles
Gómez-Tato, Antonio
Carracedo, Ángel
Parson, Walther
Phillips, Christopher
Lareu, María Victoria
author_sort de la Puente, María
collection PubMed
description The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components.
format Online
Article
Text
id pubmed-7606911
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-76069112020-11-13 Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data de la Puente, María Ruiz-Ramírez, Jorge Ambroa-Conde, Adrián Xavier, Catarina Amigo, Jorge Casares de Cal, María Ángeles Gómez-Tato, Antonio Carracedo, Ángel Parson, Walther Phillips, Christopher Lareu, María Victoria Front Genet Genetics The development of microhaplotype (MH) panels for massively parallel sequencing (MPS) platforms is gaining increasing relevance for forensic analysis. Here, we expand the applicability of a 102 autosomal and 11 X-chromosome panel of MHs, previously validated with both MiSeq and Ion S5 MPS platforms and designed for identification purposes. We have broadened reference population data for identification purposes, including data from 240 HGDP-CEPH individuals of native populations from North Africa, the Middle East, Oceania and America. Using the enhanced population data, the panel was evaluated as a marker set for bio-geographical ancestry (BGA) inference, providing a clear differentiation of the five main continental groups of Africa, Europe, East Asia, Native America, and Oceania. An informative degree of differentiation was also achieved for the population variation encompassing North Africa, Middle East, Europe, South Asia, and East Asia. In addition, we explored the potential for individual BGA inference from simple mixed DNA, by simulation of mixed profiles followed by deconvolution of mixture components. Frontiers Media S.A. 2020-10-20 /pmc/articles/PMC7606911/ /pubmed/33193704 http://dx.doi.org/10.3389/fgene.2020.581041 Text en Copyright © 2020 de la Puente, Ruiz-Ramírez, Ambroa-Conde, Xavier, Amigo, Casares de Cal, Gómez-Tato, Carracedo, Parson, Phillips and Lareu. http://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
de la Puente, María
Ruiz-Ramírez, Jorge
Ambroa-Conde, Adrián
Xavier, Catarina
Amigo, Jorge
Casares de Cal, María Ángeles
Gómez-Tato, Antonio
Carracedo, Ángel
Parson, Walther
Phillips, Christopher
Lareu, María Victoria
Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title_full Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title_fullStr Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title_full_unstemmed Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title_short Broadening the Applicability of a Custom Multi-Platform Panel of Microhaplotypes: Bio-Geographical Ancestry Inference and Expanded Reference Data
title_sort broadening the applicability of a custom multi-platform panel of microhaplotypes: bio-geographical ancestry inference and expanded reference data
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606911/
https://www.ncbi.nlm.nih.gov/pubmed/33193704
http://dx.doi.org/10.3389/fgene.2020.581041
work_keys_str_mv AT delapuentemaria broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT ruizramirezjorge broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT ambroacondeadrian broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT xaviercatarina broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT amigojorge broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT casaresdecalmariaangeles broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT gomeztatoantonio broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT carracedoangel broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT parsonwalther broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT phillipschristopher broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata
AT lareumariavictoria broadeningtheapplicabilityofacustommultiplatformpanelofmicrohaplotypesbiogeographicalancestryinferenceandexpandedreferencedata