Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q

Autores
Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Ossa, Humberto; Parolin, María Laura; Quiroz, Alfredo; Toscanini, Ulises Faustino; Vullo, Carlos; Børsting, Claus; Gusmão, Leonor; Pereira, Vania
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy. Recently, MPS based panels were introduced in the forensic genetics community for Y-SNP typing and identification of a broad range of haplogroups. The panels are based on an amplicon strategy and allow the detection of up to 15,600 Y-SNPs. The panels target up to 210,000 bps, which should be compared to the overall 8.9 Mbps comprising the unique regions of the non-recombining portion of the Y chromosome (NRY). We present an alternative approach of sequencing unique regions within the NRY using target enrichment probes and hybridization capture. A total of 359,954 probes were designed using the SureDesign software, representing 7.5 Mbps of the NRY. Library preparation and capture were performed using the Agilent SureSelect XT HS2 Target Enrichment method and sequencing was performed in a NovaSeq 6000 System. Besides individual barcodes, the method also included unique molecular barcodes for additional quality screening. The method was tested on admixed South Americans that carry a Y chromosome of haplogroup Q. We successfully identified novel variation that could potentially help refining haplogroup Q phylogeny.
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
Fil: Burgos, Germán. Universidad de Santiago de Compostela; España. Universidad de Las Américas; Ecuador
Fil: Carvalho, Elizeu. Universidade do Estado de Rio do Janeiro; Brasil
Fil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Laboratório de Genética y Biología Molecular; Colombia
Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Quiroz, Alfredo. Instituto de Previsión Social; Paraguay
Fil: Toscanini, Ulises Faustino. Fundación Favaloro; Argentina
Fil: Vullo, Carlos. Argentine Forensic Anthropology Team; Argentina
Fil: Børsting, Claus. Universidad de Copenhagen; Dinamarca
Fil: Gusmão, Leonor. Universidade do Estado de Rio do Janeiro; Brasil
Fil: Pereira, Vania. Universidad de Copenhagen; Dinamarca
Materia
HAPLOGROUP Q
MPS
NGS
TARGETED CAPTURE
Y CHROMOSOME
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/218413
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/218413
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup QKöksal, ZehraBurgos, GermánCarvalho, ElizeuOssa, HumbertoParolin, María LauraQuiroz, AlfredoToscanini, Ulises FaustinoVullo, CarlosBørsting, ClausGusmão, LeonorPereira, VaniaHAPLOGROUP QMPSNGSTARGETED CAPTUREY CHROMOSOMEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy. Recently, MPS based panels were introduced in the forensic genetics community for Y-SNP typing and identification of a broad range of haplogroups. The panels are based on an amplicon strategy and allow the detection of up to 15,600 Y-SNPs. The panels target up to 210,000 bps, which should be compared to the overall 8.9 Mbps comprising the unique regions of the non-recombining portion of the Y chromosome (NRY). We present an alternative approach of sequencing unique regions within the NRY using target enrichment probes and hybridization capture. A total of 359,954 probes were designed using the SureDesign software, representing 7.5 Mbps of the NRY. Library preparation and capture were performed using the Agilent SureSelect XT HS2 Target Enrichment method and sequencing was performed in a NovaSeq 6000 System. Besides individual barcodes, the method also included unique molecular barcodes for additional quality screening. The method was tested on admixed South Americans that carry a Y chromosome of haplogroup Q. We successfully identified novel variation that could potentially help refining haplogroup Q phylogeny.Fil: Köksal, Zehra. Universidad de Copenhagen; DinamarcaFil: Burgos, Germán. Universidad de Santiago de Compostela; España. Universidad de Las Américas; EcuadorFil: Carvalho, Elizeu. Universidade do Estado de Rio do Janeiro; BrasilFil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Laboratório de Genética y Biología Molecular; ColombiaFil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Quiroz, Alfredo. Instituto de Previsión Social; ParaguayFil: Toscanini, Ulises Faustino. Fundación Favaloro; ArgentinaFil: Vullo, Carlos. Argentine Forensic Anthropology Team; ArgentinaFil: Børsting, Claus. Universidad de Copenhagen; DinamarcaFil: Gusmão, Leonor. Universidade do Estado de Rio do Janeiro; BrasilFil: Pereira, Vania. Universidad de Copenhagen; DinamarcaElsevier2022-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/218413Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Ossa, Humberto; Parolin, María Laura; et al.; Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q; Elsevier; Forensic Science International: Genetics Supplement Series; 8; 12-2022; 97-981875-17681875-175XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.fsigss.2022.09.034info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S187517682200035Xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:49:09Zoai:ri.conicet.gov.ar:11336/218413instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:49:10.15CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
title Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
spellingShingle Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
Köksal, Zehra
HAPLOGROUP Q
MPS
NGS
TARGETED CAPTURE
Y CHROMOSOME
title_short Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
title_full Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
title_fullStr Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
title_full_unstemmed Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
title_sort Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q
dc.creator.none.fl_str_mv Köksal, Zehra
Burgos, Germán
Carvalho, Elizeu
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises Faustino
Vullo, Carlos
Børsting, Claus
Gusmão, Leonor
Pereira, Vania
author Köksal, Zehra
author_facet Köksal, Zehra
Burgos, Germán
Carvalho, Elizeu
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises Faustino
Vullo, Carlos
Børsting, Claus
Gusmão, Leonor
Pereira, Vania
author_role author
author2 Burgos, Germán
Carvalho, Elizeu
Ossa, Humberto
Parolin, María Laura
Quiroz, Alfredo
Toscanini, Ulises Faustino
Vullo, Carlos
Børsting, Claus
Gusmão, Leonor
Pereira, Vania
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv HAPLOGROUP Q
MPS
NGS
TARGETED CAPTURE
Y CHROMOSOME
topic HAPLOGROUP Q
MPS
NGS
TARGETED CAPTURE
Y CHROMOSOME
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy. Recently, MPS based panels were introduced in the forensic genetics community for Y-SNP typing and identification of a broad range of haplogroups. The panels are based on an amplicon strategy and allow the detection of up to 15,600 Y-SNPs. The panels target up to 210,000 bps, which should be compared to the overall 8.9 Mbps comprising the unique regions of the non-recombining portion of the Y chromosome (NRY). We present an alternative approach of sequencing unique regions within the NRY using target enrichment probes and hybridization capture. A total of 359,954 probes were designed using the SureDesign software, representing 7.5 Mbps of the NRY. Library preparation and capture were performed using the Agilent SureSelect XT HS2 Target Enrichment method and sequencing was performed in a NovaSeq 6000 System. Besides individual barcodes, the method also included unique molecular barcodes for additional quality screening. The method was tested on admixed South Americans that carry a Y chromosome of haplogroup Q. We successfully identified novel variation that could potentially help refining haplogroup Q phylogeny.
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
Fil: Burgos, Germán. Universidad de Santiago de Compostela; España. Universidad de Las Américas; Ecuador
Fil: Carvalho, Elizeu. Universidade do Estado de Rio do Janeiro; Brasil
Fil: Ossa, Humberto. Pontificia Universidad Javeriana; Colombia. Laboratório de Genética y Biología Molecular; Colombia
Fil: Parolin, María Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; Argentina
Fil: Quiroz, Alfredo. Instituto de Previsión Social; Paraguay
Fil: Toscanini, Ulises Faustino. Fundación Favaloro; Argentina
Fil: Vullo, Carlos. Argentine Forensic Anthropology Team; Argentina
Fil: Børsting, Claus. Universidad de Copenhagen; Dinamarca
Fil: Gusmão, Leonor. Universidade do Estado de Rio do Janeiro; Brasil
Fil: Pereira, Vania. Universidad de Copenhagen; Dinamarca
description Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy. Recently, MPS based panels were introduced in the forensic genetics community for Y-SNP typing and identification of a broad range of haplogroups. The panels are based on an amplicon strategy and allow the detection of up to 15,600 Y-SNPs. The panels target up to 210,000 bps, which should be compared to the overall 8.9 Mbps comprising the unique regions of the non-recombining portion of the Y chromosome (NRY). We present an alternative approach of sequencing unique regions within the NRY using target enrichment probes and hybridization capture. A total of 359,954 probes were designed using the SureDesign software, representing 7.5 Mbps of the NRY. Library preparation and capture were performed using the Agilent SureSelect XT HS2 Target Enrichment method and sequencing was performed in a NovaSeq 6000 System. Besides individual barcodes, the method also included unique molecular barcodes for additional quality screening. The method was tested on admixed South Americans that carry a Y chromosome of haplogroup Q. We successfully identified novel variation that could potentially help refining haplogroup Q phylogeny.
publishDate 2022
dc.date.none.fl_str_mv 2022-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/218413
Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Ossa, Humberto; Parolin, María Laura; et al.; Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q; Elsevier; Forensic Science International: Genetics Supplement Series; 8; 12-2022; 97-98
1875-1768
1875-175X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/218413
identifier_str_mv Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Ossa, Humberto; Parolin, María Laura; et al.; Targeted Y chromosome capture enrichment in admixed South American samples with haplogroup Q; Elsevier; Forensic Science International: Genetics Supplement Series; 8; 12-2022; 97-98
1875-1768
1875-175X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.fsigss.2022.09.034
info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S187517682200035X
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1842268957263790080
score 13.13397

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