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dc.contributor.author
Köksal, Zehra
dc.contributor.author
Burgos, Germán
dc.contributor.author
Carvalho, Elizeu
dc.contributor.author
Loiola, Silvia
dc.contributor.author
Parolin, María Laura
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dc.contributor.author
Quiroz, Alfredo
dc.contributor.author
Ribeiro dos Santos, Ândrea
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Toscanini, Ulises
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Vullo, Carlos
dc.contributor.author
Børsting, Claus
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Gusmão, Leonor
dc.contributor.author
Pereira, Vania
dc.date.available
2023-11-07T13:00:00Z
dc.date.issued
2022-07
dc.identifier.citation
Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Loiola, Silvia; Parolin, María Laura; et al.; Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q; Elsevier Ireland; Forensic Science International: Genetics; 59; 7-2022; 1-8
dc.identifier.issn
1872-4973
dc.identifier.uri
http://hdl.handle.net/11336/217280
dc.description.abstract
Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy, which is important for population, evolutionary and forensic genetics. In this study, Y-SNPs were typed and haplogroups inferred with the MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1, as a high-throughput approach. Firstly, the performance of the panel was evaluated with different DNA input amounts, reagent volumes and cycle numbers. DNA-inputs from 0.5 to 1 ng generated the most balanced read depth. Combined with full reagent and 19 cycles, this offered the highest number of amplicons with a sequencing read depth of at least 20 reads. Secondly, the sub-haplogroups of 182 admixed South Americans and Greenlanders belonging to haplogroup Q were inferred and tested for potential improvement in resolution. Most samples were assigned to lineage Q-M3 with some samples assigned to lineages upstream (Q-M346, L56, L57; Q-L331, L53; Q-L54; Q-CTS11969, CTS11970) or parallel (Q-L330, L334; Q-Z780/M971) to Q-M3. Only one sample was assigned to a downstream lineage (Q-Z35615, Z35616). Most individuals of haplogroup Q with NAM ancestry could neither be distinguished from each other, nor from half of the Greenlandic samples. Typing additional, known SNPs within lineage Q-M3, Z19483 and SA05, increased the resolution of predicted haplogroups. The search for novel variants in the sequenced regions allowed the detection of 42 variants and the subdivision of lineage Q-M3 into new subclades. The variants found in six of these subclades were exclusive to certain South American countries. In light of the limited differentiation of haplogroup Q samples, the additional information on known or novel SNPs disclosed in this study when using MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1 should be included in the Yleaf software, to increase the differentiation of lineage Q-M3.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Elsevier Ireland
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by/2.5/ar/
dc.subject
AMPLISEQ PANEL
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MASSIVELY PARALLEL SEQUENCING
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NATIVE AMERICAN
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POPULATION GENETICS
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Y HAPLOGROUP Q
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Y-SNP ANALYSIS
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Genética y Herencia
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Ciencias Biológicas
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dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
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dc.title
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2023-11-06T15:33:52Z
dc.journal.volume
59
dc.journal.pagination
1-8
dc.journal.pais
Irlanda
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dc.description.fil
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
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Fil: Burgos, Germán. Universidad de Santiago de Compostela; España
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Fil: Carvalho, Elizeu. Universidade do Estado de Rio do Janeiro; Brasil
dc.description.fil
Fil: Loiola, Silvia. Universidade do Estado de Rio do Janeiro; Brasil
dc.description.fil
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
dc.description.fil
Fil: Quiroz, Alfredo. Hospital Central Instituto de Previsiín Social; Paraguay
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Fil: Ribeiro dos Santos, Ândrea. Universidade Federal do Pará; Brasil
dc.description.fil
Fil: Toscanini, Ulises. Fundación Favaloro; Argentina
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Fil: Vullo, Carlos. No especifíca;
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Fil: Børsting, Claus. Universidad de Copenhagen; Dinamarca
dc.description.fil
Fil: Gusmão, Leonor. Universidade do Estado de Rio do Janeiro; Brasil
dc.description.fil
Fil: Pereira, Vania. Universidad de Copenhagen; Dinamarca
dc.journal.title
Forensic Science International: Genetics
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1016/j.fsigen.2022.102708
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