Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q.
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-throughpu...
Published in: | Forensic Science International: Genetics |
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Main Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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2022
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Online Access: | https://curis.ku.dk/portal/da/publications/testing-the-ion-ampliseq-hid-ysnp-research-panel-v1-for-performance-and-resolution-in-admixed-south-americans-of-haplogroup-q(81321796-397f-4900-b05a-735f84320d0c).html https://doi.org/10.1016/j.fsigen.2022.102708 https://curis.ku.dk/ws/files/305171081/1_s2.0_S1872497322000497_main.pdf |
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ftcopenhagenunip:oai:pure.atira.dk:publications/81321796-397f-4900-b05a-735f84320d0c 2023-05-15T16:30:59+02:00 Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Köksal, Zehra Burgos, Gérman Carvalho, Elizeu F Loiola, Silvia Parolin, Maria Laura Quiroz, Alfredo Ribeiro-dos-Santos, Ândrea Toscanini, Ulises Vullo, Carlos Børsting, Claus Gusmão, Leonor Pereira, Vania 2022 application/pdf https://curis.ku.dk/portal/da/publications/testing-the-ion-ampliseq-hid-ysnp-research-panel-v1-for-performance-and-resolution-in-admixed-south-americans-of-haplogroup-q(81321796-397f-4900-b05a-735f84320d0c).html https://doi.org/10.1016/j.fsigen.2022.102708 https://curis.ku.dk/ws/files/305171081/1_s2.0_S1872497322000497_main.pdf eng eng info:eu-repo/semantics/openAccess Köksal , Z , Burgos , G , Carvalho , E F , Loiola , S , Parolin , M L , Quiroz , A , Ribeiro-dos-Santos , Â , Toscanini , U , Vullo , C , Børsting , C , Gusmão , L & Pereira , V 2022 , ' Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. ' , Forensic Science International: Genetics , vol. 59 , 102708 . https://doi.org/10.1016/j.fsigen.2022.102708 article 2022 ftcopenhagenunip https://doi.org/10.1016/j.fsigen.2022.102708 2022-07-27T22:51:02Z 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. Article in Journal/Newspaper greenlander* greenlandic University of Copenhagen: Research Forensic Science International: Genetics 59 102708 |
institution |
Open Polar |
collection |
University of Copenhagen: Research |
op_collection_id |
ftcopenhagenunip |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Köksal, Zehra Burgos, Gérman Carvalho, Elizeu F Loiola, Silvia Parolin, Maria Laura Quiroz, Alfredo Ribeiro-dos-Santos, Ândrea Toscanini, Ulises Vullo, Carlos Børsting, Claus Gusmão, Leonor Pereira, Vania |
spellingShingle |
Köksal, Zehra Burgos, Gérman Carvalho, Elizeu F Loiola, Silvia Parolin, Maria Laura Quiroz, Alfredo Ribeiro-dos-Santos, Ândrea Toscanini, Ulises Vullo, Carlos Børsting, Claus Gusmão, Leonor Pereira, Vania Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
author_facet |
Köksal, Zehra Burgos, Gérman Carvalho, Elizeu F Loiola, Silvia Parolin, Maria Laura Quiroz, Alfredo Ribeiro-dos-Santos, Ândrea Toscanini, Ulises Vullo, Carlos Børsting, Claus Gusmão, Leonor Pereira, Vania |
author_sort |
Köksal, Zehra |
title |
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
title_short |
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
title_full |
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
title_fullStr |
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
title_full_unstemmed |
Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. |
title_sort |
testing the ion ampliseq™ hid y-snp research panel v1 for performance and resolution in admixed south americans of haplogroup q. |
publishDate |
2022 |
url |
https://curis.ku.dk/portal/da/publications/testing-the-ion-ampliseq-hid-ysnp-research-panel-v1-for-performance-and-resolution-in-admixed-south-americans-of-haplogroup-q(81321796-397f-4900-b05a-735f84320d0c).html https://doi.org/10.1016/j.fsigen.2022.102708 https://curis.ku.dk/ws/files/305171081/1_s2.0_S1872497322000497_main.pdf |
genre |
greenlander* greenlandic |
genre_facet |
greenlander* greenlandic |
op_source |
Köksal , Z , Burgos , G , Carvalho , E F , Loiola , S , Parolin , M L , Quiroz , A , Ribeiro-dos-Santos , Â , Toscanini , U , Vullo , C , Børsting , C , Gusmão , L & Pereira , V 2022 , ' Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. ' , Forensic Science International: Genetics , vol. 59 , 102708 . https://doi.org/10.1016/j.fsigen.2022.102708 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1016/j.fsigen.2022.102708 |
container_title |
Forensic Science International: Genetics |
container_volume |
59 |
container_start_page |
102708 |
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1766020789002305536 |