Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q

Autor: Zehra Köksal, Germán Burgos, Elizeu Carvalho, Silvia Loiola, María Laura Parolin, Alfredo Quiroz, Ândrea Ribeiro dos Santos, Ulises Toscanini, Carlos Vullo, Claus Børsting, Leonor Gusmão, Vania Pereira
Rok vydání: 2022
Předmět:
Zdroj: 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
ISSN: 1872-4973
DOI: 10.1016/j.fsigen.2022.102708
Popis: 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.
Databáze: OpenAIRE
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