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

• Published in: Forensic Science International: Genetics
• Main Authors: 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
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2022
• Subjects: greenlander*; greenlandic
• 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

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.