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

• Autores: Köksal, Zehra; Burgos, Germán; Carvalho, Elizeu; Loiola, Silvia; Parolin, María Laura; Quiroz, Alfredo; Ribeiro dos Santos, Ândrea; Toscanini, Ulises; Vullo, Carlos; Børsting, Claus; Gusmão, Leonor; Pereira, Vania
• Año de publicación: 2022
• Idioma: inglés
• Tipo de recurso: artículo
• Materia: AMPLISEQ PANEL; MASSIVELY PARALLEL SEQUENCING; NATIVE AMERICAN; POPULATION GENETICS; Y HAPLOGROUP Q; Y-SNP ANALYSIS
• Institución: Consejo Nacional de Investigaciones Científicas y Técnicas

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.
Fil: Köksal, Zehra. Universidad de Copenhagen; Dinamarca
Fil: Burgos, Germán. Universidad de Santiago de Compostela; España
Fil: Carvalho, Elizeu. Universidade do Estado de Rio do Janeiro; Brasil
Fil: Loiola, Silvia. Universidade do Estado de Rio do Janeiro; Brasil
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. Hospital Central Instituto de Previsiín Social; Paraguay
Fil: Ribeiro dos Santos, Ândrea. Universidade Federal do Pará; Brasil
Fil: Toscanini, Ulises. Fundación Favaloro; Argentina
Fil: Vullo, Carlos. No especifíca;
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