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Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q.
Forensic Sci Int Genet. 2022 07; 59:102708.FS

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.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Köksal Z
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address: Zehra.koksal@sund.ku.dk.
Burgos G
Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad de Las Américas (UDLA), Quito, Ecuador; Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain. Electronic address: german.burgos@udla.edu.ec.
Carvalho E
DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil. Electronic address: elizeufc@hotmail.com.
Loiola S
DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil. Electronic address: silvia.labdna@gmail.com.
Parolin ML
Instituto de Diversidad y Evolución Austral (IDEAus), Centro Nacional Patagónico, CONICET, Puerto Madryn, Argentina. Electronic address: parolinml@gmail.com.
Quiroz A
fInstituto de Previsión Social, Asunción 100153, Paraguay. Electronic address: alfredoquiroz1974@me.com.
Ribeiro Dos Santos Â
Human and Medical Genetics Laboratory, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil; Center for Oncology Research, Federal University of Pará, Belém, Pará, Brazil. Electronic address: akelyufpa@gmail.com.
Toscanini U
Primer Centro Argentino de Inmunogenética (PRICAI), Fundación Favaloro, Buenos Aires, Argentina. Electronic address: utoscanini@pricai.com.ar.
Vullo C
DNA Forensic Laboratory, Argentine Forensic Anthropology Team (EAAF), Córdoba, Argentina. Electronic address: cvullo@yahoo.com.ar.
Børsting C
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address: claus.boersting@sund.ku.dk.
Gusmão L
DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Rio de Janeiro 20550-013, Brazil. Electronic address: leonorbgusmao@gmail.com.
Pereira V
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. Electronic address: vania.pereira@sund.ku.dk.

MeSH

Chromosomes, Human, YDNADNA FingerprintingGenetics, PopulationHaplotypesHigh-Throughput Nucleotide SequencingHumansPolymorphism, Single NucleotideSequence Analysis, DNA

Pub Type(s)

Journal Article

Language

eng

PubMed ID

35453088

Citation

Köksal, Zehra, et al. "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, 2022, p. 102708.
Köksal Z, Burgos G, Carvalho E, et al. Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. Forensic Sci Int Genet. 2022;59:102708.
Köksal, Z., Burgos, G., Carvalho, E., 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, 59, 102708. https://doi.org/10.1016/j.fsigen.2022.102708
Köksal Z, et al. Testing the Ion AmpliSeq™ HID Y-SNP Research Panel V1 for Performance and Resolution in Admixed South Americans of Haplogroup Q. Forensic Sci Int Genet. 2022;59:102708. PubMed PMID: 35453088.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Testing the Ion AmpliSeq™ HID Y-SNP Research Panel v1 for performance and resolution in admixed South Americans of haplogroup Q. AU - Köksal,Zehra, AU - Burgos,Germán, AU - Carvalho,Elizeu, AU - Loiola,Silvia, AU - Parolin,María Laura, AU - Quiroz,Alfredo, AU - Ribeiro Dos Santos,Ândrea, AU - Toscanini,Ulises, AU - Vullo,Carlos, AU - Børsting,Claus, AU - Gusmão,Leonor, AU - Pereira,Vania, Y1 - 2022/04/15/ PY - 2022/01/21/received PY - 2022/04/04/revised PY - 2022/04/11/accepted PY - 2022/4/23/pubmed PY - 2022/6/22/medline PY - 2022/4/22/entrez KW - AmpliSeq panel KW - Massively parallel sequencing KW - Native American KW - Population genetics KW - Y haplogroup Q KW - Y-SNP analysis SP - 102708 EP - 102708 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 59 N2 - 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. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/35453088/Testing_the_Ion_AmpliSeq™_HID_Y_SNP_Research_Panel_v1_for_performance_and_resolution_in_admixed_South_Americans_of_haplogroup_Q_ DB - PRIME DP - Unbound Medicine ER -