Abstract
The application of massively parallel sequencing (MPS) data from whole genomes has allowed very many more Y-SNP loci to be genotyped simultaneously than previously possible. Although this greatly increases the resolution of Y-SNP haplogroups to link common ancestors, it remains a great challenge to provide a phylogenetic tree to clearly display the relationship of varying haplogroups. Y-SNP Haplogroup Hierarchy Finder is a web tool to generate hierarchical haplogroups based on Y-SNP data with the derived allele at the terminal of a haplogroup tree. The input data can include that from whole-genome sequencing. Confidence in assignment using Y-SNP Haplogroup Hierarchy Finder was demonstrated using Y-SNP genotypes of 1233 samples, sourced from the 1000 genomes project phase 3, used to generate the expected haplogroups. The outcome includes 2 reports: a ‘Haplogroup Report’ lists mutation types from the submitted Y-SNPs and their corresponding haplogroups, and a ‘Haplogroup Hierarchy Report’ lists all possible hierarchical haplogroups and ranks the three most supported haplogroups. Each layer of the descending haplogroups from one step to the next is shown and the supporting numbers of Y-SNPs are also included in these reports. All haplogroups that exhibited a clear relationship between the ancestral through to the derived SNPs can be clustered into a hierarchy of haplogroups. The assigned 1233 haplogroups were compared with 2 other software programs designed to assemble haplogroups, which resulted in one where there were many differences and the other one where there was only minor difference. The advantage of this web-based tool is that it provides an easy way to assign Y-SNP haplogroup based on the visualized hierarchical pattern.
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References
Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, Graziosi G, et al. Evaluation of Y-chromosomal STRs: a multicenter study. Int J Leg Med. 1997;110:125–33.
de Knijff P, Kayser M, Caglià A, Corach D, Fretwell N, Gehrig C, et al. Chromosome Y microsatellites: population genetic and evolutionary aspects. Int J Leg Med. 1997;110:134–40.
Sobrino B, Brión M, Carracedo A. SNPs in forensic genetics: a review on SNP typing methodologies. Forensic Sci Int. 2005;154:181–94.
Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet. 2017;136:621–35.
Ralf A, van Oven M, Montiel González D, de Knijff P, van der Beek K, Wootton S, et al. Forensic Y-SNP analysis beyond SNaPshot: High-resolution Y-chromosomal haplogrouping from low quality and quantity DNA using Ion AmpliSeq and targeted massively parallel sequencing. Forensic Sci Int Genet. 2019;41:93–106.
van Oven M, Ralf A, Kayser M. An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups. Int J Leg Med. 2011;125:879–85.
Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, et al. Antiquity and diversity of aboriginal Australian Y-chromosomes. Am J Phys Anthropol. 2016;159:367–81.
Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C, et al. Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™. Forensic Sci Int Genet. 2015;17:110–21.
Silvia AL, Shugarts N, Smith J. A preliminary assessment of the ForenSeq™ FGx System: next generation sequencing of an STR and SNP multiplex. Int J Leg Med. 2017;131:73–86.
Tillmar A, Sjölund P, Lundqvist B, Klippmark T, Älgenäs C, Green H. Whole-genome sequencing of human remains to enable genealogy DNA database searches - a case report. Forensic Sci Int Genet. 2020;46:102233.
Van Geystelen A, Decorte R, Larmuseau MHD. AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications. BMC Genomics. 2013;14:101.
Ralf A, van Oven M, Zhong K, Kayser M. Simultaneous analysis of hundreds of Y-chromosomal SNPs for high-resolution paternal lineage classification using targeted semiconductor sequencing. Hum Mutat. 2015;36:151–9.
Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Sayres MAW, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat Genet. 2016;48:593–9.
Ralf A, Montiel González D, Zhong K, Kayser M. Yleaf: software for human Y-chromosomal haplogroup inference from next-generation sequencing data. Mol Biol Evol. 2018;35:1291–4.
Jagadeesan A, Ebenesersdóttir SS, Guðmundsdóttir VB, Thordardottir EL, Moore KHS, Helgason A. HaploGrouper: A generalized approach to haplogroup classification. Bioinformatics. 2020;37:570–2.
Chen H, Lu Y, Lu D, Xu S. Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data. BMC Bioinform. 2021;22:114.
Acknowledgements
We thank the Ministry of Science and Technology of Taiwan by a grant [MOST 107-2320-B-002-045-MY3] and the Taiwan Biobank for advising data analysis.
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BT conducted the creation of new software. HLH, CYL and YJY carried data analyses. AL and JCL designed the study and drafted the manuscript.
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10038_2022_1033_MOESM2_ESM.pdf
Y-SNP Haplogroup comparison between results reported by HaploGrouper,Y-LineageTracker and Y-Finder based on 1,233 samples taken from 1000 Genome Project
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Tseng, B., Hwa, HL., Lin, CY. et al. Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J Hum Genet 67, 487–493 (2022). https://doi.org/10.1038/s10038-022-01033-0
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DOI: https://doi.org/10.1038/s10038-022-01033-0