Highlights
- •This novel Y-SNP panel contains 256 Y-SNPs and allows inferring 253 Y haplogroups.
- •This Y-SNP MPS panel could provide an achievable high-resolution in the Chinese populations.
- •This Y-SNP MPS panel performs highly accurate, is sensitive, reliable, specific and robust.
Abstract
Y-chromosomal haplogroups determined by Y-chromosomal single nucleotide polymorphisms
(Y-SNPs) allow paternal lineage identification and paternal biogeographic ancestry
inference, which has attracted a lot of interest in the forensic community. Recently,
a comprehensive Y-SNP tool with dominant markers targeting haplogroups in R, E and
I branches has been reported, which allows the inference of 640 Y haplogroups. It
had a very good performance and could provide a high level of Y haplogroup resolution
in most populations. However, the predominant haplogroups in the Chinese populations
are O, C and N, suggesting that more Y-SNPs under these clades are needed to achieve
the population-specific high resolution. Herein, aiming at the Chinese population,
we presented a largely improved custom Y-SNP MPS panel that contains 256 carefully
ascertained Y-SNPs based on our previous studies, and evaluated this panel via a series
of tests, including the tests for concordance, repeatability, sensitivity, specificity,
and stability, as well as the mixture, degraded and case-type sample analysis. The
preliminary developmental validation demonstrated that this panel was highly reliable,
sensitive, specific, and robust. In the sensitivity test, even when the DNA input
was reduced to as low as 0.5 ng, the sample could still be assigned to the correct
Y haplogroup. For mixture analysis, even the 1:99 (Male: Female) mixtures had no effects
on the assignation of the Y haplogroup of the male contributor. In summary, this assay
has provided a high-resolution Y-chromosomal haplogrouping workflow to determine a
male’s paternal lineage and/or paternal biogeographic ancestry and could be widely
used for Chinese Y-chromosomal haplogroups dissection.
Keywords
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References
- Forensic use of Y-chromosome DNA: a general overview.Hum. Genet. 2017; 136: 621-635https://doi.org/10.1007/s00439-017-1776-9
- Y chromosome STR typing in crime casework.Forensic Sci. Med. Pathol. 2009; 5: 77-84https://doi.org/10.1007/s12024-009-9089-5
- Human Y-chromosome variation in the genome-sequencing era.Nat. Rev. Genet. 2017; 18: 485-497https://doi.org/10.1038/nrg.2017.36
- The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.Hum. Genet. 2017; 136: 559-573https://doi.org/10.1007/s00439-016-1740-0
- Detecting past male-mediated expansions using the Y chromosome.Hum. Genet. 2017; 136: 547-557https://doi.org/10.1007/s00439-017-1781-z
- Founders, drift, and infidelity: the relationship between Y chromosome diversity and patrilineal surnames.Mol. Biol. Evol. 2009; 26: 1093-1102https://doi.org/10.1093/molbev/msp022
- Inheritance of coronary artery disease in men: an analysis of the role of the Y chromosome.Lancet. 2012; 379: 915-922https://doi.org/10.1016/s0140-6736(11)61453-0
- Forensic applications of Y chromosomal properties.Leg. Med. 2017; 26: 86-91https://doi.org/10.1016/j.legalmed.2017.04.002
- Toward a consensus on SNP and STR mutation rates on the human Y-chromosome.Hum. Genet. 2017; 136: 575-590https://doi.org/10.1007/s00439-017-1805-8
- 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: 93-106https://doi.org/10.1016/j.fsigen.2019.04.001
- Simultaneous analysis of hundreds of Y‐Chromosomal SNP s for high‐resolution paternal lineage classification using targeted semiconductor sequencing.Hum. Mutat. 2015; 36: 151-159https://doi.org/10.1002/humu.22713
- SNaPshot® minisequencing analysis of multiple ancestry-informative Y-SNPs using capillary electrophoresis.Methods Mol. Biol. 2012; 830: 127-140https://doi.org/10.1007/978-1-61779-461-2_9
- Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.Sci. Rep. 2017; 7: 11324https://doi.org/10.1038/s41598-017-11955-x
- Y chromosome homogeneity in the Korean population.Int. J. Leg. Med. 2010; 124: 653-657https://doi.org/10.1007/s00414-010-0501-1
- Development of a single base extension method to resolve Y chromosome haplogroups in sub-Saharan African populations.Investig. Genet. 2010; 1: 6https://doi.org/10.1186/2041-2223-1-6
- Hierarchical Y-SNP assay to study the hidden diversity and hylogenetic relationship of native populations in South America.Forensic Sci. Int. Genet. 2011; 5: 100-104https://doi.org/10.1016/j.fsigen.2010.08.016
- Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra.Nat. Commun. 2011; 2: 228https://doi.org/10.1038/ncomms1235
- The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa.Mol. Ecol. 2011; 20: 2693-2708https://doi.org/10.1111/j.1365-294X.2011.05130.x
- An efficient multiplex genotyping approach for detecting the major worldwide human Y-chromosome haplogroups.Int. J. Leg. Med. 2011; 125: 879https://doi.org/10.1007/s00414-011-0605-2
- A multiplex SNP assay for the dissection of human Y-chromosome haplogroup O representing the major paternal lineage in East and Southeast Asia.J. Hum. Genet. 2012; 57: 65https://doi.org/10.1038/jhg.2011.120
- Multiplex genotyping assays for fine‐resolution subtyping of the major human Y‐chromosome haplogroups E, G, I, J, and R in anthropological, genealogical, and forensic investigations.Electrophoresis. 2013; 34: 3029-3038https://doi.org/10.1002/elps.201300210
- Identification of new SNPs in native South American populations by resequencing the Y chromosome.Forensic Sci. Int. Genet. 2015; 15: 111-114https://doi.org/10.1016/j.fsigen.2014.09.014
- Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.Hum. Mutat. 2014; 35: 187-191https://doi.org/10.1002/humu.22468
- 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; 59102708https://doi.org/10.1016/j.fsigen.2022.102708
- Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route.Mol. Biol. Evol. 2011; 28: 717-727https://doi.org/10.1093/molbev/msq247
- Forensic characteristics and genetic analysis of both 27 Y-STRs and 143 Y-SNPs in Eastern Han Chinese population.Forensic Sci. Int. Genet. 2019; 42: e13-e20https://doi.org/10.1016/j.fsigen.2019.07.011
- Next-generation sequencing of 74 Y-SNPs to construct a concise consensus phylogeny tree for Chinese population.Forensic Sci. Int. Genet. Suppl. Ser. 2017; 6: e96-e98https://doi.org/10.1016/j.fsigss.2017.09.043
- Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China.Forensic Sci. Int. Genet. 2019; 39: e14-e20https://doi.org/10.1016/j.fsigen.2018.11.016
- Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs.Forensic Sci. Int. Genet. 2019; 41: 11-18https://doi.org/10.1016/j.fsigen.2019.03.022
- Exploitation of a novel slowly mutating Y-STRs set and evaluation of slowly mutating Y-STRs plus Y-SNPs typing strategy in forensic genetics and evolutionary research.Electrophoresis. 2021; 42: 774-785https://doi.org/10.1002/elps.202000302
- Developmental validation of a custom panel including 165 Y-SNPs for Chinese Y-chromosomal haplogroups dissection using the ion S5 XL system.Forensic Sci. Int. Genet. 2019; 38: 70-76https://doi.org/10.1016/j.fsigen.2018.10.009
- Genetic reconstruction and phylogenetic analysis by 193 Y-SNPs and 27 Y-STRs in a Chinese Yi ethnic group.Electrophoresis. 2021; 42: 1480-1487https://doi.org/10.1002/elps.202100003
- Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels.Forensic Sci. Int. Genet. 2021; 54102565https://doi.org/10.1016/j.fsigen.2021.102565
- Genetic structure and paternal admixture of the modern Chinese Zhuang population based on 37 Y-STRs and 233 Y-SNPs.Forensic Sci. Int. Genet. 2022; 58102681https://doi.org/10.1016/j.fsigen.2022.102681
- Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.Forensic Sci. Int. 2001; 118: 106-113https://doi.org/10.1016/s0379-0738(00)00478-3
- Y chromosome haplotype reference database (YHRD): update.Forensic Sci. Int. Genet. 2007; 1: 83-87https://doi.org/10.1016/j.fsigen.2007.01.017
- A global reference for human genetic variation.Nature. 2015; 526: 68-74https://doi.org/10.1038/nature15393
- The revised World Medical Association’s Declaration of Helsinki 2013: enhancing the protection of human research subjects and empowering ethics review committees.World Med. Health Policy. 2014; 6: 1-3
- Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations.Electrophoresis. 2020; 41: 194-201https://doi.org/10.1002/elps.201900278
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.Brief. Bioinform. 2013; 14: 178-192https://doi.org/10.1093/bib/bbs017
- Developmental validation of a custom panel including 273 SNPs for forensic application using Ion Torrent PGM.Forensic Sci. Int. Genet. 2017; 27: 50-57https://doi.org/10.1016/j.fsigen.2016.12.003
- Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.Nat. Genet. 2016; 48: 593-599https://doi.org/10.1038/ng.3559
- Inhibition mechanisms of hemoglobin, immunoglobulin G, and whole blood in digital and real-time PCR.Anal. Bioanal. Chem. 2018; 410: 2569-2583https://doi.org/10.1007/s00216-018-0931-z
- The impact of common PCR inhibitors on forensic MPS analysis.Forensic Sci. Int. Genet. 2019; 40: 182-191https://doi.org/10.1016/j.fsigen.2019.03.001
Article info
Publication history
Published online: October 08, 2022
Accepted:
October 4,
2022
Received in revised form:
August 25,
2022
Received:
June 19,
2022
Identification
Copyright
© 2022 Elsevier B.V. All rights reserved.
