Highlights
- •A NGS-based 68-plex panel including 67 Y-STRs and Amelogenin was developed.
- •The 68-plex panel was accurate and sensitive in genotyping DNA samples.
- •Sequence characteristics of 67 forensic Y-STRs were reported.
- •A total of 466 length-based and 806 sequence-based Y-STR alleles were observed.
- •A total of 201 sequence-based alleles across 42 loci were newly discovered.
Abstract
Sequence polymorphisms of Y chromosome short tandem repeat (Y-STR) markers can be
unveiled using next generation sequencing (NGS). Compared to capillary electrophoresis,
NGS has the advantage of distinguishing between some alleles of the same length. Here,
a 68-plex in-house panel covering 67 Y-STR loci and the sex determinant Amelogenin
locus, was developed. The accuracy of this panel was 100% concordant with three standard
reference samples. The sensitive was as low as 250 pg. A total of 466 length-based
alleles, 806 sequence-based alleles, and 149 haplotypes were observed across 149 Chinese
Han individuals. The total haplotype diversity and discrimination capacity was 1.0000
in detected samples. The DYS710 locus possessed the highest diversity by sequence
among these Y-STRs, with 109 sequence-based alleles observed. Micro-variant alleles
with the same length were observed in 39 Y-STR loci, with their sequence variations
mainly attributable to repeat pattern variations. While the number of sequence-based
alleles identified for DYS447, DYS449, DYS710, DYS720 and DYF387S1a/b was approximately
three times that of their length-based alleles, flanking sequence variations were
observed in 18 alleles. In addition, 201 sequence-based alleles in 42 loci were newly
discovered. This significantly expanded the knowledge of human Y-STR sequence polymorphisms.
Collectively, the 68-plex panel provided reliable Y-STR results as well as higher
resolution for paternal lineage analysis.
Keywords
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References
- Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases.Forensic Sci. Int Genet. 2015; 19: 238-242https://doi.org/10.1016/j.fsigen.2015.08.002
- Forensic molecular biomarkers for mixture analysis.Forensic Sci. Int Genet. 2019; 41: 107-119https://doi.org/10.1016/j.fsigen.2019.04.003
- Application of Y-chromosomal microdeletions in a homicide case.Forensic Sci. Int. 2020; 314110370https://doi.org/10.1016/j.forsciint.2020.110370
- Forensic use of Y-chromosome DNA: a general overview.Hum. Genet. 2017; 136: 621-635https://doi.org/10.1007/s00439-017-1776-9
- Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing.Sci. Rep. 2020; 10: 12225https://doi.org/10.1038/s41598-020-69137-1
- , D. Consortium, Massively parallel sequence data of 31 autosomal STR loci from 496 Spanish individuals revealed concordance with CE-STR technology and enhanced discrimination power.Forensic Sci. Int Genet. 2019; 42: 49-55https://doi.org/10.1016/j.fsigen.2019.06.009
- Genetic polymorphism and population structure of Torghut Mongols and comparison with a Mongolian population 3000 kilometers away.Forensic Sci. Int Genet. 2019; 42: 235-243https://doi.org/10.1016/j.fsigen.2019.07.017
- Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations.J. Forensic Sci. 2002; 47: 513-519
- Y.C.U.G. International Forensic, Y chromosome haplotype reference database (YHRD): update.Forensic Sci. Int Genet. 2007; 1: 83-87https://doi.org/10.1016/j.fsigen.2007.01.017
- Haplotype diversity and phylogenetic relationship analysis of Chinese Yulin Han population using 59 Y-STR loci of two novel Y-STR typing systems.Leg. Med (Tokyo). 2021; 50101871https://doi.org/10.1016/j.legalmed.2021.101871
- RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates.Forensic Sci. Int Genet. 2021; 55102595https://doi.org/10.1016/j.fsigen.2021.102595
- Haplotype diversity and phylogenetic characteristics for Guanzhong Han population from Northwest China via 38 Y-STRs using Yfiler Platinum Amplification System.Mol. Genet Genom. Med. 2020; 8e1187https://doi.org/10.1002/mgg3.1187
- Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM).Forensic Sci. Int Genet. 2015; 19: 192-196https://doi.org/10.1016/j.fsigen.2015.06.012
- Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing.Forensic Sci. Int Genet. 2016; 25: 132-141https://doi.org/10.1016/j.fsigen.2016.08.010
- Novel Y-chromosome Short Tandem Repeat Variants Detected Through the Use of Massively Parallel Sequencing.Genom. Proteom. Bioinforma. 2015; 13: 250-257https://doi.org/10.1016/j.gpb.2015.08.001
- Evaluation of Promega PowerSeq Auto/Y systems prototype on an admixed sample of Rio de Janeiro, Brazil: Population data, sensitivity, stutter and mixture studies.Forensic Sci. Int Genet. 2021; 53102516https://doi.org/10.1016/j.fsigen.2021.102516
- Genetic analysis of Southern Brazil subjects using the PowerSeq AUTO/Y system for short tandem repeat sequencing.Forensic Sci. Int Genet. 2018; 33: 129-135https://doi.org/10.1016/j.fsigen.2017.12.008
- Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710.Forensic Sci. Int Genet. 2010; 4: 104-110https://doi.org/10.1016/j.fsigen.2009.06.011
- Genetic polymorphism of DYS19 DYS385 DYS389 DYS390 DYS635 DYS713 DYS720 loci and their forensic applications in Hebei Han population, Hebei Medical University.He Bei. 2007; : 1-74
- Allele frequencies for 27 Y-STR loci with U.S. Caucasian, African American, and Hispanic samples.Forensic Sci. Int. 2006; 156: 250-260https://doi.org/10.1016/j.forsciint.2005.02.011
- Forensic evaluation and population data on the new Y-STRs DYS434, DYS437, DYS438, DYS439 and GATA A10.Int J. Leg. Med. 2002; 116: 139-147https://doi.org/10.1007/s00414-001-0275-6
- Fast STR allele identification with STRait Razor 3.0.Forensic Sci. Int Genet. 2017; 30: 18-23https://doi.org/10.1016/j.fsigen.2017.05.008
- Clustal W and Clustal X version 2.0.Bioinformatics. 2007; 23: 2947-2948https://doi.org/10.1093/bioinformatics/btm404
- Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV).Genome Res. 2021; 31: 159-169https://doi.org/10.1101/gr.266932.120
- Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.Mol. Ecol. Resour. 2010; 10: 564-567https://doi.org/10.1111/j.1755-0998.2010.02847.x
- DNA polymorphism detectable by restriction endonucleases.Genetics. 1981; 97: 145-163https://doi.org/10.1093/genetics/97.1.145
- Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.Am. J. Hum. Genet. 2010; 87: 341-353https://doi.org/10.1016/j.ajhg.2010.08.006
- Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx forensic genomics system.Forensic Sci. Int Genet. 2016; 24: 18-23https://doi.org/10.1016/j.fsigen.2016.05.008
- Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population.Mol. Genet Genom. Med. 2021; 9e1626https://doi.org/10.1002/mgg3.1626
- Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing.Int J. Leg. Med. 2021; https://doi.org/10.1007/s00414-021-02738-1
- A game of hide and seq: Identification of parallel Y-STR evolution in deep-rooting pedigrees.Eur. J. Hum. Genet. 2019; 27: 637-646https://doi.org/10.1038/s41431-018-0312-2
- Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population.Forensic Sci. Int. 2004; 145: 47-55https://doi.org/10.1016/j.forsciint.2004.03.009
- STRSeq: A catalog of sequence diversity at human identification Short Tandem Repeat loci.Forensic Sci. Int Genet. 2017; 31: 111-117https://doi.org/10.1016/j.fsigen.2017.08.017
- Massively parallel sequencing of forensic STRs and SNPs using the Illumina((R)) ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System.Forensic Sci. Int Genet. 2017; 31: 135-148https://doi.org/10.1016/j.fsigen.2017.09.003
- A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing.Forensic Sci. Int Genet. 2018; 35: 97-106https://doi.org/10.1016/j.fsigen.2018.03.012
- Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449.Int J. Leg. Med. 2019; 133: 1681-1689https://doi.org/10.1007/s00414-019-02056-7
- Population study and evaluation of 20 Y-chromosome STR loci in Germans.Int J. Leg. Med. 2007; 121: 24-27https://doi.org/10.1007/s00414-005-0075-5
- Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups.Forensic Sci. Int Genet. 2019; 41: e1-e7https://doi.org/10.1016/j.fsigen.2019.03.004
- New, male-specific microsatellite markers from the human Y chromosome.Genomics. 1999; 57: 433-437https://doi.org/10.1006/geno.1999.5782
- Structure and polymorphism of 16 novel Y-STRs in Chinese Han population.Genet Mol. Res. 2012; 11: 4487-4500https://doi.org/10.4238/2012.October.11.1
- Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance.Electrophoresis. 2015; 36: 2908-2913https://doi.org/10.1002/elps.201500204
- Identification of 5 novel Y chromosome STR loci and haplotype distribution in Chinese Han population（Guangzhou）.J. Sun Yat-Sen. Univ. (Med. Sci. ). 2010; 31: 7-12https://doi.org/10.13471/j.cnki.j.sun.yat-sen.univ(med.sci).2010.0001
Article info
Publication history
Published online: May 25, 2022
Accepted:
May 23,
2022
Received in revised form:
May 3,
2022
Received:
January 30,
2022
Identification
Copyright
© 2022 Elsevier B.V. All rights reserved.
