Highlights
- •Novel sequence structure at locus DYS533.
- •Upstream insertion explains a new variant allele DYS533/16.3.
- •New variant allele associated to south american Y haplotypes.
Abstract
We typed 1541 Y-STR haplotypes from reference samples along forensic casework investigations.
In three haplotypes, we detected a variant allele designed as 16.3 at locus DYS533.
This was confirmed by amplification using two commercial kits. Sanger sequencing revealing
a novel motif corresponding to [TATC]12 repeats with a 19-bp insertion in the flanking upstream region. We propose its origin
as an insertion at − 9.1 upstream of the repeat motifs. We searched other local databases
and found this allele in various geographical areas of Argentina and neighbouring
countries. The haplotypes share a common core of 10 Y-STRs (DYS389-I/13; DYS389-II/30;
DYS19/14; DYS481/22; DYS438/12; DYS437/16; DYS635/23; DYS392/13; DYS393/13; GATA H4/11)
and belong to the R1b haplogroup. This 16.3 allele is restricted to southern South
America, which allows us to propose a local and relatively recent origin. The sequence
described herein constitutes a novelty that could be considered in future criteria
for the nomenclature of STRs based on massively parallel sequencing.
Keywords
To read this article in full you will need to make a payment
Purchase one-time access:
Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online accessOne-time access price info
- For academic or personal research use, select 'Academic and Personal'
- For corporate R&D use, select 'Corporate R&D Professionals'
Subscribe:
Subscribe to Forensic Science International: GeneticsAlready a print subscriber? Claim online access
Already an online subscriber? Sign in
Register: Create an account
Institutional Access: Sign in to ScienceDirect
References
- A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP–CEPH populations.Mol. Biol. Evol. 2010; 27: 385-393https://doi.org/10.1093/molbev/msp243
- 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
- A single nucleotide substitution in the flanking region of DYS533 with low peak height.Jpn. J. Forensic Sci. Technol. 2021; 26: 225-229
- Characterization of genetic sequence variation of 58 STR loci in four major population groups.Forensic Sci. Int. Genet. 2016; 25: 214-226https://doi.org/10.1016/j.fsigen.2016.09.007
- The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration.Forensic Sci. Int. Genet. 2020; 48102345https://doi.org/10.1016/j.fsigen.2020.102345
- Human DNA degradation assessment and male DNA detection by quantitative-PCR followed by high-resolution melting analysis.Forensic Sci. Int. Genet. 2019; 295: 1-7https://doi.org/10.1016/j.forsciint.2018.11.013
- Rapid screening for Native American mitochondrial and Y-chromosome haplogroups detection in routine DNA analysis.Forensic Sci. Int. Genet. 2011; 5: 105-108https://doi.org/10.1016/j.fsigen.2010.08.018
- A comprehensive survey of human Y-chromosomal microsatellites.Am. J. Hum. Genet. 2004; 74: 1183-1197https://doi.org/10.1086/421531
- “The devil’s in the detail”: release of an expanded, enhanced and dynamically revised forensic STR sequence guide.Forensic Sci. Int. Genet. 2018; 34: 162-169
- Recommendations of the DNA commission of the international society for forensic genetics (ISFG) on quality control of autosomal short tandem repeat allele frequency databasing (STRidER).Forensic Sci. Int. Genet. 2016; 24: 97-102
- Median-joining networks for inferring intraspecific phylogenies.Mol. Biol. Evol. 1999; 16: 37-48
- Y-chromosomal DNA variation in Pakistan.Am. J. Hum. Genet. 2002; 70: 1107-1124https://doi.org/10.1086/339929
- Genomic complexity of the Y-STR DYS19: inversions, deletions and founder lineages carrying duplications.Int J. Leg. Med. 2009; 123: 15-23https://doi.org/10.1007/s00414-008-0253-3
- The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.Genome Res. 2013; 23: 749-761https://doi.org/10.1101/gr.148718.112
- Analysis of 23 Y-STRs in a population sample from eastern Paraguay.Forensic Sci. Int. Genet. 2018; 37: e20-e22
- Male lineages in Brazilian populations and performance of haplogroup prediction tools.Forensic Sci. Int. Genet. 2020; 44102163https://doi.org/10.1016/j.fsigen.2019.102163
- Flanking region variation of ForenSeq DNA signature prep kit STR and SNP loci in Yavapai native Americans.Forensic Sci. Int. Genet. 2017; 28: 146-154https://doi.org/10.1016/j.fsigen.2017.02.014
- Length and repeat-sequence variation in 58 STRs and 94 SNPs in two Spanish populations.Forensic Sci. Int. Genet. 2017; 30: 66-70
- Genetic analysis of Southern Brazil subjects using the PowerSeq AUTO/Y system for short tandem repeat sequencing.Forensic Sci. Int. Genet. 2018; 33: 129-135
- Massive parallel sequencing of short tandem repeats in the Korean population.Electrophoresis. 2018; 39: 2702-2707
- Variation of 52 new Y-STR loci in the Y chromosome consortium worldwide panel of 76 diverse individuals.Int J. Leg. Med. 2007; 121: 124-127https://doi.org/10.1007/s00414-006-0124-8
- Novel Y-chromosome short tandem repeat variants detected through the use of massively parallel sequencing.Genom. Proteom. Bioinforma. 2015; : 250-257https://doi.org/10.1016/j.gpb.2015.08.001
- Sequence variation observed in 27 Y-STR markers with U.S. population samples.Forensic Sci. Int Genet.: Suppl. Ser. 2019; 7: 520-521https://doi.org/10.1016/j.fsigss.2019.10.074
- Evaluation of the MiSeq FGx system for use in forensic casework.Int. J. Leg. Med. 2019; 133: 689-697https://doi.org/10.1007/s00414-018-01987-
- 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
- Global patterns of STR sequence variation: sequencing the CEPH human genome diversity panel for 58 forensic STRs using the Illumina ForenSeq DNA Signature Prep Kit.Electrophoresis. 2018; 39: 2708-2724
- Inferring continental ancestry of argentineans from Autosomal, Y-chromosomal and mitochondrial DNA.Ann. Hum. Genet. 2010; 74: 65-76https://doi.org/10.1111/j.1469-1809.2009.00556.x
- Massively parallel sequencing of forensic STRs: considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements.Forensic Sci. Int. Genet. 2016; 22: 54-63
- Report from the STRAND Working Group on the 2019 STR sequence nomenclature meeting.Forensic Sci. Int. Genet. 2019; 43102165https://doi.org/10.1016/j.fsigen.2019.102165
- The devil's in the detail: release of an expanded, enhanced and dynamically revised forensic STR sequence guide.Forensic Sci. Int. Genet. 2018; 34: 162-169https://doi.org/10.1016/j.fsigen.2018.02.017
- STRNaming: generating simple, informative names for sequenced STR alleles in a standardised and automated manner.Forensic Sci. Int. Genet. 2021; 52102473https://doi.org/10.1016/j.fsigen.2021.102473
Article info
Publication history
Published online: October 10, 2022
Accepted:
October 7,
2022
Received in revised form:
August 24,
2022
Received:
May 31,
2022
Identification
Copyright
© 2022 Elsevier B.V. All rights reserved.
