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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 07; 41:93-106.FS

Abstract

Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the "minimal reference phylogeny for the human Y chromosome" (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man's paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Ralf A
Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands.
van Oven M
Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands.
Montiel González D
Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands.
de Knijff P
Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands.
van der Beek K
Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB, The Hague, the Netherlands.
Wootton S
Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA.
Lagacé R
Human Identification Group, Thermo Fisher Scientific, 180 Oyster Point Blvd, South San Francisco, CA, 94080, USA.
Kayser M
Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Wytemaweg 80, 3000 CA, Rotterdam, the Netherlands. Electronic address: m.kayser@erasmusmc.nl.

MeSH

Chromosomes, Human, YDNADNA Degradation, NecroticForensic GeneticsHaplotypesHigh-Throughput Nucleotide SequencingHumansMalePolymerase Chain ReactionPolymorphism, Single NucleotideReproducibility of ResultsSequence Analysis, DNA

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

31063905

Citation

Ralf, Arwin, 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 Science International. Genetics, vol. 41, 2019, pp. 93-106.
Ralf A, van Oven M, Montiel González D, 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.
Ralf, A., van Oven, M., Montiel González, D., de Knijff, P., van der Beek, K., Wootton, S., Lagacé, R., & Kayser, M. (2019). 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 Science International. Genetics, 41, 93-106. https://doi.org/10.1016/j.fsigen.2019.04.001
Ralf A, 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. PubMed PMID: 31063905.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - 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. AU - Ralf,Arwin, AU - van Oven,Mannis, AU - Montiel González,Diego, AU - de Knijff,Peter, AU - van der Beek,Kees, AU - Wootton,Sharon, AU - Lagacé,Robert, AU - Kayser,Manfred, Y1 - 2019/04/27/ PY - 2019/01/11/received PY - 2019/04/08/revised PY - 2019/04/08/accepted PY - 2019/5/8/pubmed PY - 2019/7/25/medline PY - 2019/5/8/entrez KW - Bio-geographic ancestry KW - Forensic Y-chromosome analysis KW - MPS: AmpliSeq KW - Massively parallel sequencing KW - Paternal lineage KW - Y haplogrouping SP - 93 EP - 106 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 41 N2 - Y-chromosomal haplogroups assigned from male-specific Y-chromosomal single nucleotide polymorphisms (Y-SNPs) allow paternal lineage identification and paternal bio-geographic ancestry inference, both being relevant in forensic genetics. However, most previously developed forensic Y-SNP tools did not provide Y haplogroup resolution on the high level needed in forensic applications, because the limited multiplex capacity of the DNA technologies used only allowed the inclusion of a relatively small number of Y-SNPs. In a proof-of-principle study, we recently demonstrated that high-resolution Y haplogrouping is feasible via two AmpliSeq PCR analyses and simultaneous massively parallel sequencing (MPS) of 530 Y-SNPs allowing the inference of 432 Y-haplogroups. With the current study, we present a largely improved Y-SNP MPS lab tool that we specifically designed for the analysis of low quality and quantity DNA often confronted with in forensic DNA analysis. Improvements include i) Y-SNP marker selection based on the "minimal reference phylogeny for the human Y chromosome" (PhyloTree Y), ii) strong increase of the number of targeted Y-SNPs allowing many more Y haplogroups to be inferred, iii) focus on short amplicon length enabling successful analysis of degraded DNA, and iv) combination of all amplicons in a single AmpliSeq PCR and simultaneous sequencing allowing single DNA aliquot use. This new MPS tool simultaneously analyses 859 Y-SNPs and allows inferring 640 Y haplogroups. Preliminary forensic developmental validation testing revealed that this tool performs highly accurate, is sensitive and robust. We also provide a revised software tool for analysing the sequencing data produced by the new MPS lab tool including final Y haplogroup assignment. We envision the tools introduced here for high-resolution Y-chromosomal haplogrouping to determine a man's paternal lineage and/or paternal bio-geographic ancestry to become widely used in forensic Y-chromosome DNA analysis and other applications were Y haplogroup information from low quality / quantity DNA samples is required. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/31063905/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_ DB - PRIME DP - Unbound Medicine ER -