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A SNaPshot of next generation sequencing for forensic SNP analysis.
Forensic Sci Int Genet. 2015 Jan; 14:50-60.FS

Abstract

Forensic phenotyping can provide useful intelligence regarding the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of an evidentiary sample. Currently, single nucleotide polymorphism (SNP) based inference of BGA and EVCs is performed most commonly using SNaPshot(®), a single base extension (SBE) assay. However, a single SNaPshot multiplex PCR is limited to 30-40 SNPs. Next generation sequencing (NGS) offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. The PCR multiplexes from five SNaPshot assays (SNPforID 52plex, SNPforID 34plex, Eurasiaplex, IrisPlex and an unpublished BGA assay) were applied to three different DNA template amounts (0.1, 0.2 and 0.3 ng) in three samples (9947A and 007 control DNAs and a male donor). The pooled PCR amplicons containing 136 unique SNPs were sequenced using Life Technologies' Ion Torrent™ PGM system. Approximately 72 Mb of sequence was generated from two 10 Mb Ion 314™ v1 chips. Accurate genotypes were readily obtained from all three template amounts. Of a total of 408 genotypes, 395 (97%) were fully concordant with SNaPshot across all three template amounts. Of those genotypes discordant with SNaPshot, six Ion Torrent sequences (1.5%) were fully concordant with Sanger sequencing across the three template amounts. Seven SNPs (1.7%) were either discordant between template amounts or discordant with Sanger sequencing. Sequence coverage observed in the negative control, and, allele coverage variation for heterozygous genotypes highlights the need to establish a threshold for background levels of sequence output and heterozygous balance. This preliminary study of the Ion Torrent PGM system has demonstrated considerable potential for use in forensic DNA analyses as a low to medium throughput NGS platform using established SNaPshot assays.

Authors+Show Affiliations

Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia. Electronic address: runa.daniel@police.vic.gov.au.Forensic Genetics Unit, Institute of Forensic Science "Luis Concheiro", University of Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Science "Luis Concheiro", University of Santiago de Compostela, Spain.Forensic Genetics Unit, Institute of Forensic Science "Luis Concheiro", University of Santiago de Compostela, Spain.Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Australia.Forensic Genetics Unit, Institute of Forensic Science "Luis Concheiro", University of Santiago de Compostela, Spain; CIBERER, Genomic Medicine Group, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.Forensic Genetics Unit, Institute of Forensic Science "Luis Concheiro", University of Santiago de Compostela, Spain.National Centre for Forensic Studies, University of Canberra, Australia.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

25282603

Citation

Daniel, R, et al. "A SNaPshot of Next Generation Sequencing for Forensic SNP Analysis." Forensic Science International. Genetics, vol. 14, 2015, pp. 50-60.
Daniel R, Santos C, Phillips C, et al. A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Sci Int Genet. 2015;14:50-60.
Daniel, R., Santos, C., Phillips, C., Fondevila, M., van Oorschot, R. A., Carracedo, A., Lareu, M. V., & McNevin, D. (2015). A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Science International. Genetics, 14, 50-60. https://doi.org/10.1016/j.fsigen.2014.08.013
Daniel R, et al. A SNaPshot of Next Generation Sequencing for Forensic SNP Analysis. Forensic Sci Int Genet. 2015;14:50-60. PubMed PMID: 25282603.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A SNaPshot of next generation sequencing for forensic SNP analysis. AU - Daniel,R, AU - Santos,C, AU - Phillips,C, AU - Fondevila,M, AU - van Oorschot,R A H, AU - Carracedo,A, AU - Lareu,M V, AU - McNevin,D, Y1 - 2014/08/30/ PY - 2014/07/02/received PY - 2014/08/14/revised PY - 2014/08/25/accepted PY - 2014/10/6/entrez PY - 2014/10/6/pubmed PY - 2015/7/21/medline KW - Biogeographical ancestry (BGA) KW - Externally visible characteristics (EVCs) KW - Molecular photofitting KW - Next generation sequencing (NGS) KW - SNaPshot KW - Single nucleotide polymorphisms (SNPs) SP - 50 EP - 60 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 14 N2 - Forensic phenotyping can provide useful intelligence regarding the biogeographical ancestry (BGA) and externally visible characteristics (EVCs) of the donor of an evidentiary sample. Currently, single nucleotide polymorphism (SNP) based inference of BGA and EVCs is performed most commonly using SNaPshot(®), a single base extension (SBE) assay. However, a single SNaPshot multiplex PCR is limited to 30-40 SNPs. Next generation sequencing (NGS) offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. The PCR multiplexes from five SNaPshot assays (SNPforID 52plex, SNPforID 34plex, Eurasiaplex, IrisPlex and an unpublished BGA assay) were applied to three different DNA template amounts (0.1, 0.2 and 0.3 ng) in three samples (9947A and 007 control DNAs and a male donor). The pooled PCR amplicons containing 136 unique SNPs were sequenced using Life Technologies' Ion Torrent™ PGM system. Approximately 72 Mb of sequence was generated from two 10 Mb Ion 314™ v1 chips. Accurate genotypes were readily obtained from all three template amounts. Of a total of 408 genotypes, 395 (97%) were fully concordant with SNaPshot across all three template amounts. Of those genotypes discordant with SNaPshot, six Ion Torrent sequences (1.5%) were fully concordant with Sanger sequencing across the three template amounts. Seven SNPs (1.7%) were either discordant between template amounts or discordant with Sanger sequencing. Sequence coverage observed in the negative control, and, allele coverage variation for heterozygous genotypes highlights the need to establish a threshold for background levels of sequence output and heterozygous balance. This preliminary study of the Ion Torrent PGM system has demonstrated considerable potential for use in forensic DNA analyses as a low to medium throughput NGS platform using established SNaPshot assays. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/25282603/A_SNaPshot_of_next_generation_sequencing_for_forensic_SNP_analysis_ DB - PRIME DP - Unbound Medicine ER -