Abstract
Massively parallel sequencing (MPS) of identity informative single-nucleotide polymorphisms (IISNPs) enables hundreds of forensically relevant markers to be analysed simultaneously. Generating DNA sequence data enables more detailed analysis including identification of sequence variations between individuals. The GeneRead DNAseq 140 IISNP MPS panel (QIAGEN) has been evaluated on both the MiSeq (Illumina) and Ion PGM™ (Applied Biosystems) MPS platforms using the GeneRead DNAseq Targeted Panels V2 library preparation workflow (QIAGEN). The aims of this study were to (1) determine if the GeneRead DNAseq panel is effective for identity testing by assessing deviation from Hardy-Weinberg (HWE) and pairwise linkage equilibrium (LE); (2) sequence samples with the GeneRead DNAseq panel on the Ion PGM™ using the QIAGEN workflow and assess specificity, sensitivity and accuracy; (3) assess the efficacy of adding biological samples directly to the GeneRead DNAseq PCR, without prior DNA extraction; and (4) assess the effect of varying coverage and allele frequency thresholds on genotype concordance. Analyses of the 140 SNPs for HWE and LE using Fisher’s exact tests and the sequential Bonferroni correction revealed that one SNP was out of HWE in the Japanese population and five SNP combinations were commonly out of LE in 13 of 14 populations. The panel was sensitive down to 0.3125 ng of DNA input. A direct-to-PCR approach (without DNA extraction) produced highly concordant genotypes. The setting of appropriate allele frequency thresholds is more effective for reducing erroneous genotypes than coverage thresholds.
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References
Budowle B, Van Daal A (2008) Forensically relevant SNP classes. BioTechniques 44(5):603–610
Butler JM, Coble MD, Vallone PM (2007) STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol 3(3):200–205
Daniel R, Santos C, Phillips C, Fondevila M, van Oorschot RAH, Carracedo Á, Lareu MV, McNevin D (2015) A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Sci Int Genet 14:50–60
Kidd KK et al (2015) Genetic markers for massively parallel sequencing in forensics. Forensic Sci Int 5:e677–e679
Lou C, Cong B, Li S, Fu L, Zhang X, Feng T, Su S, Ma C, Yu F, Ye J, Pei L (2011) A SNaPshot assay for genotyping 44 individual identification single nucleotide polymorphisms. Electrophoresis 32(3–4):368–378
Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A, SNPforID Consortium (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3):273–280
Sanchez JJ, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9):1713–1724
Mehta B, Daniel R, Phillips C, Doyle S, Elvidge G, McNevin D (2016) Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. ELECTROPHORESIS 37(21):2832–2840
Grandell I, Samara R, Tillmar AO (2016) A SNP panel for identity and kinship testing using massive parallel sequencing. Int J Legal Med 130(4):905–914
de la Puente M, Phillips C, Santos C, Fondevila M, Carracedo Á, Lareu MV (2017) Evaluation of the Qiagen 140-SNP forensic identification multiplex for massively parallel sequencing. Forensic Sci Int Genet 28:35–43
Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Børsting C, Johansen P, Fondevila M, Morling N, Schneider P, EUROFORGEN-NoE Consortium, Carracedo A, Lareu MV (2014) Building a forensic ancestry panel from the ground up: the EUROFORGEN global AIM-SNP set. Forensic Sci Int Genet 11:13–25
Al-Asfi M, McNevin D, Mehta B, Power D, Gahan ME, Daniel R (2018) Assessment of the Precision ID Ancestry panel. Int J Legal Med 132(6):1581–1594
Seo SB, King JL, Warshauer DH, Davis CP, Ge J, Budowle B (2013) Single nucleotide polymorphism typing with massively parallel sequencing for human identification. Int J Legal Med 127(6):1079–1086
Pakstis AJ, Speed WC, Fang R, Hyland FCL, Furtado MR, Kidd JR, Kidd KK (2010) SNPs for a universal individual identification panel. Hum Genet 127(3):315–324
Ottens R et al (2013) Application of direct PCR in forensic casework. Forensic Sci Int 4(1):e47–e48
McNevin D (2016) Preservation of and DNA Extraction from Muscle Tissue. Methods Mol Biol 1420:43–53
QIAGEN(2014) Investigator Quantiplex HYres Handbook. Version 1:1–16
Amigo J, Salas A, Phillips C, Carracedo Á (2008) SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics 9(1):428
Weir BS, Cockerham C (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Assoc. Inc., Sunderland
Fisher RA (1922) On the interpretation of χ 2 from contingency tables, and the calculation of P. J R Stat Soc 85(1):87–94
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57(1):289–300
Council, N.R (1996) The evaluation of forensic DNA evidence. The National Academies Press, Washington, DC, p 272
Tillmar AO, Phillips C (2017) Evaluation of the impact of genetic linkage in forensic identity and relationship testing for expanded DNA marker sets. Forensic Sci Int Genet 26:58–65
Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N (2014) Evaluation of the ion torrent™ HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 12:144–154
Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C, Sobrino B, Ballard D, Schneider PM, Carracedo Á, Lareu MV, Parson W, Phillips C (2015) Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the ion PGM™. Forensic Sci Int Genet 17:110–121
Sorensen A, Berry C, Bruce D, Gahan ME, Hughes-Stamm S, McNevin D (2016) Direct-to-PCR tissue preservation for DNA profiling. Int J Legal Med 130(3):607–613
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The authors were supported by QIAGEN through their financial and technical contributions to this project.
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This study was partially funded by QIAGEN. N. Jones and I. Petermann are employed by QIAGEN.
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Ethics approval was obtained from the University of Canberra Human Research Ethics Committee (Project Number CEHR 14-70), in accordance with the Helsinki Declaration.
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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed. The Chimpanzee blood sample was donated from the sample collection of the Australian Federal Police (AFP).
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Avent, I., Kinnane, A.G., Jones, N. et al. The QIAGEN 140-locus single-nucleotide polymorphism (SNP) panel for forensic identification using massively parallel sequencing (MPS): an evaluation and a direct-to-PCR trial. Int J Legal Med 133, 677–688 (2019). https://doi.org/10.1007/s00414-018-1975-5
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DOI: https://doi.org/10.1007/s00414-018-1975-5