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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

  • I. Avent
  • A. G. Kinnane
  • N. Jones
  • I. Petermann
  • R. Daniel
  • M. E. Gahan
  • D. McNevin
Original Article

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.

Keywords

MPS Forensic Identity SNP DNAseq panel Direct-to-PCR 

Notes

Funding information

The authors were supported by QIAGEN through their financial and technical contributions to this project.

Compliance with ethical standards

Conflict of interest

This study was partially funded by QIAGEN. N. Jones and I. Petermann are employed by QIAGEN.

Research involving human participants

Ethics approval was obtained from the University of Canberra Human Research Ethics Committee (Project Number CEHR 14-70), in accordance with the Helsinki Declaration.

Research involving animal participants

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).

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

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References

  1. 1.
    Budowle B, Van Daal A (2008) Forensically relevant SNP classes. BioTechniques 44(5):603–610CrossRefGoogle Scholar
  2. 2.
    Butler JM, Coble MD, Vallone PM (2007) STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol 3(3):200–205CrossRefGoogle Scholar
  3. 3.
    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 14:50–60CrossRefGoogle Scholar
  4. 4.
    Kidd KK et al (2015) Genetic markers for massively parallel sequencing in forensics. Forensic Sci Int 5:e677–e679Google Scholar
  5. 5.
    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):368–378CrossRefGoogle Scholar
  6. 6.
    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):273–280CrossRefGoogle Scholar
  7. 7.
    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):1713–1724CrossRefGoogle Scholar
  8. 8.
    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):2832–2840CrossRefGoogle Scholar
  9. 9.
    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):905–914CrossRefGoogle Scholar
  10. 10.
    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 28:35–43CrossRefGoogle Scholar
  11. 11.
    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 11:13–25CrossRefGoogle Scholar
  12. 12.
    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):1581–1594CrossRefGoogle Scholar
  13. 13.
    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):1079–1086CrossRefGoogle Scholar
  14. 14.
    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):315–324CrossRefGoogle Scholar
  15. 15.
    Ottens R et al (2013) Application of direct PCR in forensic casework. Forensic Sci Int 4(1):e47–e48Google Scholar
  16. 16.
    McNevin D (2016) Preservation of and DNA Extraction from Muscle Tissue. Methods Mol Biol 1420:43–53Google Scholar
  17. 17.
    QIAGEN(2014) Investigator Quantiplex HYres Handbook. Version 1:1–16Google Scholar
  18. 18.
    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):428CrossRefGoogle Scholar
  19. 19.
    Weir BS, Cockerham C (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Assoc. Inc., SunderlandGoogle Scholar
  20. 20.
    Fisher RA (1922) On the interpretation of χ 2 from contingency tables, and the calculation of P. J R Stat Soc 85(1):87–94CrossRefGoogle Scholar
  21. 21.
    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):289–300Google Scholar
  22. 22.
    Council, N.R (1996) The evaluation of forensic DNA evidence. The National Academies Press, Washington, DC, p 272Google Scholar
  23. 23.
    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 26:58–65CrossRefGoogle Scholar
  24. 24.
    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 12:144–154CrossRefGoogle Scholar
  25. 25.
    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 17:110–121CrossRefGoogle Scholar
  26. 26.
    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):607–613CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.National Centre for Forensic Studies, Faculty of Science & TechnologyUniversity of CanberraCanberraAustralia
  2. 2.QIAGEN Pty Ltd, Chadstone CentreChadstoneAustralia
  3. 3.Office of the Chief Forensic Scientist, Victoria Police Forensic Services DepartmentMacleodAustralia
  4. 4.Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of ScienceUniversity of Technology SydneySydneyAustralia

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