International Journal of Legal Medicine

, Volume 133, Issue 3, pp 677–688 | Cite as

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


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.


MPS Forensic Identity SNP DNAseq panel Direct-to-PCR 


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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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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