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.

Autor: Avent I; National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, ACT, Australia. Isabelle.Avent@canberra.edu.au., Kinnane AG; National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, ACT, Australia., Jones N; QIAGEN Pty Ltd, Chadstone Centre, Chadstone, VIC, Australia., Petermann I; QIAGEN Pty Ltd, Chadstone Centre, Chadstone, VIC, Australia., Daniel R; Office of the Chief Forensic Scientist, Victoria Police Forensic Services Department, Macleod, VIC, Australia., Gahan ME; National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, ACT, Australia., McNevin D; National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, Canberra, ACT, Australia.; Centre for Forensic Science, School of Mathematical & Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
Jazyk: angličtina
Zdroj: International journal of legal medicine [Int J Legal Med] 2019 May; Vol. 133 (3), pp. 677-688. Date of Electronic Publication: 2018 Dec 05.
DOI: 10.1007/s00414-018-1975-5
Abstrakt: 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.
Databáze: MEDLINE
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