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

Avent, I; Kinnane, AG; Jones, N; Petermann, I; Daniel, R; Gahan, ME; McNevin, D

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

Avent, I Kinnane, AG Jones, N Petermann, I Daniel, R Gahan, ME McNevin, D

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Publication Type:: Journal Article
Citation:: International Journal of Legal Medicine, 2019, 133 (3), pp. 677 - 688
Issue Date:: 2019-05-01

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Field	Value	Language
dc.contributor.author	Avent, I	en_US
dc.contributor.author	Kinnane, AG	en_US
dc.contributor.author	Jones, N	en_US
dc.contributor.author	Petermann, I	en_US
dc.contributor.author	Daniel, R	en_US
dc.contributor.author	Gahan, ME	en_US
dc.contributor.author	McNevin, D https://orcid.org/0000-0003-1665-3367	en_US
dc.date.available	2018-11-23	en_US
dc.date.issued	2019-05-01	en_US
dc.identifier.citation	International Journal of Legal Medicine, 2019, 133 (3), pp. 677 - 688	en_US
dc.identifier.issn	0937-9827	en_US
dc.identifier.uri	http://hdl.handle.net/10453/131090
dc.description.abstract	© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. 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.	en_US
dc.relation.ispartof	International Journal of Legal Medicine	en_US
dc.relation.isbasedon	10.1007/s00414-018-1975-5	en_US
dc.subject.classification	Legal & Forensic Medicine	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Sensitivity and Specificity	en_US
dc.subject.mesh	Polymerase Chain Reaction	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Species Specificity	en_US
dc.subject.mesh	Gene Frequency	en_US
dc.subject.mesh	Genotype	en_US
dc.subject.mesh	Linkage Disequilibrium	en_US
dc.subject.mesh	Polymorphism, Single Nucleotide	en_US
dc.subject.mesh	Continental Population Groups	en_US
dc.subject.mesh	Ethnic Groups	en_US
dc.subject.mesh	High-Throughput Nucleotide Sequencing	en_US
dc.title	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	en_US
dc.type	Journal Article
utslib.citation.volume	3	en_US
utslib.citation.volume	133	en_US
utslib.for	0399 Other Chemical Sciences	en_US
utslib.for	0699 Other Biological Sciences	en_US
utslib.for	1103 Clinical Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
pubs.organisational-group	/University of Technology Sydney/Strength - CFS - Centre for Forensic Science
utslib.copyright.status	closed_access
pubs.issue	3	en_US
pubs.publication-status	Published	en_US
pubs.volume	133	en_US

Abstract:

© 2018, Springer-Verlag GmbH Germany, part of Springer Nature. 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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http://hdl.handle.net/10453/131090