Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq.

Mehta, B; Daniel, R; Phillips, C; Doyle, S; Elvidge, G; McNevin, D

Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq.

Mehta, B Daniel, R Phillips, C Doyle, S Elvidge, G McNevin, D

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Publisher:: WILEY
Publication Type:: Journal Article
Citation:: Electrophoresis, 2016, 37, (21), pp. 2832-2840
Issue Date:: 2016-10

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Field	Value	Language
dc.contributor.author	Mehta, B
dc.contributor.author	Daniel, R
dc.contributor.author	Phillips, C
dc.contributor.author	Doyle, S
dc.contributor.author	Elvidge, G
dc.contributor.author	McNevin, D https://orcid.org/0000-0003-1665-3367
dc.date.accessioned	2022-01-31T22:28:13Z
dc.date.available	2016-08-23
dc.date.available	2022-01-31T22:28:13Z
dc.date.issued	2016-10
dc.identifier.citation	Electrophoresis, 2016, 37, (21), pp. 2832-2840
dc.identifier.issn	0173-0835
dc.identifier.issn	1522-2683
dc.identifier.uri	http://hdl.handle.net/10453/153998
dc.description.abstract	Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.
dc.format	Print
dc.language	eng
dc.publisher	WILEY
dc.relation	http://purl.org/au-research/grants/arc/LP110100121
dc.relation.ispartof	Electrophoresis
dc.relation.isbasedon	10.1002/elps.201600190
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	0301 Analytical Chemistry, 0601 Biochemistry and Cell Biology, 0904 Chemical Engineering
dc.subject.classification	Analytical Chemistry
dc.subject.mesh	DNA
dc.subject.mesh	Female
dc.subject.mesh	Forensic Genetics
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.subject.mesh	Humans
dc.subject.mesh	Humic Substances
dc.subject.mesh	Male
dc.subject.mesh	Polymerase Chain Reaction
dc.subject.mesh	Polymorphism, Single Nucleotide
dc.subject.mesh	Reproducibility of Results
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Humans
dc.subject.mesh	Humic Substances
dc.subject.mesh	DNA
dc.subject.mesh	Reproducibility of Results
dc.subject.mesh	Polymerase Chain Reaction
dc.subject.mesh	Sequence Analysis, DNA
dc.subject.mesh	Polymorphism, Single Nucleotide
dc.subject.mesh	Female
dc.subject.mesh	Male
dc.subject.mesh	Forensic Genetics
dc.subject.mesh	High-Throughput Nucleotide Sequencing
dc.title	Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq.
dc.type	Journal Article
utslib.citation.volume	37
utslib.location.activity	Germany
utslib.for	0301 Analytical Chemistry
utslib.for	0601 Biochemistry and Cell Biology
utslib.for	0904 Chemical Engineering
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - CFS - Centre for Forensic Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
utslib.copyright.status	open_access	*
dc.date.updated	2022-01-31T22:28:12Z
pubs.issue	21
pubs.publication-status	Published
pubs.volume	37
utslib.citation.issue	21

Abstract:

Forensic DNA-based intelligence, or forensic DNA phenotyping, utilises SNPs to infer the biogeographical ancestry and externally visible characteristics of the donor of evidential material. SNaPshot® is a commonly employed forensic SNP genotyping technique, which is limited to multiplexes of 30-40 SNPs in a single reaction and prone to PCR contamination. Massively parallel sequencing has the ability to genotype hundreds of SNPs in multiple samples simultaneously by employing an oligonucleotide sample barcoding strategy. This study of the Illumina MiSeq massively parallel sequencing platform analysed 136 unique SNPs in 48 samples from SNaPshot PCR amplicons generated by five established forensic DNA phenotyping assays comprising the SNPforID 52-plex, SNPforID 34-plex, Eurasiaplex, Pacifiplex and IrisPlex. Approximately 3 GB of sequence data were generated from two MiSeq flow cells and profiles were obtained from just 0.25 ng of DNA. Compared with SNaPshot, an average 98% genotyping concordance was achieved. Our customised approach was successful in attaining SNP profiles from extremely degraded, inhibited, and compromised casework samples. Heterozygote imbalance and sequence coverage in negative controls highlight the need to establish baseline sequence coverage thresholds and refine allele frequency thresholds. This study demonstrates the potential of the MiSeq for forensic SNP analysis.

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http://hdl.handle.net/10453/153998