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

Bhavik MEHTA, Runa Daniel, C. Phillips, Stephen Doyle, Gareth Elvidge, Dennis MCNEVIN

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)2832-2840
Number of pages9
JournalElectrophoresis
Volume37
Issue number21
DOIs
Publication statusPublished - 2016

Fingerprint

High-Throughput Nucleotide Sequencing
Single Nucleotide Polymorphism
DNA
Oligonucleotides
Genotyping Techniques
Assays
Contamination
Polymerase Chain Reaction
Aptitude
Heterozygote
Intelligence
Gene Frequency
Genotype

Cite this

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), 2832-2840. https://doi.org/10.1002/elps.201600190
MEHTA, Bhavik ; Daniel, Runa ; Phillips, C. ; Doyle, Stephen ; Elvidge, Gareth ; MCNEVIN, Dennis. / Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. In: Electrophoresis. 2016 ; Vol. 37, No. 21. pp. 2832-2840.
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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{\circledR} 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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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, vol. 37, no. 21, pp. 2832-2840. https://doi.org/10.1002/elps.201600190

Massively parallel sequencing of customised forensically informative SNP panels on the MiSeq. / MEHTA, Bhavik; Daniel, Runa; Phillips, C.; Doyle, Stephen; Elvidge, Gareth; MCNEVIN, Dennis.

In: Electrophoresis, Vol. 37, No. 21, 2016, p. 2832-2840.

Research output: Contribution to journalArticle

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AU - MCNEVIN, Dennis

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