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Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples
Swedish National Forensic Centre, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden.
Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.
Swedish National Forensic Centre, Linköping, Sweden.
Swedish National Forensic Centre, Linköping, Sweden.
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2017 (English)In: Forensic Science International: Genetics Supplement Series, ISSN 1875-1768, E-ISSN 1875-175X, Vol. 6, p. e267-e269Article in journal (Refereed) Published
Abstract [en]

Massive parallel sequencing (MPS) is increasingly used for human identification purposes in forensic DNA laboratories. Forensic DNA samples are by nature heterogeneous and of varying quality, both concerning DNA integrity and matrices, creating a need for assays that can handle low amounts of DNA as well as impurities. Commercial short tandem repeat (STR) analysis kits for capillary electrophoresis-based separation have evolved drastically over the past years to handle low-template samples and high amounts of various PCR inhibitors. If MPS is to be used extensively in forensic laboratories there is a need to ascertain a similar performance. We have evaluated the GeneRead Individual Identity SNP panel (Qiagen) that includes 140 SNP markers, following the GeneRead DNAseq Targeted Panels V2 handbook for library preparation, applying low levels of DNA and relevant impurities. Analysis of down to 0.1 ng DNA generated SNP profiles with at least 85% called SNPs, after increasing the number of PCR cycles in the initial PCR from 20 to 24. The SNP assay handled extracts from four different DNA extraction methods, including Chelex with blood and saliva, without detrimental effects. Further, the assay was shown to tolerate relevant amounts of inhibitor solutions from soil, cigarettes, snuff and chewing gum. In conclusion, the performance of the SNP panel was satisfactory for casework-like samples. © 2017 Elsevier B.V.

Place, publisher, year, edition, pages
Elsevier, 2017. Vol. 6, p. e267-e269
Keywords [en]
Forensic DNA analysis; Human identification; Massive parallel sequencing; Next generation sequencing; Single nucleotide polymorphism
National Category
Analytical Chemistry
Identifiers
URN: urn:nbn:se:liu:diva-146972DOI: 10.1016/j.fsigss.2017.09.088Scopus ID: 2-s2.0-85029660404OAI: oai:DiVA.org:liu-146972DiVA, id: diva2:1196109
Available from: 2018-04-09 Created: 2018-04-09 Last updated: 2018-04-09

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Gréen, HenrikTillmar, Andreas

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Forensic Science International: Genetics Supplement Series
Analytical Chemistry

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