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Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples

Sidstedt, Maja LU ; Grandell, Ida ; Boiso, Samuel ; Sanga, Malin ; Green, Henrik ; Hedman, Johannes LU and Tillmar, Andreas (2017) In Forensic Science International: Genetics Supplement Series 6. p.267-269
Abstract

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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Forensic DNA analysis, Human identification, Massive parallel sequencing, Next generation sequencing, Single nucleotide polymorphism
in
Forensic Science International: Genetics Supplement Series
volume
6
pages
267 - 269
publisher
Elsevier
external identifiers
  • scopus:85029660404
ISSN
1875-1768
DOI
10.1016/j.fsigss.2017.09.088
language
English
LU publication?
yes
id
1f353650-9de7-4111-91eb-9168cad5c5e5
date added to LUP
2018-01-25 07:14:55
date last changed
2022-04-25 05:17:31
@article{1f353650-9de7-4111-91eb-9168cad5c5e5,
  abstract     = {{<p>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.</p>}},
  author       = {{Sidstedt, Maja and Grandell, Ida and Boiso, Samuel and Sanga, Malin and Green, Henrik and Hedman, Johannes and Tillmar, Andreas}},
  issn         = {{1875-1768}},
  keywords     = {{Forensic DNA analysis; Human identification; Massive parallel sequencing; Next generation sequencing; Single nucleotide polymorphism}},
  language     = {{eng}},
  month        = {{12}},
  pages        = {{267--269}},
  publisher    = {{Elsevier}},
  series       = {{Forensic Science International: Genetics Supplement Series}},
  title        = {{Assessing the GeneRead SNP panel for analysis of low-template and PCR-inhibitory samples}},
  url          = {{http://dx.doi.org/10.1016/j.fsigss.2017.09.088}},
  doi          = {{10.1016/j.fsigss.2017.09.088}},
  volume       = {{6}},
  year         = {{2017}},
}