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Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity

Staadig, Adam ; Hedman, Johannes LU and Tillmar, Andreas (2023) In Genes 14(4).
Abstract

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main... (More)

One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (>99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs.

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author
; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
forensic genetics, kinship, massively parallel sequencing, single nucleotide polymorphism, UMI, unique molecular indices
in
Genes
volume
14
issue
4
article number
818
publisher
MDPI AG
external identifiers
  • pmid:37107576
  • scopus:85154559422
ISSN
2073-4425
DOI
10.3390/genes14040818
language
English
LU publication?
yes
id
7e3a97fd-a625-4a46-8c82-64b41fcf4975
date added to LUP
2023-09-20 16:04:42
date last changed
2024-04-19 02:14:30
@article{7e3a97fd-a625-4a46-8c82-64b41fcf4975,
  abstract     = {{<p>One of the major challenges in forensic genetics is being able to detect very small amounts of DNA. Massively parallel sequencing (MPS) enables sensitive detection; however, genotype errors may exist and could interfere with the interpretation. Common errors in MPS-based analysis are often induced during PCR or sequencing. Unique molecular indices (UMIs) are short random nucleotide sequences ligated to each template molecule prior to amplification. Applying UMIs can improve the limit of detection by enabling accurate counting of initial template molecules and removal of erroneous data. In this study, we applied the FORCE panel, which includes ~5500 SNPs, with a QIAseq Targeted DNA Custom Panel (Qiagen), including UMIs. Our main objective was to investigate whether UMIs can enhance the sensitivity and accuracy of forensic genotyping and to evaluate the overall assay performance. We analyzed the data both with and without the UMI information, and the results showed that both genotype accuracy and sensitivity were improved when applying UMIs. The results showed very high genotype accuracies (&gt;99%) for both reference DNA and challenging samples, down to 125 pg. To conclude, we show successful assay performance for several forensic applications and improvements in forensic genotyping when applying UMIs.</p>}},
  author       = {{Staadig, Adam and Hedman, Johannes and Tillmar, Andreas}},
  issn         = {{2073-4425}},
  keywords     = {{forensic genetics; kinship; massively parallel sequencing; single nucleotide polymorphism; UMI; unique molecular indices}},
  language     = {{eng}},
  number       = {{4}},
  publisher    = {{MDPI AG}},
  series       = {{Genes}},
  title        = {{Applying Unique Molecular Indices with an Extensive All-in-One Forensic SNP Panel for Improved Genotype Accuracy and Sensitivity}},
  url          = {{http://dx.doi.org/10.3390/genes14040818}},
  doi          = {{10.3390/genes14040818}},
  volume       = {{14}},
  year         = {{2023}},
}