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Ultrasensitive sequ...
Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method
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- Sidstedt, Maja (författare)
- Swedish National Forensic Center,National Forensic Centre, Sweden
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- Gynnå, Arvid H. (författare)
- Swedish National Forensic Center,National Forensic Centre, Sweden
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- Kiesler, Kevin M. (författare)
- National Institute of Standards and Technology (NIST),NIST, USA
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- Jansson, Linda (författare)
- Lund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Swedish National Forensic Center,National Forensic Centre, Sweden; Lund University, Sweden
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- Steffen, Carolyn R. (författare)
- National Institute of Standards and Technology (NIST),NIST, USA
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- Håkansson, Joakim, 1975 (författare)
- RISE,Gothenburg University,Göteborgs universitet,University of Gothenburg,Research Institutes of Sweden (RISE),Institutionen för kemi och molekylärbiologi,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Department of Chemistry and Molecular Biology,Department of Laboratory Medicine,Metodik, textil och medicinteknik,University of Gothenburg, Sweden
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- Johansson, Gustav (författare)
- SIMSEN Diagnostics, Sweden
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- Österlund, Tobias, 1984 (författare)
- Gothenburg University,Göteborgs universitet,University of Gothenburg,University of Gothenburg, Sweden; Sahlgrenska University Hospital, Sweden,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Sahlgrenska Centrum för Cancerforskning (SCCR),Wallenberg Centre for Molecular and Translational Medicine,Department of Laboratory Medicine,Sahlgrenska Center for Cancer Research (SCCR)
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- Bogestål, Yalda (författare)
- RISE,Metodik, textil och medicinteknik
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- Tillmar, Andreas (författare)
- Swedish National Board of Forensic Medicine, Linköping,National Board of Forensic Medicine, Sweden
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- Rådström, Peter (författare)
- Lund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Lund University, Sweden
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- Ståhlberg, Anders, 1975 (författare)
- Gothenburg University,Göteborgs universitet,University of Gothenburg,University of Gothenburg, Sweden;Sahlgrenska University Hospital, Sweden,Sahlgrenska Academy,Institutionen för biomedicin, avdelningen för laboratoriemedicin,Wallenberg Centre for Molecular and Translational Medicine,Sahlgrenska Centrum för Cancerforskning (SCCR),Department of Laboratory Medicine,Sahlgrenska Center for Cancer Research (SCCR)
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- Vallone, Peter M. (författare)
- National Institute of Standards and Technology (NIST),NIST, USA
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- Hedman, Johannes (författare)
- Lund University,Lunds universitet,Teknisk mikrobiologi,Centrum för tillämpade biovetenskaper,Kemiska institutionen,Institutioner vid LTH,Lunds Tekniska Högskola,Applied Microbiology,Center for Applied Life Sciences,Department of Chemistry,Departments at LTH,Faculty of Engineering, LTH,Swedish National Forensic Center,National Forensic Centre, Sweden; Lund University, Sweden
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(creator_code:org_t)
- Elsevier Ireland Ltd, 2024
- 2024
- Engelska.
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Ingår i: Forensic Science International: Genetics. - : Elsevier Ireland Ltd. - 1872-4973 .- 1878-0326. ; 71
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://doi.org/10.1...
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https://ri.diva-port... (primary) (Raw object)
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https://lup.lub.lu.s...
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https://doi.org/10.1...
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https://gup.ub.gu.se...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1–15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Annan medicin och hälsovetenskap -- Rättsmedicin (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Other Medical and Health Sciences -- Forensic Science (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Forensic DNA
- Machine learning
- Massively parallel sequencing
- Short tandem repeats
- Targeted PCR
- UMI
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
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Sidstedt, Maja
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Gynnå, Arvid H.
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Kiesler, Kevin M ...
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Jansson, Linda
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Steffen, Carolyn ...
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Håkansson, Joaki ...
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visa fler...
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Johansson, Gusta ...
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Österlund, Tobia ...
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Bogestål, Yalda
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Tillmar, Andreas
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Rådström, Peter
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Ståhlberg, Ander ...
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Vallone, Peter M ...
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Hedman, Johannes
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- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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och Genetik
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Annan medicin oc ...
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och Rättsmedicin
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Medicinska och f ...
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och Medicinsk geneti ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Data och informa ...
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och Bioinformatik
- Artiklar i publikationen
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Forensic Science ...
- Av lärosätet
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Lunds universitet
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Göteborgs universitet
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RISE