PMID- 35769342
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240119
IS  - 2631-9268 (Electronic)
IS  - 2631-9268 (Linking)
VI  - 4
IP  - 2
DP  - 2022 Jun
TI  - OPUSeq simplifies detection of low-frequency DNA variants and uncovers 
      fragmentase-associated artifacts.
PG  - lqac048
LID - 10.1093/nargab/lqac048 [doi]
LID - lqac048
AB  - Detection of low-frequency DNA variants (below 1%) is becoming increasingly 
      important in biomedical research and clinical practice, but is challenging to do 
      with standard sequencing approaches due to high error rates. The use of 
      double-stranded unique molecular identifiers (dsUMIs) allows correction of errors 
      by comparing reads arising from the same original DNA duplex. However, the 
      implementation of such approaches is still challenging. Here, we present a novel 
      method, one-pot dsUMI sequencing (OPUSeq), which allows incorporation of dsUMIs 
      in the same reaction as the library PCR. This obviates the need for adapter 
      pre-synthesis or additional enzymatic steps. OPUSeq can be incorporated into 
      standard DNA library preparation approaches and coupled with hybridization target 
      capture. We demonstrate successful error correction and detection of variants 
      down to allele frequency of 0.01%. Using OPUSeq, we also show that the use of 
      enzymatic fragmentation can lead to the appearance of spurious double-stranded 
      variants, interfering with detection of variant fractions below 0.1%.
CI  - (c) The Author(s) 2022. Published by Oxford University Press on behalf of NAR 
      Genomics and Bioinformatics.
FAU - Alekseenko, Alisa
AU  - Alekseenko A
AUID- ORCID: 0000-0002-4269-4894
AD  - SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska 
      Institutet, Tomtebodavagen 23A, 17165, Solna, Sweden.
FAU - Wang, Jingwen
AU  - Wang J
AUID- ORCID: 0000-0001-9688-8793
AD  - SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska 
      Institutet, Tomtebodavagen 23A, 17165, Solna, Sweden.
FAU - Barrett, Donal
AU  - Barrett D
AUID- ORCID: 0000-0001-5381-5391
AD  - SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska 
      Institutet, Tomtebodavagen 23A, 17165, Solna, Sweden.
FAU - Pelechano, Vicent
AU  - Pelechano V
AUID- ORCID: 0000-0002-9415-788X
AD  - SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska 
      Institutet, Tomtebodavagen 23A, 17165, Solna, Sweden.
LA  - eng
PT  - Journal Article
DEP - 20220627
PL  - England
TA  - NAR Genom Bioinform
JT  - NAR genomics and bioinformatics
JID - 101756213
PMC - PMC9235115
EDAT- 2022/07/01 06:00
MHDA- 2022/07/01 06:01
PMCR- 2022/06/27
CRDT- 2022/06/30 02:32
PHST- 2022/05/26 00:00 [received]
PHST- 2022/06/15 00:00 [accepted]
PHST- 2022/06/30 02:32 [entrez]
PHST- 2022/07/01 06:00 [pubmed]
PHST- 2022/07/01 06:01 [medline]
PHST- 2022/06/27 00:00 [pmc-release]
AID - lqac048 [pii]
AID - 10.1093/nargab/lqac048 [doi]
PST - epublish
SO  - NAR Genom Bioinform. 2022 Jun 27;4(2):lqac048. doi: 10.1093/nargab/lqac048. 
      eCollection 2022 Jun.