PMID- 33043294
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20210914
IS  - 2631-9268 (Electronic)
IS  - 2631-9268 (Linking)
VI  - 2
IP  - 4
DP  - 2020 Dec
TI  - Characterization and mitigation of fragmentation enzyme-induced dual stranded 
      artifacts.
PG  - lqaa070
LID - 10.1093/nargab/lqaa070 [doi]
LID - lqaa070
AB  - High-throughput short-read sequencing relies on fragmented DNA for optimal sampling 
      of input nucleic acid. Several vendors now offer proprietary enzyme cocktails as a 
      cheaper and more streamlined method of fragmentation when compared to acoustic 
      shearing. We have discovered that these enzymes induce the formation of library 
      molecules containing regions of nearby DNA from opposite strands. Sequencing reads 
      derived from these molecules can lead to artifact-derived variant calls appearing at 
      variant allele frequencies <5%. We present Fragmentation Artifact Detection and 
      Elimination (FADE), software to remove these artifacts from mapped reads and 
      mitigate artifact-related effects on downstream analysis. We find that the artifacts 
      principally affect downstream analyses that are sensitive to a 1-3% artifact bias in 
      the sequencing reads, such as targeted resequencing and rare variant discovery.
CI  - © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics 
      and Bioinformatics.
FAU - Gregory, Thomas
AU  - Gregory T
AUID- ORCID: 0000-0001-9357-369X
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Ngankeu, Apollinaire
AU  - Ngankeu A
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Orwick, Shelley
AU  - Orwick S
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Kautto, Esko A
AU  - Kautto EA
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Woyach, Jennifer A
AU  - Woyach JA
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Byrd, John C
AU  - Byrd JC
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
FAU - Blachly, James S
AU  - Blachly JS
AUID- ORCID: 0000-0002-4275-5562
AD  - Division of Hematology, Ohio State University, Columbus, OH 43210, USA.
LA  - eng
GR  - R01 CA183444/CA/NCI NIH HHS/United States
GR  - R35 CA197734/CA/NCI NIH HHS/United States
GR  - T32 GM068412/GM/NIGMS NIH HHS/United States
PT  - Journal Article
DEP - 20201002
TA  - NAR Genom Bioinform
JT  - NAR genomics and bioinformatics
JID - 101756213
PMC - PMC7531576
EDAT- 2020/10/13 06:00
MHDA- 2020/10/13 06:01
CRDT- 2020/10/12 05:34
PHST- 2020/01/30 00:00 [received]
PHST- 2020/07/27 00:00 [revised]
PHST- 2020/09/22 00:00 [accepted]
PHST- 2020/10/12 05:34 [entrez]
PHST- 2020/10/13 06:00 [pubmed]
PHST- 2020/10/13 06:01 [medline]
AID - lqaa070 [pii]
AID - 10.1093/nargab/lqaa070 [doi]
PST - ppublish
SO  - NAR Genom Bioinform. 2020 Dec;2(4):lqaa070. doi: 10.1093/nargab/lqaa070. Epub 2020 
      Oct 2.