ArticleNAR genomics and bioinformatics2020
Characterization and mitigation of fragmentation enzyme-induced dual stranded artifacts.
Article in NAR genomics and bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 22 citations in OpenAlex.
- Comparative metagenomic assessment of Illumina-compatible library preparation methods, short-read lengths, and PacBio HiFi sequencing reveals differences in microbial and functional diversity recovery from a complex environmental sample.Microbiology spectrum · 2026Article
- 96 sample parallel acoustic fragmentation for high throughput next generation sequencing library preparation.PloS one · 2026Article
- Stable clonal contribution of lineage-restricted stem cells to human hematopoiesis.Nature genetics · 2025Article
- Replication stress induces POLQ-mediated structural variant formation throughout common fragile sites after entry into mitosis.Nature communications · 2024Article
- Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome.BMC genomics · 2024Article
- A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.Nature cancer · 2023Article
- Validation of genetic variants from NGS data using deep convolutional neural networks.BMC bioinformatics · 2023Article
- CRISPR-KRISPR: a method to identify on-target and random insertion of donor DNAs and their characterization in knock-in mice.Genome biology · 2022Article
- OPUSeq simplifies detection of low-frequency DNA variants and uncovers fragmentase-associated artifacts.NAR genomics and bioinformatics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
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.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.