Evidence map›Paper›PMID 33301893›Full record

ArticleGenomics2021

Sequencing facility and DNA source associated patterns of virus-mappable reads in whole-genome sequencing data.

Xun Chen, Dawei Li

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Xun ChenDepartment of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA.
Dawei LiDepartment of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Department of Computer Science, University of Vermont, Burlington, VT 05405, USA; Neuroscience, Behavior, Health Initiative, University of Vermont, Burlington, VT 05405, USA. Electronic address: dawei.li@uvm.edu.

Funding

Comprehensive analyses of endogenous retroviruses with severe chronic fatigue syndromeR03AI147084 · NIAID · UNIVERSITY OF VERMONT & ST AGRIC COLLEGE · PI LI, DAWEI · 2019 to 2020
$152k
NIAID NIH HHS R03 AI147084
6 · The paper itself

Abstract

Numerous viral sequences have been reported in the whole-genome sequencing (WGS) data of human blood. However, it is not clear to what degree the virus-mappable reads represent true viral sequences rather than random-mapping or noise originating from sample preparation, sequencing processes, or other sources. Identification of patterns of virus-mappable reads may generate novel indicators for evaluating the origins of these viral sequences. We characterized paired-end unmapped reads and reads aligned to viral references in human WGS datasets, then compared patterns of the virus-mappable reads among DNA sources and sequencing facilities which produced these datasets. We then examined potential origins of the source- and facility-associated viral reads. The proportions of clean unmapped reads among the seven sequencing facilities were significantly different (P < 2 × 10

Indexed as

Genes, ViralGenome, HumanBloodClinical Laboratory ServicesDNA ContaminationHumansMetagenomeSignal-To-Noise RatioViromeWhole Genome SequencingBatch effectHigh-throughput sequencingHuman viromeUnmapped reads

Identifiers

PMID33301893
PMCPMC7856238

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.