Evidence map›Paper›PMID 34845444›Full record

ArticlebioRxiv : the preprint server for biology2021

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.

Omary Mzava, Alexandre Pellan Cheng, Adrienne Chang, Sami Smalling, Liz-Audrey Djomnang Kounatse, Joan Lenz, Randy Longman, Amy Steadman, Mirella Salvatore, Manikkam Suthanthiran and 4 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors at 3 institutions in 1 country.

Omary MzavaNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Alexandre Pellan ChengNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Adrienne ChangNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Sami SmallingNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Liz-Audrey Djomnang KounatseNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Joan LenzNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Randy LongmanJill Roberts Center for IBD, Weill Cornell Medicine, Division of Gastroenterology and Hepatology, New York, NY, USA.
Amy SteadmanGlobal Health Labs, Bellevue, WA, USA.
Mirella SalvatoreDivision of Public Health Programs, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.
Manikkam SuthanthiranDivision of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
John R LeeDivision of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
Christopher E MasonDepartment of Physiology and Biophysics, Weill Cornell Medical College, New York City, NY, USA.
Darshana DadhaniaDivision of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
Iwijn De VlaminckNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Cornell University · USNewYork–Presbyterian Hospital · USBellevue Hospital Center · US

Funding

TRAINING IN MOLECULAR PHYSICS OF BIOLOGICAL SYSTEMST32GM008267 · NIGMS · CORNELL UNIVERSITY ITHACA · PI WANG, MICHELLE D. · 1988 to 2021
$9.6M
Biomolecular Markers for Safe Minimization of ImmunosuppressionR37AI051652 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI SUTHANTHIRAN, MANIKKAM · 2009 to 2021
$4.7M
Epigenetic Profiling of circulating cell-free DNA for the Monitoring of Graft-Versus-Host Disease after Hematopoietic Cell TransplantationR01AI146165 · NIAID · CORNELL UNIVERSITY · PI DE VLAMINCK, IWIJN, RITZ, JEROME · 2020 to 2024
$3.4M
Metagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantationR01AI151059 · NIAID · CORNELL UNIVERSITY · PI DADHANIA, DARSHANA, DE VLAMINCK, IWIJN · 2020 to 2024
$3.4M
Precision monitoring of kidney transplants via single-cell and single-molecule sequencingDP2AI138242 · NIAID · CORNELL UNIVERSITY · PI DE VLAMINCK, IWIJN · 2017 to 2017
$2.3M
Host-Pathogen Interactions From Measurements of Urinary Cell Free DNA in Kidney TransplantationR21AI133331 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI DE VLAMINCK, IWIJN, LEE, JOHN RICHARD · 2017 to 2018
$457k
Mitochondrial Cell-Free DNA as a Marker of Rejection and Damage-Associated Molecular Pattern in Organ TransplantationR21AI124237 · NIAID · CORNELL UNIVERSITY · PI DE VLAMINCK, IWIJN · 2016 to 2017
$427k
NIAID NIH HHS DP2 AI138242NIAID NIH HHS R01 AI146165NIAID NIH HHS R01 AI151059NIAID NIH HHS R21 AI124237NIAID NIH HHS R21 AI133331NIAID NIH HHS R37 AI051652NIGMS NIH HHS T32 GM008267
6 · The paper itself

Abstract

Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present contamination-free metagenomic DNA sequencing (Coffee-seq), a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied Coffee-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of inflammatory bowel disease in blood.

Identifiers

PMID34845444
PMCPMC8629186
OpenAlexW3215276240

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.