Evidence map›Paper›PMID 36974726›Full record

ArticlePersonalized medicine2023

SARS-CoV-2 variant identification using a genome tiling array and genotyping probes.

Ryota Shimada, Emily N Alden, Kendall Hoff, Xun Ding, Jiayi Sun, Adam M Halasz, Wei Zhou, Jeremy S Edwards

Abstract read
In one paragraph

Article in Personalized medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Ryota ShimadaDepartment of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
Emily N AldenDepartment of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.
Kendall HoffCentrillion Technologies, Palo Alto, CA 94303, USA.
Xun DingCentrillion Technologies, Palo Alto, CA 94303, USA.
Jiayi SunCentrillion Technologies, Palo Alto, CA 94303, USA.
Adam M HalaszDepartment of Mathematics, West Virginia University, Morgantown, WV 26506, USA.
Wei ZhouCentrillion Technologies, Palo Alto, CA 94303, USA.
Jeremy S EdwardsDepartment of Chemistry & Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.ORCID 0000-0003-3694-3716

Funding

NM-INBRE Sequencing and Bioinformatics CoreP20GM103451 · NIGMS · NEW MEXICO STATE UNIVERSITY LAS CRUCES · PI Charlotte C. Gard · 2012 to 2026
$61.2M
WOMEN'S CANCERS RESEARCH PROGRAMP30CA118100 · NCI · UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR · PI Yolanda Sanchez · 2005 to 2026
$57.1M
NCI NIH HHS P30 CA118100NIGMS NIH HHS P20 GM103451
6 · The paper itself

Abstract

With over 5.5 million deaths worldwide attributed to the respiratory disease COVID-19 caused by the novel coronavirus SARS-CoV-2, it is essential that continued efforts be made to track the evolution and spread of the virus globally. The authors previously presented a rapid and cost-effective method to sequence the entire SARS-CoV-2 genome with 95% coverage and 99.9% accuracy. This method is advantageous for identifying and tracking variants in the SARS-CoV-2 genome compared with traditional short-read sequencing methods which can be time-consuming and costly. Herein, the addition of genotyping probes to a DNA chip that targets known SARS-CoV-2 variants is presented. The incorporation of genotyping probe sets along with the advent of a moving average filter improved the sequencing coverage and accuracy of the SARS-CoV-2 genome.

Indexed as

COVID-19SARS-CoV-2Genome, ViralGenotypeHumansbioinformaticsCOVID-19genotypingpandemicSARS-CoV-2screeningsequencingtiling-arrayviral genome

Identifiers

PMID36974726
PMCPMC10350312

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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.