Evidence map›Paper›PMID 33876458›Full record

ArticleJournal of medical primatology2021

Efficiency of whole-exome sequencing in old world and new world primates using human capture reagents.

Jeannie Chan, Wen Yao, Timothy D Howard, Gregory A Hawkins, Michael Olivier, Matthew J Jorgensen, Ian H Cheeseman, Shelley A Cole, Laura A Cox

Open access · greenAbstract read
In one paragraph

Article in Journal of medical primatology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.0field-weighted citation impact, top 22% of its field
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

5 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. 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

9 authors at 3 institutions in 2 countries.

Jeannie ChanDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.ORCID 0000-0003-4346-2873
Wen YaoCollege of Life Sciences, Henan Agricultural University, Zhengzhou, China.
Timothy D HowardDepartment of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.
Gregory A HawkinsDepartment of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.
Michael OlivierDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
Matthew J JorgensenDepartment of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.
Ian H CheesemanTexas Biomedical Research Institute, San Antonio, TX, USA.
Shelley A ColeTexas Biomedical Research Institute, San Antonio, TX, USA.
Laura A CoxDepartment of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA.ORCID 0000-0002-8836-3783
Wake Forest University · USTexas Biomedical Research Institute · USHenan Agricultural University · CN

Funding

The Southwest National Primate Research Center Supplement- Infrastructure improvements of ABSL2 holding areasP51OD011133 · OD · TEXAS BIOMEDICAL RESEARCH INSTITUTE · PI Larry S. Schlesinger · 2012 to 2026
$129.7M
Wake Forest Clinical and Translational Science AwardUL1TR001420 · NCATS · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI ARD, JAMY D, FOLEY, KRISTIE L · 2015 to 2023
$32.3M
Vervet Research Colony as a Biomedical ResourceP40OD010965 · OD · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI Matthew Jorgensen · 2012 to 2026
$14.6M
Womb to Tomb: Developmental Programming and Aging Interactions in PrimatesU19AG057758 · NIA · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI CLARKE, GEOFFREY DAVID, COX, LAURA A · 2018 to 2024
$13.2M
Development of a pedigreed baboon genome resource for biomedical researchR24OD017859 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COX, LAURA A, WALL, JEFFREY D · 2014 to 2017
$3.2M
NCATS NIH HHS UL1 TR001420NIA NIH HHS U19 AG057758NIH HHS P40 OD010965NIH HHS P51 OD011133NIH HHS R24 OD017859
6 · The paper itself

Abstract

backgroundWhole-exome sequencing (WES) can expedite research on genetic variation in non-human primate (NHP) models of human diseases. However, NHP-specific reagents for exome capture are not available. This study reports the use of human-specific capture reagents in WES for olive baboons, marmosets, and vervet monkeys.

methodsExome capture was carried out using the SureSelect Human All Exon V6 panel from Agilent Technologies, followed by high-throughput sequencing. Capture of protein-coding genes and detection of single nucleotide variants were evaluated.

resultsExome capture and sequencing results showed that more than 97% of old world and 93% of new world monkey protein coding genes were detected. Single nucleotide variants were detected across the genomes and missense variants were found in genes associated with human diseases.

conclusionsA cost-effective approach based on commercial, human-specific reagents can be used to perform WES for the discovery of genetic variants in these NHP species.

Indexed as

ExomeHigh-Throughput Nucleotide SequencingAnimalsChlorocebus aethiopsExome SequencingHumansIndicators and ReagentsPrimatesIndicators and Reagentsexome capturegenetic variantsmarmosetsolive baboonsvervet monkeys

Identifiers

PMID33876458
PMCPMC8407272
OpenAlexW3154856190

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.