Evidence map›Paper›PMID 36569460›Full record

ArticleAnimal genetics2022

Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants.

Nathan A Kinsey, Janelle M Belanger, Dog Biomedical Variant Database Consortium, Anita M Oberbauer

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Animal genetics, 2022. 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. Review of Molecular Technologies for Investigating Canine Cancer.Animals : an open access journal from MDPI · 2024
    Review
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

4 authors.

Nathan A KinseyDepartment of Animal Science, University of California, Davis, USA.ORCID 0000-0003-2789-1299
Janelle M BelangerDepartment of Animal Science, University of California, Davis, USA.
Dog Biomedical Variant Database Consortium
Anita M OberbauerDepartment of Animal Science, University of California, Davis, USA.

Funding

The role of zinc transporters and dietary zinc in calcium oxalate urolithiasisK01OD019912 · OD · UNIVERSITY OF MINNESOTA · PI FURROW, EVA · 2015 to 2021
$760k
Novel Genetic Models for Vertebral AbnormalitiesK01OD027051 · OD · PURDUE UNIVERSITY · PI EKENSTEDT, KARI J · 2019 to 2023
$627k
NIH HHS K01 OD019912NIH HHS K01 OD027051
6 · The paper itself

Abstract

Deficient homozygosity of a variant maintained in a population suggests that the variant may be embryonic lethal. We examined whole genome sequence data from 675 canids to investigate for variants with missing homozygosity and high predicted impact. Our analysis identified 45 variants, in 32 genes. However, further scrutiny of the sequence reads revealed that all but one of these variants were artifacts of the variant calling process when using CanFam3.1, a widely utilized canine reference genome. We demonstrate that the use of multiple, newer reference genomes could reduce artifacts and lead to more accurate variant identification.

Indexed as

GenomeHigh-Throughput Nucleotide SequencingAnimalsDogsHomozygoteSequence Analysis, DNASoftwareWhole Genome Sequencingbioinformaticscanis lupus familiarisgenomicslethal recessivesequence mappingwhole genome sequencing

Identifiers

PMID36569460
PMCPMC9784012

What Socratic holds

Textmetadata
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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 Socratic graph.