Evidence map›Paper›PMID 38260597›Full record

ArticlebioRxiv : the preprint server for biology2024

Pangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery.

Flavia Villani, Andrea Guarracino, Rachel R Ward, Tomomi Green, Madeleine Emms, Michal Pravenec, Pjotr Prins, Erik Garrison, Robert W Williams, Hao Chen and 1 more

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

Article in bioRxiv : the preprint server for biology, 2024. 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, 2 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 3 institutions in 3 countries.

Flavia VillaniDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0003-3633-0610
Andrea GuarracinoDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0001-9744-131X
Rachel R WardDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center.ORCID 0009-0009-4842-4885
Tomomi GreenDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center.ORCID 0009-0008-1860-7341
Madeleine EmmsInstitute of Genetics and Biophysics, National Research Council, Naples, 80111, Italy.ORCID 0000-0002-1850-9919
Michal PravenecInstitute of Physiology, Czech Academy of Sciences, 14200 Prague, Czech Republic.ORCID 0000-0001-9197-5871
Pjotr PrinsDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0002-8021-9162
Erik GarrisonDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0003-3821-631X
Robert W WilliamsDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0001-8924-4447
Hao ChenDepartment of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center.ORCID 0000-0002-2680-6921
Vincenza ColonnaDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID 0000-0002-3966-0474
University of Tennessee Health Science Center · USCzech Academy of Sciences · CZInstitute of Genetics and Biophysics · IT

Funding

System genetics of menthol and nicotine addictionU01DA047638 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI CHEN, HAO, WILLIAMS, ROBERT W. · 2019 to 2023
$3.1M
NIDA NIH HHS U01 DA047638
6 · The paper itself

Abstract

The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between

Indexed as

Chromogranin expressionGenotype-PhenotypeGlucoseInsulinPangenomeRatRecombinant Inbred

Identifiers

PMID38260597
PMCPMC10802574
OpenAlexW4390765858

What OpenQuestion holds

Textmetadata
LicenceCC BY-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.