Pangenome reconstruction in rats enhances genotype-phenotype mapping and variant discovery
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985823%3A_____%2F25%3A00617646" target="_blank" >RIV/67985823:_____/25:00617646 - isvavai.cz</a>
Result on the web
<a href="https://doi.org/10.1016/j.isci.2025.111835" target="_blank" >https://doi.org/10.1016/j.isci.2025.111835</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1016/j.isci.2025.111835" target="_blank" >10.1016/j.isci.2025.111835</a>
Alternative languages
Result language
angličtina
Original language name
Pangenome reconstruction in rats enhances genotype-phenotype mapping and variant discovery
Original language description
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 Pirl1l1, chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
30101 - Human genetics
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
iScience
ISSN
2589-0042
e-ISSN
2589-0042
Volume of the periodical
28
Issue of the periodical within the volume
2
Country of publishing house
US - UNITED STATES
Number of pages
9
Pages from-to
111835
UT code for WoS article
001449314500001
EID of the result in the Scopus database
2-s2.0-85217644363