ArticleBMC genomics2015
Genomic landscape of rat strain and substrain variation.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 4 of them syntheses that pooled it.
What it found
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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.
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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.
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Who cites it
57 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Conservation and divergence of canonical and non-canonical imprinting in murids.Genome biology · 2023Pooled it
- Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies.PLoS genetics · 2022Pooled it
- Genetic quality assurance and genetic monitoring of laboratory mice and rats: FELASA Working Group Report.Laboratory animals · 2020Guideline
- The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption.The FEBS journal · 2015Pooled it
- Source-dependent variability in gut barrier disruption, bacterial translocation, and immune activation after ischemic stroke in Wistar rats.Animal models and experimental medicine · 2026Article
- Mapping of EFO terms from the GWAS catalog data to multiple ontologies at the Rat Genome Database.Database : the journal of biological databases and curation · 2026Article
- Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.bioRxiv : the preprint server for biology · 2025Article
- Genetic modulation of protein expression in rat brain.iScience · 2025Article
- Establishing the hybrid rat diversity program: a resource for dissecting complex traits.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.Cell genomics · 2024Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks.Cell reports · 2023Article
- Genetic background in the rat affects endocrine and metabolic outcomes of bisphenol F exposure.Toxicological sciences : an official journal of the Society of Toxicology · 2023Article
- Animal Models of Hypertension (ISIAH Rats), Catatonia (GC Rats), and Audiogenic Epilepsy (PM Rats) Developed by Breeding.Biomedicines · 2023Review
- The Assembled Genome of the Stroke-Prone Spontaneously Hypertensive Rat.Hypertension (Dallas, Tex. : 1979) · 2023Article
- Intrinsic base substitution patterns in diverse species reveal links to cancer and metabolism.Genetics · 2022Article
- Coding variants in mouse and rat model organisms: mousepost and ratpost.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel.Frontiers in genetics · 2022Article
- Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel.Frontiers in genetics · 2022Article
- CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.GigaScience · 2021Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
backgroundSince the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004).
resultsHere we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs.
conclusionsIn summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs.
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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.