ArticleScientific data2019
Extended regions of suspected mis-assembly in the rat reference genome.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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.
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.
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Who cites it
23 citing papers in PubMed.
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.Molecular biology and evolution · 2026Article
- Integrative multi-omics uncovers skeletal muscle enhancer programming of cardiorespiratory fitness.bioRxiv : the preprint server for biology · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
- Ligand-Independent Vitamin D Receptor Actions Essential for Keratinocyte Homeostasis in the Skin.International journal of molecular sciences · 2025Article
- A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations.bioRxiv : the preprint server for biology · 2024Article
- 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
- Whole-genome Analyses Reveal Past Population Fluctuations and Low Genetic Diversities of the North Pacific Albatrosses.Molecular biology and evolution · 2023Article
- Genetic Mapping of Multiple Traits Identifies Novel Genes for Adiposity, Lipids, and Insulin Secretory Capacity in Outbred Rats.Diabetes · 2023Article
- The Wistar Kyoto Rat: A Model of Depression Traits.Current neuropharmacology · 2023Article
- mRatBN7.2: familiar and unfamiliar features of a new rat genome reference assembly.Physiological genomics · 2022Review
- Transcriptome-wide analyses of adipose tissue in outbred rats reveal genetic regulatory mechanisms relevant for human obesity.Physiological genomics · 2022Article
- Whole genome sequencing of nearly isogenic WMI and WLI inbred rats identifies genes potentially involved in depression and stress reactivity.Scientific reports · 2021Article
- The genome sequence of the Norway rat,Wellcome open research · 2021Article
- Genome-to-phenome research in rats: progress and perspectives.International journal of biological sciences · 2021Review
- Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans.Brain sciences · 2020Review
- Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose.Obesity (Silver Spring, Md.) · 2020Article
- Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.G3 (Bethesda, Md.) · 2020Article
- Using Genetic and Species Diversity to Tackle Kidney Disease.Trends in genetics : TIG · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
We performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with unusually high levels of heterozygosity. These regions are consistent across the eight inbred strains, including Brown Norway, which is the basis of the rat reference genome. These regions show higher read depths than other regions in the genome and contain higher rates of apparent tri-allelic variant sites. The evidence suggests that these regions may correspond to duplicated segments that were incorrectly overlaid as a single segment in the reference genome. We provide masks for these regions of suspected mis-assembly as a resource for the community to flag potentially false interpretations of mapping or functional results.
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Registered trials
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.