ArticleG3 (Bethesda, Md.)2020
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis 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.
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
22 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies.PLoS genetics · 2022Pooled it
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Genomic prediction in insects: a case study on wing morphology traits in the jewel wasp Nasonia vitripennis.G3 (Bethesda, Md.) · 2026Article
- Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats.Nature communications · 2025Article
- Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats.bioRxiv : the preprint server for biology · 2025Article
- Genetic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats.Genes, brain, and behavior · 2025Article
- RatXcan: A framework for cross-species integration of genome-wide association and gene expression data.PLoS genetics · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
- STICI: Split-Transformer with integrated convolutions for genotype imputation.Nature communications · 2025Article
- Y and mitochondrial chromosomes in the heterogeneous stock rat population.G3 (Bethesda, Md.) · 2024Article
- 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
- Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats.bioRxiv : the preprint server for biology · 2024Article
- Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population.bioRxiv : the preprint server for biology · 2023Article
- 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
- The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats.Nucleic acids research · 2022Article
- Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats.Frontiers in genetics · 2022Article
- Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders.Frontiers in psychiatry · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.
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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.