ArticleG3 (Bethesda, Md.)2025
A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.
Article in G3 (Bethesda, Md.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide association study of cocaine self-administration behavior in Heterogeneous Stock rats.Nature communications · 2026Article
- Identification of novel candidate neural genes for diet-induced obesity in outbred heterogeneous stock rats.Research square · 2026Article
- Leveraging low-cost short-read sequencing: revolutionizing complex trait genetics.Molecular biology and evolution · 2026Article
- The missing data problem in population genomics and statistical methods to address them.G3 (Bethesda, Md.) · 2026Article
- Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats.Nature communications · 2025Article
- A low-coverage skim-sequencing and imputation pipeline for genomic selection.The plant genome · 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
- Y and mitochondrial chromosomes in the heterogeneous stock rat population.G3 (Bethesda, Md.) · 2024Article
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Abstract
Affordable sequencing and genotyping methods are essential for large-scale genome-wide association studies. While genotyping microarrays and reference panels for imputation are available for human subjects, nonhuman model systems often lack such options. Our lab previously demonstrated an efficient and cost-effective method to genotype heterogeneous stock rats using double-digest genotyping by sequencing. However, low-coverage whole-genome sequencing offers an alternative method that has several advantages. Here, we describe a cost-effective, high-throughput, high-accuracy genotyping method for N/NIH heterogeneous stock rats that can use a combination of sequencing data previously generated by double-digest genotyping by sequencing and more recently generated by low-coverage whole-genome sequencing data. Using double-digest genotyping-by-sequencing data from 5,745 heterogeneous stock rats (mean 0.21× coverage) and low-coverage whole-genome sequencing data from 8,760 heterogeneous stock rats (mean 0.27× coverage), we can impute 7.32 million biallelic single-nucleotide polymorphisms with a concordance rate > 99.76% compared to high-coverage (mean 33.26× coverage) whole-genome sequencing data for a subset of the same individuals. Our results demonstrate the feasibility of using sequencing data from double-digest genotyping by sequencing or low-coverage whole-genome sequencing for accurate genotyping and demonstrate techniques that may also be useful for other genetic studies in nonhuman subjects.
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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.