A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations

Area of Science:

• Genomics
• Animal Models
• Bioinformatics

Background:

• Genome-wide association studies (GWAS) require affordable genotyping methods.
• Non-human model systems often lack the resources available for human genetic studies.
• Previous work established double-digest genotyping-by-sequencing for rat genotyping.

Purpose of the Study:

• To develop a cost-effective, high-throughput, and accurate genotyping method for N/NIH heterogeneous stock rats.
• To evaluate the utility of combining double-digest genotyping-by-sequencing and low-coverage whole-genome sequencing data.
• To enable large-scale genetic studies in rat models.

Main Methods:

• Utilized existing double-digest genotyping-by-sequencing data from 5,745 rats (0.21x coverage).
• Incorporated new low-coverage whole-genome sequencing data from 8,760 rats (0.27x coverage).
• Imputed 7.32 million single-nucleotide polymorphisms and compared results to high-coverage sequencing data (>33x).

Main Results:

• Achieved a high imputation concordance rate of >99.76% compared to high-coverage sequencing.
• Demonstrated the feasibility of using low-coverage sequencing data for accurate genotyping.
• Successfully imputed millions of bi-allelic single-nucleotide polymorphisms in a large cohort.

Conclusions:

• Low-coverage whole-genome sequencing and double-digest genotyping-by-sequencing are effective for accurate rat genotyping.
• This approach provides a cost-effective solution for large-scale genetic studies in non-human models.
• The methods developed can be applied to other genetic studies in various non-human subjects.