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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
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A cost-effective, high-throughput, highly accurate genotyping method for outbred populations
Denghui Chen1, Apurva S Chitre1, Khai-Minh H Nguyen2
1Bioinformatics and System Biology Program, University of California San Diego, La Jolla, CA 92093, USA.
G3 (Bethesda, Md.)
|December 13, 2024
Summary
Accurate genotyping for N/NIH heterogeneous stock rats is now feasible using combined low-coverage whole-genome sequencing and double-digest genotyping by sequencing data. This cost-effective method enables imputation of millions of single-nucleotide polymorphisms for large-scale genetic studies.
Area of Science:
- Genomics
- Animal Models
- Bioinformatics
Background:
- Genome-wide association studies (GWAS) require affordable and scalable genotyping methods.
- Nonhuman model systems often lack the comprehensive genotyping resources available for human subjects.
- Previous work established double-digest genotyping by sequencing (ddGBS) for heterogeneous stock rats.
Purpose of the Study:
- To develop a cost-effective, high-throughput, and accurate genotyping method for N/NIH heterogeneous stock rats.
- To leverage existing and new sequencing data for improved genetic analysis.
- To demonstrate the utility of low-coverage whole-genome sequencing (lcWGS) in conjunction with ddGBS.
Main Methods:
- Combined ddGBS data from 5,745 rats (0.21× coverage) and lcWGS data from 8,760 rats (0.27× coverage).
- Imputation of 7.32 million biallelic single-nucleotide polymorphisms (SNPs).
- Validation against high-coverage whole-genome sequencing (hcWGS) data (33.26× coverage) from a subset of individuals.
Main Results:
- Achieved a high concordance rate (>99.76%) between imputed and hcWGS data.
- Demonstrated the feasibility of accurate SNP imputation using combined low-depth sequencing data.
- Successfully genotyped a large cohort of N/NIH heterogeneous stock rats.
Conclusions:
- Combining ddGBS and lcWGS provides a powerful and cost-effective genotyping solution for N/NIH heterogeneous stock rats.
- This approach significantly enhances the potential for large-scale genetic studies in this model organism.
- The developed techniques are adaptable for genetic studies in other nonhuman subjects.
