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A reference panel of 64,976 haplotypes for genotype imputation
Shane McCarthy1, Sayantan Das2,3, Warren Kretzschmar4
1Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Nature Genetics
|August 23, 2016
Summary
This study presents a large human haplotype reference panel for accurate genotype imputation and increased SNP testing in genetic association studies. This resource aids in discovering and refining causal genetic loci efficiently.
Area of Science:
- Genetics
- Genomics
- Bioinformatics
Background:
- Genetic association studies require large reference panels for accurate imputation.
- Existing panels may have limitations in SNP coverage and imputation accuracy for low-frequency variants.
Purpose of the Study:
- To create a comprehensive human haplotype reference panel using whole-genome sequence data.
- To improve genotype imputation accuracy, especially for low-frequency variants.
- To enhance the discovery and refinement of causal loci in genetic studies.
Main Methods:
- Construction of a reference panel with 64,976 human haplotypes and 39,235,157 single nucleotide polymorphisms (SNPs).
- Utilized whole-genome sequence data from 20 studies, primarily of European ancestry.
- Developed remote server resources for consistent and efficient imputation and phasing.
Main Results:
- The reference panel enables accurate genotype imputation down to 0.1% minor allele frequency.
- Significant increase in the number of SNPs testable in association studies.
- Facilitates the discovery and refinement of causal genetic loci.
Conclusions:
- The developed reference panel is a valuable resource for genetic research.
- It enhances the power and precision of genetic association studies.
- Remote server access ensures efficient and widespread use by researchers.
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