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HLA-IMPUTER: an easy to use web application for HLA imputation and association analysis using population-specific
Jiangshan J Shen1, Chao Yang2, Yong-Fei Wang1
1Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, SAR China.
Bioinformatics (Oxford, England)
|September 1, 2018
Summary
HLA allele imputation accuracy improves with population-specific reference panels, like the new Han Chinese panel. HLA-IMPUTER offers a platform for imputing human leukocyte antigen (HLA) alleles and conducting association studies.
Area of Science:
- Genetics and Genomics
- Immunogenetics
- Computational Biology
Background:
- Human Leukocyte Antigen (HLA) allele imputation from single nucleotide polymorphism (SNP) genotypes is crucial for genetic association studies.
- The accuracy of HLA imputation is highly dependent on the quality and population specificity of reference panels.
- Existing reference panels may not adequately represent diverse global populations, potentially limiting imputation accuracy.
Purpose of the Study:
- To introduce HLA-IMPUTER, a novel platform for HLA allele imputation.
- To integrate the HIBAG algorithm with diverse, population-specific reference panels.
- To provide a user-friendly tool for researchers to perform HLA imputation and association analyses, particularly for underrepresented populations.
Main Methods:
- Implementation of the HIBAG algorithm for HLA imputation.
- Development and inclusion of population-specific reference panels, including a new Han Chinese panel from 10,689 samples.
- Creation of a web-based platform for accessible HLA imputation and downstream analysis.
Main Results:
- Demonstrated the utility of population-specific reference panels in enhancing HLA imputation accuracy.
- Successfully developed and validated a Han Chinese reference panel for HLA imputation.
- Provided a functional platform enabling researchers to impute HLA alleles from SNP data.
Conclusions:
- HLA-IMPUTER, utilizing population-specific reference panels, significantly improves HLA imputation accuracy.
- The availability of diverse reference panels, such as the Han Chinese panel, is essential for precise genetic studies in various ethnicities.
- The platform facilitates broader research applications in immunogenetics and population genetics.
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