Background: Asia is the largest continent in the world with a large group of populations. However, we are still in lack of an imputation server with an Asian-specific reference panel to estimate genotypes for genome wide association study in Asia. Currently, two well-known imputation servers are available, i.e., Michigan imputation server in the US and Sanger in the UK. However, the quality of imputation for Southeast Asia's populations is not satisfying by using their genotype imputation services and reference panels.
Objective: In this paper, we develop ModStore imputation server with a specially designed reference panel to offer genotype imputation as a service, aiming to increase the power of genome wide association study of Singapore in the context of National Precision Medicine.
Method: We present the implementation and customization of ModStore imputation server on high performance computing infrastructure. Meanwhile, we construct a reference panel based on whole-genome sequencing of Singaporeans, referred to as the SG10K reference panel, for improving the imputation accuracy of Southeast Asia's populations.
Results: Experiment results show that by using the SG10K reference panel, over 79% improvement of mean Rsq can be achieved for the imputation of three Singapore ethnic populations data set, i.e., Malay, Chinese, and Indian, under MAF<0.005 compared to the 1000 Genome reference panel.
Conclusion: With ModStore imputation server, genotype imputation can be performed more accurately for data derived from array-based pharmacogenomics and pre-existing Southeast Asia's population-scale genetic.