A new model calling procedure for Illumina BeadArray data.

Background: Accurate genotype calling for high throughput Illumina data is an important step to extract more genetic information for a large scale genome wide association studies. Many popular calling algorithms use mixture models to infer genotypes of a large number of single nucleotide polymorphisms in a fast and efficient way. In practice, mixture models are mostly restricted to infer genotypes for common SNPs where their minor allele frequencies are quite large. However, it is still challenging to accurately genotype rare variants, especially for some rare variants where the boundaries of their genotypes are not clearly defined.

Results: To further improve the call accuracy and the quality of genotypes on rare variants, a new model calling procedure, named M-D, is proposed to infer genotypes for the Illumina BeadArray data. In this calling procedure, a Gaussian Mixture Model and a Dirichlet Process Gaussian Mixture Model are integrated to infer genotypes.

Conclusions: Applications to Illumina data illustrate that this new approach can improve calling performance compared to other popular genotyping algorithms.