ArticleBMC genetics2016
A new model calling procedure for Illumina BeadArray data.
Article in BMC genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- MGV-seq: a sensitive and culture-independent method for detecting microbial genetic variation.Frontiers in microbiology · 2025Article
- Rare protein-coding variants implicate genes involved in risk of suicide death.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2021Article
- Estimation of DNA contamination and its sources in genotyped samples.Genetic epidemiology · 2019Article
- A user guide to the Brassica 60K Illumina Infinium™ SNP genotyping array.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
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Abstract
backgroundAccurate 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.
resultsTo 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.
conclusionsApplications to Illumina data illustrate that this new approach can improve calling performance compared to other popular genotyping algorithms.
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