BRLMM-P: a Genotype Calling Method for the SNP 5.0

Highly accurate and reliable genotype calling is an essential component of any highthroughput SNP genotyping technology. BRLMM, the method of choice for the Mapping 500K product, is effective, but requires the presence of mismatched probes (MM) probes on the array to create “seed” genotypes. We present here a method that only uses perfect-match probes, BRLMM-P. The primary difference between BRLMM-P and BRLMM is that BRLMM-P derives seed genotypes directly from the clustering properties of the data (as opposed to BRLMM’s reliance on initial genotype seeds from DM). Several secondary differences exist, such as using only the most informative dimension for clustering and some modifications to the exact choices for likelihood function.