Algorithm for automatic genotype calling of single nucleotide polymorphisms using the full course of TaqMan real-time data.

ABSTRACT: Single nucleotide polymorphisms (SNPs) are often determined using TaqMan real-time PCR assays (Applied Biosystems) and commercial software that assigns genotypes based on reporter probe signals at the end of amplification. Limitations to the large-scale application of this approach include the need for positive controls or operator intervention to set signal thresholds when one allele is rare. In the interest of optimizing real-time PCR genotyping, we developed an algorithm for automatic genotype calling based on the full course of real-time PCR data. Best cycle genotyping algorithm (BCGA), written in the open source language R, is based on the assumptions that classification depends on the time (cycle) of amplification and that it is possible to identify a best discriminating cycle for ea

SUBMITTER: Callegaro A 

PROVIDER: S-EPMC1440877 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature