SNP Calling from Microarray Data

Each SNP typed by this array is at a bi-allelic locus, as determined from extensive sequencing of global P. falciparum isolates [8 (link)]. The heuristic algorithm therefore focuses on the two intensities of each possible allele. This algorithm then identifies the global mean intensity for every probe with the identical center base and adjusts each individual intensity by the difference in intensity between the global means of the two bases being interrogated. Intensities are evaluated and adjusted independently for the sense and anti-sense direction. After adjusting the intensity, a SNP is called after fulfilling the following criteria: 1) the contrast of intensities is greater than or equal to 0.98, 2) the forward and reverse SNP calls are concordant, and 3) all intensities are above global background levels determined by the average value of the random probes. Multiple thresholds were tested for background levels up to average random plus two standard deviations (data not shown). SNP calling accuracy changed minimally when thresholds were raised, however SNP call rate dropped more significantly. This algorithm was written in the PERL programming language and uses standard outputs from the Roche NimbleScan (v2.6) software. Given the discontinuation of this microarray the algorithm will be made publically available when the probe set is validated on a new platform.