In this study, we sought to evaluate the accuracy of Nimblegen's microarray-based CGS resequencing technology so that the results obtained from experimental samples can be interpreted judiciously. Our results indicate that the false positive rate for SNPs was one per 244,193 bp of sequence. The false positive rate for clusters of ROI probes was one per 309,312 bp of sequence. These rates have been shown to depend on the thresholds chosen for mutation-calling [17] . In theory, low thresholds should be used for mutation mapping, increasing the number of false positives but reducing the number of false negatives. The methods used by Nimblegen to identify ROI's and to determine sequence differences have been described elsewhere [2] [18] . ROIs are identified by discarding erroneous probes then picking probes for which the ratio on both strands exceeds 3.5 standard deviations of the 80 th percentile within a 1800 bp local window [2] . For sequence determination, Molla et al. [18] . describe a machine-learning algorithm that uses relative positions within "feature space" rather than a training set and describe the effects of changing thresholds on sensitivity.