[i] For each sample, an RQPS probe, consisting of an exon fragment (∼50 bp) from within a randomly selected query gene residing within the CNV region fused to a NOTCH2 fragment, was prepared. Both fragments were mutated to contain an SNV. These probes were then used to estimate the copy number of seven loci in a semi-blind test. After RQPS, the results were compared to previously determined array-CGH data. Two discrepancies were found, which were resolved when RQPS was repeated with query sequences matching the CGH probe.

[ii] ^aRepeat reaction with RQPS probe matching the CGH probe.

[iii] ^bInconsistent result between RQPS probe to a region not covered by a CGH probe and the CGH array.

[iv] ^cBoth RQPS and array-CGH data detected amplification; they differ in estimating copy number.