deCODE has developed a unique set of validation tools which it used to calibrate the new content. deCODE examined 20 previously unknown as well as documented CNVs in 96 HapMap CEU and Icelandic control triads. These variants varied in complexity and size with the largest being over 200 kb in size. deCODE defined the actual copy number of each variant in all individuals by pulsed field Southern Blots and quantitative PCR gene dosage (qPCR). deCODE compared these results with the data produced by the new content on an Illumina chip and found that the copy number and inheritance pattern correlate perfectly.

Below is an example of the validation of a region in which deCODE has discovered a novel polymorphic megasatellite, D11W4. As shown in figure 1, this megasatellite is not covered by other genotyping platforms. The deCODE CNV content includes 5 probes in this region. Copy number for the novel megasatellite was determined in a trio by pulsed field Southern Blot and qPCR. The copy number determined by the CNV content on an Illumina BeadChip correlated perfectly with these results (figure 2).

Fig. 1 Illustration of the coverage by different platforms in a region in which deCODE has discovered a novel polymorphic megasatellite, D11W4. The deCODE CNV content includes 5 probes in this region.

Fig. 2 Copy number determined for novel megasatellite, D11W4, in a trio by TaqMan quantitative PCR (a) and Southern blot (b) correlates well with the copy number measured using the CNV content on an Illumina BeadChip (c).

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