I do CNV analysis. I use Affymetrix Cytoscape 750K array. There are 14 probes inside a genomic region chr7:126.229.425-126.308.312 (half of them - CGH probes for CNV detection, half - SNP probes). And these probes indicate a presence of a CNV.
We also have analysis of CNVs in the same sample in shallow NGS data of 4x. The usual resolution where we can guarantee the detection of CNV in shallow WGS of this depth is 25kbps. The variant is much bigger - 70kbps.
We don't see any signal in the abovementioned region. Coverage is exactly equal to diploid - somewhat higher, somewhat lower in different parts. Mosaic variant can usually be seen by moderate increase/decrease of coverage - it is not the case.
As a comparison for aCGH analysis we've 30 non-related samples, so the presence of duplication there may be excluded.
The array sample is not very noisy. Noisy, yes, - but the drop of signal there is absolutely clear and can not be explained by the noisyness. Sample swap is not the case - the other rare variants match perfectly.
Does anyone know how it may occur? We had several such cases, idk, 4 CNVs per 300 analysed pairs array/NGS.
That's how array intensity looks like (+region around the CNV, only aCGH probes are shown)
This sample was sequenced with shallow NGS twice. Each dot at the IGV plot is 5kb coverage. In theory, in the center there should be a drop of 14 dots - visible drop. But nothing.