The pitfalls of platform comparison: DNA copy number array technologies assessed

BMC Genomics

Table 4 CNVs observed between two HapMap samples

Platform	Clear	Tentative	Not Covered
Affymetrix	20	14	10
Agilent	19	16	18
Illumina	8	21	5
Nimblegen	9	13	14

Detection of reported germline CNVs between two HapMap samples across each platform, as adjudged from the plots in Additional File 4 by three analysts. Differences in probe density prohibited the blinding of analysts, but each platform was scored independent of the others. Indicated are the number of CNVs that are clearly apparent, the number for which there may be some evidence, which are labelled tentative, and those which are not covered. Naturally, there is a fourth category (not shown), which includes regions that are covered, but appear not to be CNVs.

ISSN: 1471-2164