Improved ability to detect CNVs in segmental duplication regions. In this CNV region associated with two segmental duplications, there is one SNP probe on the edge of the region (54347071 bp on chromosome 16, represented by the black dot) on the 500 K EA array, but multiple probes present on the Nsp CN array. The three panels represent three independent replicates (one training replicate (data set 2) and two test replicates (data set 1 and data set3)) of the test sample NA15510 and the reference sample NA10851 on the Nsp CN array. The log intensity ratios are plotted on the Y axis and the genomic location on the X axis. The red horizontal line represents the CNV region identified by the Nsp CN array and algorithm, while the purple horizontal lines represent segmental duplication regions. The green arrows indicate location of primers used for QPCR verification (listed in Additional File 6).