Improved boundary delineation with Nsp CN arrays compared to 500 K EA. The CNV in these examples were identified by both the 500 K EA platform (black lines) as well as the Nsp CN array (red lines). The three panels represent three independent replicates of the test sample NA15510 and the reference sample NA10851 on the Nsp CN array (data set 1 and data set 3 are test data sets and data set 2 is used as training set). The blue lines represent the log intensity ratios, with the dots indicating the location of each probe from the Nsp CN array. Colored vertical lines indicate different primer pairs, with green indicating a confirmed copy number change, and red indicating no detectable copy number change. The black dots on the black horizontal line represent SNP markers tiled on the 500 K EA arrays. A) This CNV was identified as a 40 kb insertion using the Nsp CN array, and a 65 kb insertion using the 500 K EA arrays. The primer pairs, ordered from left to right on the figure, are named 1 to 19 in Additional File 6C. B) This CNV was identified as a 95 kb insertion using the Nsp CN array and a 23 kb insertion using 500 K EA. In addition, the CNV is flanked by segmental duplications (purple lines). Primers 1 through 9 are numbered from left to right in Additional file 6C.