Figure 7

Platform differences in narrow frequent amplification peaks. a.) The Agilent platform identifies a small amplification peak at chromosome 3, between 50.36–50.64 Mb (for exact probe localization, aberration calling, reporter coverage and gene identification see Additional file 8). The area is called as amplified using the Agilent platform due to two strongly amplified reporters covering the genes CACNA2D2 (H.s. calcium channel, alpha 2/delta subunit 2) and CISH (H.s. cytokine inducible SH2-containing protein). b.) A larger unique amplification region is detected by the Agilent platform at chromosome 20q, between 60.00–60.50 Mb. Reporters covering SS18L4, OSBPL2, and LAMA5 are highly amplified, causing this region to be called as amplification in the Agilent platform. Reporters in the other platforms either miss these genes or are located nearby at different positions (for exact probe localization, aberration calling, reporter coverage, and gene identification see Additional file 12). c.) The ROMA/NimbleGen platform detects a unique small amplification peak at chromosome 15, between 18.40–20.40 Mb (for details of exact probe localization, aberration calling, reporter coverage and gene identification see Additional file 11), while the Agilent platform has one single reporter and Illumina platform provides only 2 reporters in this specific area, and are therefore unable to detect amplifications in this region.