Genomic DNA Labeling and Analysis

Four hundred nanograms of genomic DNA was labeled with Cy3-dCTP (GE Healthcare, Machelen, Belgium) using a Bioprime array CGH genomic labeling system (Thermo Fisher Scientific, Waltham, MA, USA). In parallel, Kreatech gender-matched controls were labeled with Cy5-dCTP. Samples were hybridized on the custom array CGH arrays for 40 h at 65 °C. After washing, the samples were scanned at 5 µm resolution using a DNA microarray scanner, G2505B (Agilent Technologies, Santa Clara, CA, USA). The scan images were analyzed using the feature extraction software 9.5.3.1 (Agilent Technologies). Segmentation was achieved using the circular binary segmentation algorithm in the DNACopy R package. Visual inspection and creation of the copy number profile plots were performed with ‘Vivar’ [29 (link)]. All of the raw array CGH data files were made publically available through the GEO website using the accession number GSE85444.