Chromosomal microarray analysis and validation assays by quantitative PCR. (A) A genome-wide scanning of copy number variations in the patient DNA. The plots show the relative copy numbers (Y-axis) against the chromosome regions (X-axis). Green and red dots represent the genomic regions with duplication and deletion, respectively. Arrows indicate the three chromosomal regions with CNVs (1p36, 2q37 and 20p12.3). (B–D) Magnified views and gene mapping in the CNV regions at 1p36.33–p36.32 (B), 2q37.1–37.3 (C) and 20p12.3 (D). Solid and dashed vertical lines represent the maximum and minimum breakpoints of CNVs, respectively. Chromosomal bands, genomic scale and the gene loci (blue diagrams) were obtained from the UCSC genome browser (hg19). Red squares highlight the loci of the DVL1 (B), HDAC4 (C) and GPCPD1 (D) genes. Only the genes that were selected for qPCR and DIS3L2 are annotated for simplicity. (E) Quantitative PCR data for the copy numbers of HDAC4, DVL1, and GPCPD1 to those of the reference genes (PSMD1, TP73 and MCM8). Bar plots represent mean ± SD values with triplicated PCR assays. *, P < 0.05 (Student’s t-test).