Fig. 2

Chromosome view showing the subtelomeric 3q29 microdeletion region. Each red and blue dot represents an oligonucleotide probe along the length of chromosome 3 with its cytobands shown on the x-axis and the log₂ ratio plotted on the y-axis. The dotted lines provide a focused view of a portion the 3q29 cytoband, annotations of UCSC genes (hg19) (http://genome.ucsc.edu/), user-defined tracks indicating the recurrent 1.6 Mb deletion interval [(reported in [10]], and the 1.21 Mb deletion reported in our index patient. Immediately below, the presence of copy number variants (CNVs) annotated in the Database of Genomic Variants (DGV; blue: gain; red: loss) and region-specific segmental duplications (SDs) are shown in context (a). Zoomed-in views of chromosomal microarray (CMA) plots (X axis: hg19 genomic coordinates; Y axis: mean log₂ ratio; Agilent Technologies) depicting heterozygous copy number loss in the proband (top panel). Refinement of the deletion with a higher resolution CMA platform (Affymetrix; bottom panel arr[GRCh37]3q29(195806608_197029439)× 1) (b). CMA plots of the mother detailing the same heterozygous deletion as in the proband, whereas the sibling did not inherit the pathogenic chromosome 3q29 deletion (c). Metaphase and interphase FISH specific to the subtelomeric region of chromosome 3q (D3S4560 Abbott Molecular TelVysion, red signal), and an internal control probe specific to the subtelomeric region of chromosome 3p (D3S4559 Abbott Molecular TelVysion, green signal) in the proband. A red signal is absent at 3q29 on one of the chromosome 3 homologs (arrow), which confirms the heterozygous deletion identified by CMA testing (d)