Fig. 1
The patient’s 1q21.1 duplication CNV and the ddPCR assay strategy for HYDIN2. a Read depth of ~40× whole-genome sequencing across 1q21.1 (top panel) and 16q22.2 (bottom panel) for Patient T and HapMap DNA NA12878, plotted using Integrative Genomics Viewer.24 CNVnator16 called a heterozygous duplication CNV (copy number = 3, yellow dashed vertical lines) on chr1:146370001-148580000 (2.21 Mb, hg38) for Patient T and no CNV for NA12878. No CNV is observed over HYDIN on 16q22.2 (chr16:70700000-71400000) for either individual. Y-axis: read count from 0–80. b Shown is the region of overlap between the paralogous genes HYDIN2 (1q21.1) and HYDIN (16q22.2, minus strand). Across the ~274 kb overlapping region, the two genes are estimated to share 99.4% sequence identity, with 264 Indels and 2049 mismatched bases.9,25,26 A detailed analysis of the evolution of HYDIN2 demonstrated a more complex set of structural changes than can be shown here.9 Also shown are the three regions targeted by the ddPCR copy number assays reported here: the two insertions (1 and 6 kbp) that are unique to HYDIN2, and a segment of unique sequence in HYDIN (outside the overlap region)
