Fig. 2: Genetic analysis of the patient.

A CMA. Top: each blue (positive) and red (negative) dot represents a comparative genomic hybridization (CGH) probe along the length of chromosome 20, with cytobands shown on the X axis and the log₂ ratio on the Y axis. Bottom: each green dot represents a single nucleotide polymorphism (SNP) probe, indicating genotypes of homozygotes (0/0 and 1/1) and heterozygotes (0/1) on the Y axis. Although no pathogenic copy number variants or ROHs were detected on chromosome 20 under default settings, a region within 20q13.12 lacking heterozygous SNP probes was observed (highlighted in pink). B Homozygosity mapping using PLINK. A 1.82-Mb ROH was identified within 20q13.12 (highlighted in pink). Each black dot represents a genotype call obtained from ES, displayed in the same format as in the SNP profile above. C Gene content within the ROH. The 1.82-Mb ROH includes 53 RefSeq genes, including CTSA. D Integrative Genomics Viewer (IGV) view of ES data. A pathogenic variant, c.692+3A>G in CTSA, was identified in the homozygous state. Note that a nearby variant, c.692+55A>G, located to the right of c.692+3A>G, is a common benign variant.