Figure 1.

The computational framework for HMZDupFinder. (A–D) The HMZDupFinder workflow demonstrates the harmonization of exome capture design, nearest reference selection, Z-TPM normalization, and homozygous duplication enrichment process. (E) Estimated numbers of candidate CNVs after each ES data computational step. (F, G) An example of combined visualization of Z-TPM and log₂ ratio validating a homozygous intragenic duplication. (F) The line plot displays Z-TPM values for exons that match the annotations from the MANE transcript of the investigated gene, which is shown at the bottom. A red, jagged horizontal line signifies the value from the subject, with grey lines representing the closest reference samples. The segmented log₂ ratio of the TPM value in the subject is illustrated as a blue dashed line in panel (G).