In this case study, we compared the test outcomes for PTCH1 CNV detection using the more conventional multiplex ligation-probe (MLPA) methodology and digital droplet PCR (ddPCR) based on DNA isolated from the peripheral blood lymphocytes of a female BCNS patient (index patient), where MLPA detected a heterozygous CNV duplication. The gene discussed is PTCH1; the disease is nevoid basal cell carcinoma syndrome.