Development and validation of a multiplex chip-based droplet digital PCR method for detecting CNVs in 7q11.2 and 22q11.2 regions.

Abstract

Copy number variations (CNVs) in the 7q11.2 and 22q11.2 chromosomal regions are major contributors to genetic disorders such as Williams-Beuren syndrome and 22q11.2 deletion/duplication syndromes. These disorders are characterized by facial anomalies, growth retardation, intellectual disabilities, and lethal cardiovascular abnormalities. Despite the development and clinical application of various rapid molecular tests, each has significant limitations. We developed a multiplex chip-based droplet digital PCR (ddPCR) method for detecting microdeletions and microduplications in the 7q11.2 and 22q11.2 regions. We evaluated its linearity and reproducibility and tested it on 100 clinical patients with congenital heart defects to further verify its clinical applicability. We successfully developed a method capable of simultaneously detecting four types of CNVs in a single assay, demonstrating high accuracy and reproducibility. Compared to traditional methods, our approach depicted 100% concordance for positive and negative results. Additionally, our method accurately quantified target gene concentrations, allowing for precise evaluation of CNVs in the target regions. This study introduces a rapid, technically straightforward, and efficient quantitative chip-based ddPCR method for the detailed classification of CNVs in the 7q11.2 and 22q11.2 regions. Our findings indicated that chip-based ddPCR can be seamlessly implemented as a first-line screening tool in routine diagnostics.