Copy number and structural variant analyses of VHL gene using droplet digital PCR and targeted adaptive sampling long-read sequencing.

Von Hippel–Lindau (VHL) disease is an inherited tumor syndrome characterized by tumors and cysts in various organs, such as the eyes, pancreas, adrenal glands, and kidneys. VHL is caused by pathogenic variants in the VHL gene, which plays a critical role in blood vessel formation. Although direct sequencing is effective for detecting VHL gene variants, approximately 30% of patients with VHL disease harbor large deletions, necessitating alternative detection techniques such as multiplex ligation-dependent probe amplification (MLPA) and comparative genomic hybridization (CGH) arrays. In this study, we evaluated the clinical utility of droplet digital polymerase chain reaction (ddPCR) and targeted adaptive sampling long-read sequencing (TAS-LRS) for VHL gene deletion analysis. In cases of complex deletions, adaptive sampling was shown to be a powerful method capable of precisely identifying the exact sequence alterations. Our findings suggest that these novel techniques enable rapid and accurate detection of gene deletions in clinical genetic testing.