An Integrated Whole-Genome Sequencing and In-House Targeted Testing Strategy Enhances Comprehensive Mutation Detection in Neurofibromatosis Type 1

Abstract

Neurofibromatosis type 1 (NF1) is a common autosomal dominant neurocutaneous syndrome that affects 1 in 2,500–3,000 births. The phenotypic hallmarks include Lisch nodules, optic nerve gliomas, café-au-lait spots, axillary freckling, and benign neurofibromas. NF1 patients carry an 8–13% lifetime risk of malignant peripheral nerve sheath tumors, the leading cause of NF1 mortality. Current genetic testing detects NF1 variants in 95–97% of cases. In this prospective cohort of 103 cases, we used targeted NF1 sequencing by next-generation sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-genome sequencing to identify causative variants. Pathogenic or likely pathogenic variants were identified by in-house targeted testing in 93% of cases; six cases had large deletions detected by MLPA, and two had variants identified by whole-genome sequencing. This is the largest genetically confirmed Indian NF1 cohort reported, expanding the known mutational spectrum and demonstrating the utility of whole-genome sequencing for unresolved cases (~2%), as well as highlighting the clinical and genetic heterogeneity of NF1.