The Evolution of Gene Sequencing Technologies: Unveiling Genetic Architecture of Nonsyndromic Orofacial Clefts

Nonsyndromic orofacial clefts (NSOC) are common congenital craniofacial developmental defects. Current evidence suggests that genetic factors, environmental exposures, and their interactions jointly contribute to the development of the disease. Owing to the high heritability of NSOC, identifying susceptibility genes and loci is a central focus of etiological research. This review summarizes key findings in the identification of NSOC susceptibility genes and loci across successive stages of sequencing technology development. With the evolution of sequencing approaches, from Sanger sequencing to next-generation sequencing (NGS) and third-generation sequencing (TGS), and more recently to emerging technologies including epigenomics, single-cell sequencing, spatial omics, and multiomics integration, the field of NSOC genetics has undergone a transformative shift from low-throughput to high-throughput analyses. These advancements have enabled progress from the identification of common, classical susceptibility genes to the discovery of de novo mutations, rare variants, complex genomic structural variations, and the elucidation of cell differentiation trajectories. These advances have substantially enhanced our multidimensional understanding of the genetic heterogeneity underlying NSOC and reflect a broader transition in research focus from susceptibility mapping to mechanistic elucidation. Future studies should continuously promote methodological innovations in sequencing technologies, optimize study design, and explore integrative multiomics approaches to refine ethnicity- and subtype-specific genetic databases. Accelerating the translation of basic research findings into clinical applications will provide a solid foundation for early disease screening, genetic counseling, and precision prevention.