Functional Validation of Noncoding Variants Associated With Nonsyndromic Orofacial Cleft

Over the past decade, genome-wide association studies (GWASs) have found genetic variants associated with elevated risk for nonsyndromic orofacial cleft (NSOFC). In the post-GWAS era of NSOFC genetic research, an important aim is to identify the pathogenic variants that influence craniofacial development processes, towards understanding how they lead to disease manifestation. However, two major challenges hinder the translation of GWAS results into a mechanistic understanding. Firstly, it is uncertain whether the variants pinpointed by GWAS represent the underlying pathogenic variants; secondly, the bulk of genetic variants identified through GWAS are situated in noncoding regions of the genome, complicating their biological interpretation. Presently, research on noncoding genetic variants associated with NSOFC predominantly centers on variants located in transcriptional regulatory elements. These variants modulate transcription, subsequently altering the expression of downstream target genes and disrupting gene regulatory networks. We provide a systematic summary of the recent NSOFC-associated GWAS findings for the first time. With a particular focus on variants located in noncoding regions, we delve into current statistical methods and functional approaches for identifying and validating causal variants, aiming to bridge the gap between genetic variants identified by GWAS and their underlying pathogenic mechanism responsible for NSOFC. Deciphering causal variants underlying NSOFC offers valuable clinical insights that may advance early diagnosis, enhance risk stratification, and facilitate the discovery of novel therapeutic targets.