Integrative Multi-omics Analysis Identifies Genetic Variants Contributing to Non-syndromic Cleft Lip with or without Cleft Palate.

OBJECTIVE: To provide novel insights into the aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) by integrating multi-omics data and exploring susceptibility genes associated with NSCL/P. METHODS: A two-stage genome-wide association study (GWAS) of NSCL/P was performed, involving a total of 1,069 cases and 1,724 controls. Using promoter capture Hi-C (pCHi-C) datasets in human embryonic stem cells (hESC) and chromatin immunoprecipitation sequencing (ChIP-seq) in craniofacial tissues, we filtered out single nucleotide polymorphisms (SNPs) with active cis-regulation and their target genes. Additionally, we employed expression quantitative trait loci (eQTL) analysis to identify candidate genes. RESULTS: Thirteen SNPs were identified as cis-regulation units associated with the risk of NSCL/P. Five of these were proven to be active in chromatin states in early human craniofacial development (rs7218002: odds ratio [OR] 1.50, P = 8.14E-08; rs835367: OR 0.78, P = 3.48E- 05; rs77022994: OR 0.55, P = 1.05E-04; rs961470: OR 0.73, P = 1.38E-04; rs17314727: OR 0.73, P = 1.85E-04). Additionally, pCHi-C and eQTL analysis prioritised three candidate genes (rs7218002: NTN1, rs835367: FGGY, LINC01135). NTN1 and FGGY were expressed in mouse orofacial development. Deficiencies in NTN1, FGGY and LINC01135 were associated with cleft palate and cleft lip, abnormal facial shape and bifid uvula, and abnormality of the face, respectively. CONCLUSION: Our study identified five SNPs (rs7218002, rs835367, rs77022994, rs961470 and rs17314727) and three susceptibility genes (NTN1, FGGY and LINC01135) associated with NSCL/P. These findings contribute to a better understanding of the genetic factors involved.

Exploration of Genetic Variants of Non-syndromic Cleft Lip with or without Palate and Underlying Mechanisms.

Non-syndromic cleft lip with/without cleft palate (NSCL/P) is one of the most common birth defects in humans with an overall prevalence of one per 1000 live births. Due to genetic and environmental influences, the fusion of the lips or palate may be interrupted at any stage and cause a cleft. Over decades, dozens of susceptible genes and loci have been identified using multiple genetic approaches. Our group has collected samples of NSCL/P patients since 2008 and established the biobank. We discovered numerous susceptible loci related to the occurrence of NSCL/P in the Chinese population, such as 16p13.3, 1q32.2, 10q25.3 and 17p13.1. In addition, we performed functional studies on related loci and genes by using molecular biology, cell biology, animal models and other methods to provide a basis for the construction of the NSCL/P genetic map in the Chinese population and help to implement individualised prophylaxis and treatment. Future efforts will focus on identifying functional variants, investigating pathways and other interactions, and including phenotypic and ethnic diversity in research.