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Updated: Aug 9, 2026
Separation of Mouse Embryonic Facial Ectoderm and Mesenchyme
Published on: April 12, 2013
Integrating transcriptomics and genomics to identify fibroblast growth factor/receptor candidate genes for
Bin Ge1, Yansong Lin1, Bing Shi1
1State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, China.
Objectives:
The objective of this study was to explore the relationship between fibroblast growth factor/receptor (FGF/FGFR) and non-syndromic orofacial cleft (NSOC) in individuals of Han Chinese.
Design:
Initially, we performed RNA-Seq between non-syndromic cleft lip only (NSCLO) or non-syndromic cleft palate only (NSCPO) and control groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were carried out to evaluate the functions of differentially expressed genes (DEGs) of FGF/FGFR. Then, we selected the most significant DEG FGFR2 and performed an association analysis in Chinese. Linkage disequilibrium (LD) and haplotype analyses were performed with HaploView and PLINK. Additional bioinformatics functional prediction for the notable single nucleotide polymorphisms was performed with HaploReg V4.1 and 3DSNP.
Results:
Finally, we identified 32 mRNAs related to FGF/FGFR via RNA-Seq and chose FGFR2 in the subsequent association analysis. Results indicated that the single nucleotide polymorphism (SNP) rs2288336 in FGFR2 contributed significantly to both non-syndromic cleft lip with or without cleft palate (NSCL/P) and NSCLO, with p values of 5.00E-05 (OR = 0.79, 95% CI: 0.70-0.88) and 1.38E-04 (OR = 0.76, 95% CI: 0.65-0.87), respectively. In addition, rs3793893 in FGFR2 was found to be associated with NSCLO, with a p value of 1.02E-04 (OR = 0.67, 95% CI: 0.55-0.82).
Conclusions:
Our research demonstrated that FGFR2 is significantly more involved in NSOC than other FGF/FGFRs in Chinese and further identified rs2288336 and rs3793893 in FGFR2 associated with NSOC subtypes, which provide further evidence for the genetic etiology of NSOC in Han Chinese.
