title: Rs12941170 at SOX9 gene associated with orofacial clefts in Chinese.
abstract: OBJECTIVE
  Non-syndromic orofacial cleftings (NSOCs) are considered as complex trait, which results from genetic and/or environmental modifiers. Current findings could only explain small portion of the NSOCs. SOX9 gene plays an important role during craniofacial development in animal models and the Pierre Robin sequence (PRS). However, its role in non-syndromic clefts remains unknown.
  
  
  METHODS
  In this study, we selected eight SNPs in and around SOX9 gene to make maximum coverage, and genotyped them by using RFLP-PCR and ligase detection reaction (LDR) methods to test its associations among 151 NSOCs (53 NSCLP, 52 NSCLO and 46 NSCPO) from Western Han Chinese population.
  
  
  RESULTS
  Allelic TDT results showed that G allele at rs12941170 of SOX9 was under-transmitted among NSOCs (p=0.00014, OR=0.55 and 95%CI: 0.40-0.75), which could indicate that the G allele is protective against NSOCs; parent-of-origin effect analysis showed that G allele at rs12941170 was maternally under-transmitted (p=0.002), while there was no statistically difference between the maternal and paternal transmission of it. To test if the adjacent SNPs travel together from parents to the affected individual, we carried out the sliding window haplotype analysis, it is interesting to find that the haplotypes carrying the G allele at rs12941170 also was under-transmitted for NSOCs, NSCL/P, NSCLP and NSCPO (lowest p=0.00033).
  
  
  CONCLUSIONS
  This study suggested that G allele at rs12941170 was protective, which could decrease the risk for NSOCs from Western Han Chinese population, and it will provide new reference for future research and genetic counseling in NSOCs.
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Zhong-Lin
authors.initials: ZL
authors.lastname: Jia
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China; Department of Stomatology, The third People's hospital of Chengdu, Chengdu, PR China.
authors.forename: Sha
authors.initials: S
authors.lastname: He
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Shu-Yuan
authors.initials: SY
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Bi-He
authors.initials: BH
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Shi-Jun
authors.initials: SJ
authors.lastname: Duan
authors.affiliation: Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA 90095, United States.
authors.forename: Jia-Yu
authors.initials: JY
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Ning
authors.initials: N
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
authors.forename: Wen-Chao
authors.initials: WC
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China. Electronic address: zhonglinjia@sina.com.
authors.forename: Bing
authors.initials: B
authors.lastname: Shi
mesh_terms: D000483:Alleles; D044466:Asian People / Q000235:genetics; D002681:China; D002971:Cleft Lip / Q000208:ethnology / Q000235:genetics*; D002972:Cleft Palate / Q000208:ethnology / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D008297:Male; D010641:Phenotype; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D055758:SOX9 Transcription Factor / Q000235:genetics*
chemical_list: D055758:SOX9 Transcription Factor; C527932:SOX9 protein, human
keywords: Haplotype; Non-syndromic orofacial cleftings; Parent of origin effect; SOX9; TDT