ABSTRACT
OBJECTIVE: This study aimed to identify risk factors for NSCLP by analyzing polymorphisms in IRF6 rs2013162 and MTHFR A1298C rs1801131 in the Deutero Malay Population in Indonesia. SETTING: DNA isolation from venous blood samples was done followed by PCR and PCR-RFLPs method. PATIENTS/PARTICIPANTS: 115 NSCLP subjects and 120 healthy control subjects. MAIN OUTCOME MEASURE(S): The odds ratio (OR) determined to evaluate the risk factors is the main outcome measure. MATERIAL AND METHODS: The study is a case-control design using samples from the venous blood of 115 NSCLP subjects and 120 healthy control subjects. After DNA was extracted, the PCR-RFLPs method was performed using the DdeI restriction enzyme on 100 blood samples of the IRF6 rs2013162 group and Mboll restriction enzyme on 135 blood samples of the MTHFR A1298C rs1801131 group. The Chi-Square test was used with the Exact Fisher alternatives, depending on the expected count value. RESULTS: The results showed that the T mutant allele (OR = 4.125, P < .05) and GT genotype (OR = 21.00, P < .05) of IRF6 rs2013162 and the C mutant allele (OR = 3.781, P < .05), AC genotype (OR = 5, P < .05) and CC genotype (OR = 9,681, P < .05) of the MTHFR A1298C is associated to a greater risk of NSCLP. CONCLUSIONS: IRF6 rs2013162 and MTHFR A1298C rs1801131 gene polymorphisms are strongly associated with NSCLP among the Deutero Malay population in the Indonesian population.
ABSTRACT
BACKGROUND: IRF6 AP-2α binding site polymorphism is known as IRF6 rs642961. It has been associated with a nonsyndromic orofacial cleft (NS OFC). This study aimed to determine the IRF6 rs642961 as a risk factor associated with NS OFC and its phenotypes. METHODS: The case-control design used for 264 subjects consists of 158 NS CLP subjects (42 CU CLP, 34 CB CLP, 33 CLO, 49 CPOs) and 106 healthy controls. The DNA is extracted from venous blood. The segment of IRF6 rs642961 amplified by polymerase chain reaction (PCR) followed by restriction fragment length of polymorphisms (RFLPs) used the MspI digestion enzyme. The qPCR method to identify the mRNA expression levels of the IRF6 gene rs642961 was analyzed by the Livak method. RESULTS: The study results show that in NS CB CLP phenotype as the most severe phenotype of NS OFC, the Odds Ratio (OR) of A mutant allele was 5.094 (CI=1.456-17.820; P=0.011) and the OR of AA homozygous mutant genotype was 13.481 (CI=2.648-68.635; P=0.001). There are different levels of mRNA expression changes from NS OFC and its phenotypes. It is substantial among the 2-ΔΔCt and the group of AA, GA, and GG genotypes (P<0.05); in the NS CPO phenotype, it shows IRF6 mRNA under-expression in GA, AA genotypes while in other phenotypes it shows IRF6 mRNA overexpression. CONCLUSIONS: The IRF6 AP-2α binding site polymorphism is strongly associated with the severity of NS OFC, and this polymorphism has a functional role in affecting IRF6 mRNA expression that is variable in each phenotype.
