Association between IRF6 SNPs and oral clefts in West China.

Analyses of previous data have confirmed the contribution of the IRF6 gene to susceptibility to non- syndromic oral clefts (NSOC) in some populations. We tested for associations between the rs2013162, rs2235375, and rs2235371 polymorphisms in IRF6 and the risk of NSOC, using both case-parent trio and case-control designs on samples from western China. Our study group consisted of 332 persons with NSOC, their parents (289 mothers and 243 fathers for 206 complete trios for these three SNPs), and 174 control individuals. We found strong evidence of over- and under-transmission of the C allele (the Val allele) at rs2235371, and the C allele at rs2235375 in cleft case-parent trios (P = 0.013 and P = 0.000, respectively). There were significant differences in the frequency distributions of both genotypes and alleles when cases were compared with control infants at rs2235371 and rs2235375. Five specific haplotypes showed significant over- and under-transmission. These results further support a role for IRF6 variants in western Chinese populations.

Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations.

Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.

Gene-gene and gene-environmental interactions of p53, p21, and IRF-1 polymorphisms in Korean women with cervix cancer.

BACKGROUND: The aim of this study was to identify gene-gene and gene-environmental factors affecting cervix carcinogenesis in Korean women. METHODS: We evaluated 530 subjects composed of 185 female cervix cancer patients and 345 normal healthy women. The single nucleotide polymorphisms (SNPs) of p53 codon 72, p21 codon 31, and interferon regulatory factor-1 (IRF-1) intron 6 were evaluated from extracted DNA of peripheral blood with an automatic DNA sequencer. The differences of each SNP, gene-gene and gene-environmental interactions between normal controls and patients were evaluated in the adjusted environmental background. RESULTS: In the environmental aspect, the rate of cervix cancer increased in the women with a lower level of education, a younger age at first sexual intercourse and more childbearing. The women who had p53 (Arg/Arg), IRF-1 (T/T), and <6 years of education showed a 14.7-fold increased risk of cervix cancer compared to the women who had p53 ( approximately Pro), IRF-1 ( approximately C), and >15 years of education. The women who had p53 (Arg/Arg), p21 (Ser/Ser), and >3 children showed a 6.4-fold increased risk of cervix cancer compared to the women who had p53 ( approximately Pro), p21 ( approximately Arg), and no children. The women who had p53 (Arg/Arg), IRF-1 (T/T), and first sexual intercourse before 22 years old showed a 5.5-fold increased risk of cervix cancer compared to the women who had p53 ( approximately Pro), IRF-1 ( approximately C), and first sexual intercourse after 26 years old. CONCLUSIONS: We found that the level of education, the age at first intercourse, and the number of children were independent risk factors in cervix carcinogenesis. The specific combinations of p53, p21, and IRF-1 gene-gene and gene-environmental interactions were significantly noted in the cervix carcinogenesis of Korean women.