Genome-wide association study of multiethnic nonsyndromic orofacial cleft families identifies novel loci specific to family and phenotypic subtypes

Nonsyndromic orofacial clefts (OFCs) are among the most common craniofacial birth defects worldwide, and known to exhibit phenotypic and genetic heterogeneity. Cleft lip plus cleft palate (CLP) and cleft lip only (CL) are commonly combined together as one phenotype (CL/P), separately from cleft palate alone. In comparison, our study analyzes CL and CLP separately. A sample of 2218 CL and CLP cases, 4537 unaffected relatives of cases, and 2673 pure controls with no family history of OFC were selected from the Pittsburgh Orofacial Cleft (Pitt-OFC) multiethnic study.genome-wide association studies were run for seven specific phenotypes created based on the cleft type(s) observed within these families, as well as the combined CL/P phenotype. Five novel genome-wide significant associations, 3q29 (rs62284390), 5p13.2 (rs609659), 7q22.1 (rs6465810), 19p13.3 (rs628271), and 20q13.33 (rs2427238), and nine associations (p ≤ 1.0E-05) within previously confirmed OFC loci-PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, ARID3B, NTN1, TANC2 and the WNT9B:WNT3 gene cluster-were observed. We also found that single nucleotide polymorphisms within a subset of the associated loci, both previously known and novel, differ substantially in terms of their effects across cleft- or family-specific phenotypes, indicating not only etiologic differences between CL and CLP, but also genetic heterogeneity within each of the two OFC subtypes.

Environmental Risk Factors for Nonsyndromic Cleft Lip and/or Cleft Palate in Xinjiang Province, China: A Multiethnic Study

OBJECTIVE

To determine the risk factors of the occurrence of nonsyndromic cleft lip and/or cleft palate (NSCL/P) in Xinjiang Province, China.

DESIGN

The study included 359 patients of NSCL/P and 310 controls. Information about sociodemographic characteristics, lifestyle behaviors, negative life events, possible environmental hazards exposures, and use of supplementations were collected from cases and controls. Both t test and χ² tests were used for group comparisons. Multivariable logistic regression was used to estimate the independent associations between environmental risk factors and the presence of NSCL/P. The receiver operating characteristic curve was used to establish the predictive variables for the occurrence of NSCL/P.

RESULTS

The results showed that maternal pesticide exposure (odds ratio [OR] = 11.40, 95%CI: 5.40-24.10), antibiotic drugs use (OR = 1.32, 95%CI: 1.14-1.53), paternal smoking (OR = 3.30, 95%CI: 1.87-5.83), threatened abortion (OR = 12.2, 95%CI: 3.29-45.25) were associated with increased risk of NSCL/P in offspring. In contrast, maternal moderate (OR = 0.43, 95%CI: 0.20-0.92) and middle physical workload (OR = 0.48, 95%CI: 0.0.23-0.97), vitamin-B complex supplementations (OR = 0.11, 95%CI: 0.03-0.41), calcium and iron (OR = 0.27, 95%CI: 0.08-0.90) supplementations were associated with reduced risk of NSCL/P in offspring. These variables together explain nearly 60% of the variation of occurrence of NSCL/P.

CONCLUSION

These findings from our study may help to develop primary prevention strategies for NSCL/P in Xinjiang.

Associations between single nucleotide polymorphisms in miR-221, self-reported essential hypertension, and interactions between genetic and environmental factors: a multiethnic study in China

This case-control study explored the relationship between SNPs in miR-221 and self-reported essential hypertension, as well as interactions between genetic and environmental factors, in a multiethnic Chinese cohort. A MassArray analysis was performed to genotype 462 patients with essential hypertension and 442 healthy participants. The association between four SNPs in miR-221 and essential hypertension risk was determined by investigating the differences in allelic and genotypic frequencies between case and control groups using PLINK version 1.07 software. A 4 × 2 table approach was conducted to explore the synergistic effect of SNPs and environmental factors on the risk of essential hypertension. Subjects with the C allele of rs2858060 in miR-221 had a lower risk of essential hypertension than those with the G allele (OR = 0.692; 95% CI = 0.521-0.920; P = 0.011). Logistic regression analysis showed that carriers of the CC genotype had a significantly lower risk of essential hypertension than those with the homozygous GG genotype (OR = 0.679; 95% CI = 0.498-0.925; P = 0.014). Using crossover analyses, we identified significant interactions between rs2858060 and the effect of age, triglycerides, HDL-C, ApoB, and fasting blood glucose on essential hypertension risk. We conclude that rs2858060 in miR-221 is associated with essential hypertension risk in the Chinese population, with a clear interaction between rs2858060 and classical risk factors in predicting the condition. Therefore, rs2858060 in miR-221 could play an important role as a genetic risk factor for the development of essential hypertension in the Chinese population.