Genetic polymorphism of nonsyndromic cleft lip with or without cleft palate is associated with developmental dyslexia in Chinese school-aged populations

Ocular phenotype related SNP analysis in Southern Han Chinese population from Guangdong province

Ocular phenotype is recognizable among Asians, including eyelid fold, fissure inclination, and canthal index. Here we screened 27 facial phenotype-associated SNPs and reported a preliminary study in 246 Chinese individuals of Han origin in Guangdong province. Results showed that rs17760296 could explain 6.2% of the eyelid fold variation and double eyelids were more likely to appear when one's genotype was TT. With respect to the canthal index, rs4791774 and rs642961 were significantly associated with it. However, no individual SNP was associated with fissure inclination. We further constructed two models to predict eyelid fold and canthal index and evaluated them with receiver operating characteristic (ROC) curves and support vector machine (SVM) regression, respectively. The models showed a moderate-to-high predictive capacity (AUC = 0.75, sensitivity = 76%, and specificity = 72%) for the eyelid fold while a mild performance (R² = 0.1074, MSE = 0.0005, P-value = 0.024) for the canthal index. In conclusion, our study indicates that rs17760296 could be selected into the facial phenotype prediction system for the Southern Han Chinese population. More SNPs are encouraged to improve the prediction accuracy of the canthal index besides rs4791774 and rs642961.

The genetic factors contributing to the risk of cleft lip-cleft palate and their clinical utility

Cleft lip and cleft palate (CL/P) are among the most common congenital malformations in neonates and have syndromic or nonsyndromic forms. Nonsyndromic forms of malformation are being reported to be associated with chromosomal DNA modification by teratogenic exposure and to complex genetic contributions of multiple genes. Syndromic forms are shown to be related to chromosomal aberrations or monogenic diseases. There is a growing body of data illustrating the association of several genes with risk of developing this malformation, including genetic defects in T-box transcription factor-22 (TBX22), interferon regulatory factor-6 (IRF6), and poliovirus receptor-like-1 (PVRL1), responsible for X-linked cleft palate, cleft lip/palate-ectodermal dysplasia syndrome, and Van der Woude and popliteal pterygium syndromes, respectively. Genetic variants in MTR, PCYT1A, ASS1, SLC 25A13, GSTM1, GSTT1, SUMO1 BHMT1, and BHMT2 are being reported to be linked with CL/P risk. The etiology of nonsyndromic CLP is still remained to be unknown, although mutations in candidate genes have been found. Here, we provide an overview about the potential variants to be associated with CL/P for identification of the relative risk of CLP with respect to the basis of genetic background and environmental factors (e.g., dietary factors, alcohol use).

Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?

Dyslexia, or reading disability, is found to have a genetic basis, and several related genes have been reported. We investigated whether natural selection has acted on single nucleotide polymorphisms (SNPs) that were reported to be associated with risk/non-risk for the reading disability of Chinese characters. We applied recently developed 2D SFS-based statistics to SNP data of East Asian populations to examine whether there is any sign of selective sweep. While neutrality was not rejected for most SNPs, significant signs of selection were detected for two linkage disequilibrium (LD) regions containing the reported SNPs of GNPTAB and DCDC2. Furthermore, we searched for a selection target site among the SNPs in these LD regions, because a causal site is not necessarily a reported SNP but could instead be a tightly linked site. In both LD regions, we found candidate target sites, which may have an effect on expression regulation and have been selected, although which genes these SNPs affect remains unknown. Because most people were not engaged in reading until recently, it is unlikely that there has been selective pressure on reading ability itself. Consistent with this, our results suggest a possibility of genetic hitchhiking, whereby alleles of the reported SNPs may have increased in frequency together with the selected target, which could have functions for other genes and traits apart from reading ability.

Non-syndromic cleft lip with or without palate susceptible loci is associated with tooth agenesis

OBJECTIVE

Non-syndromic tooth agenesis (NSTA) may share common genetic factors with non-syndromic cleft lip with or without cleft palate (NSCL/P). Single-nucleotide polymorphisms (SNPs) were associated with individual's susceptibility to these anomalies. We selected five NSCL/P-associated SNPs from our previous genome-wide association study (GWAS) to test for the associations with NSTA.

MATERIALS AND METHODS

A total of 677 NSTA cases and 1,144 healthy controls were recruited in this case-control study. Five genome-wide NSCL/P-associated SNPs (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) were genotyped by TaqMan platform and evaluated for the associations with NSTA using plink software.

RESULTS

No significant associations between these SNPs and risk of NSTA were observed in the overall analysis and subgroup analysis with the number of missing teeth. However, in the subgroup analysis by tooth position, rs8049367 was nominally associated with mandibular premolar agenesis (Dominant model: OR_dom  = 0.66, 95% CI_dom  = 0.47-0.93, p_dom  = 0.016; Heterozygote model: OR_het  = 0.60, 95% CI_het  = 0.41-0.88, P_het  = 0.008). Rs4791774 showed a nominal association with congenitally missing maxillary canine (Dominant model: OR_dom  = 0.53, 95% CI_dom  = 0.28-0.98, p_dom  = 0.041; Heterozygote model: OR_het  = 0.50, 95% CI_het  = 0.26-0.97, P_het  = 0.041) and premolar (Additive model: OR = 0.59, 95% CI = 0.36-0.96, p = 0.035).

CONCLUSION

This study showed that NSCL/P susceptible loci rs8049367 and rs4791774 were probably associated with the risk of NSTA.

Unfolding the genetic pathways of dyslexia in Asian population: A review

Dyslexia also known as specific reading disorder is a complex heritable disorder with unexpected difficulty in learning to read and spell despite adequate intelligence, education, environment, and normal senses. Over past decades, researchers have attempted to characterize dyslexia neurobiological and genetic levels and unfold its pathophysiology. The genetic research on dyslexia has received attention in Asia from the last decade. Though limited by different constraints the studies from Asia have been able to gather significant evidence in this field. We present a review of studies of genetics in Asian population and suggest future directions.