Novel PAX9 compound heterozygous variants in a Chinese family with non-syndromic oligodontia and genotype-phenotype analysis of PAX9 variants

Abstract Studies have reported that >91.9% of non-syndromic tooth agenesis cases are caused by seven pathogenic genes. Objective To report novel heterozygous PAX9 variants in a Chinese family with non-syndromic oligodontia and summarize the reported genotype-phenotype relationship of PAX9 variants. Methodology We recruited 28 patients with non-syndromic oligodontia who were admitted to the Hospital of Stomatology Hebei Medical University (China) from 2018 to 2021. Peripheral blood was collected from the probands and their core family members for whole-exome sequencing (WES) and variants were verified by Sanger sequencing. Bioinformatics tools were used to predict the pathogenicity of the variants. SWISS-MODEL homology modeling was used to analyze the three-dimensional structural changes of variant proteins. We also analyzed the genotype-phenotype relationships of PAX9 variants. Results We identified novel compound heterozygous PAX9 variants (reference sequence NM_001372076.1) in a Chinese family with non-syndromic oligodontia: a new missense variant c.1010C>A (p.T337K) in exon 4 and a new frameshift variant c.330_331insGT (p.D113Afs*9) in exon 2, which was identified as the pathogenic variant in this family. This discovery expands the known variant spectrum of PAX9; then, we summarized the phenotypes of non-syndromic oligodontia with PAX9 variants. Conclusion We found that PAX9 variants commonly lead to loss of the second molars.

Deafness genetic mutation spectrum in nonsyndromic hearing impairment associated with enlarged vestibular aqueducts / 中国康复理论与实践

ObjectiveTo investigate the deafness genetic mutation spectrum in nonsyndromic hearing impairment (NSHI) associated with enlarged vestibular aqueducts (EVA). MethodsFrom October, 2015 to August, 2016, 85 patients with NSHI from Hubei Yichang Special Education School were examined with temporal bone CT, and 20 deafness-related gene mutations in GJB2, GJB3, SLC26A4 and mtDNA 12S rRNA were detected with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. ResultsA total of 31 patients were found EVA with temporal bone CT. Compared with non-EVA patients, the proportion of deafness-related gene mutations was more in patients with EVA (χ2 = 11.160, P = 0.001), especially for c.919-2A>G mutation of SLC26A4 (χ2 = 23.870, P < 0.001). ConclusionThe deafness gene mutation spectrum is different in NSHI patients with or without EVA. It is needed to optimize genetic testing scheme for deafness for early diagnosis and intervention of NSHI associated with EVA.

Preliminary study of familial nonsyndromic tooth agenesis caused by ectodysplasin A mutation / 口腔疾病防治

Objective@# To explore the pathogenic genes in a Chinese family affected by nonsyndromic tooth agenesis so as to study the pathogenesis of oligodontia.@*Methods @# Hospital ethical approval and informed consent of the patients and family members were obtained. Clinical data of the proband and close family members were collected, peripheral venous blood was collected, and DNA was extracted. Gene sequencing was performed through whole-exome sequencing, and then the screened pathogenic genes were verified by Sanger sequencing. The three-dimensional structure of the mutant proteins was analyzed and compared with the wild-type using bioinformatics tools.@*Results@#The two patients with congenital majority tooth loss in this family were cousins, and there were no other patients with congenital majority tooth loss in the family. Besides congenital multiple tooth loss, the two patients had no obvious hair abnormalities, finger/toe abnormalities, sweating abnormalities or other abnormal manifestations of ectodermal tissue. We found a mutant gene that in this family by carrying out gene sequencing of the patients and their close family members. A novel EDA (ectodysplasin A) missense mutation c.983C>T (p. Pro328Leu) was identified, which changed the encoded amino acid from proline (Pro) to leucine (Leu). Analysis of the mutation site showed that the site was highly conserved, and three-dimensional structure modeling also found that it changed the structure of EDA. @* Conclusion@#A novel EDA missense variant (c.983C>T, p.Pro328Leu) was first identified in a Chinese family with nonsyndromic tooth agenesis, extending the mutation spectrum of the EDA gene.

Prevalence and Patterns of Supernumerary Teeth in a Peruvian Non-Syndromic Population: A Radiographic Study

ABSTRACT: This study aims to evaluate the prevalence and patterns of supernumerary teeth in a Peruvian non- syndromic population. This retrospective study used 2500 panoramic radiographs from the archives of a radiology center from Tacna-Peru. Radiographs were taken in 2019 and corresponded to subjects with ages between 8 to 22 years. The patterns of the supernumerary teeth were recorded in a checklist. Descriptive statistics was used for the distribution of supernumerary teeth. The Chi-square test was used to compare the distribution between the patterns. A confidence level of 5 % was used. The prevalence of supernumerary teeth was 5.32 % (n=133), with a male: female ratio of 1.56:1. The most affected arch was the maxilla (79.7 %), single presentation was the most common (87.22 %), and no differences were observed by gender (p > 0.05). Mesiodens was the most frequent (53.38 %), followed by parapremolar (34.59 %) in both genders (p > 0.05). According to the morphology, conical presentation was presented in 46.62 % of the cases, and impacted status were seen in 69.92 %. There were significance differences when the distribution of morphology was compared by the affected arch (p < 0.05). Conical form was most common in the maxilla (53.77 %), meanwhile in the mandible was the euromorphic type (40.74 %). A prevalence of supernumerary teeth of 5.32 % was estimated. The most frequent affected arch was the maxilla. Mesiodens, conical type and impacted were the most frequent patterns.

RESUMEN: Los dientes supernumerarios son anomalías del desarrollo dentario y se pueden clasificar según diferentes patrones. Este estudio tiene como objetivo evaluar la prevalencia y patrones de dientes supernumerarios en una población peruana no sindrómica. Este estudio retrospectivo utilizó 2500 radiografías panorámicas de los archivos de un centro de radiología de Tacna-Perú. Las radiografías se tomaron en 2019 y correspondieron a sujetos con edades entre 8 y 22 años. Los patrones de los dientes supernumerarios se registraron en una lista de verificación. Se utilizó estadística descriptiva para describir la distribución de dientes supernumerarios. Se utilizó la prueba de Chi-cuadrado para comparar la distribución entre los patrones. Se utilizó un nivel de confianza del 5 %. La prevalencia de dientes supernumerarios fue de 5,32 % (n = 133), con una relación hombre: mujer de 1,56:1. El arco más afectado fue el maxilar (79,7 %), la presentación única fue la más común (87,22 %) y no se observaron diferencias por sexo (p > 0,05). Mesiodens fue el más frecuente (53,38 %), seguido del parapremolar (34,59 %) en ambos sexos (p > 0,05). Según la morfología, la presentación cónica se presentó en el 46,62 % de los casos y el estado impactado en el 69,92 %. Hubo diferencias significativas cuando se comparó la distribución de la morfología por arco afectado (p < 0,05). La forma cónica fue más común en el maxilar (53,77 %), mientras que en la mandíbula fue el tipo euromórfico (40,74 %). Se estimó una prevalencia de dientes supernumerarios de 5,32 %. El arco afectado con mayor frecuencia fue el maxilar. Los mesiodens, tipo cónico e impactado fueron los patrones más frecuentes.

A Systematic Review of the Role of Mitochondria in Cleft Pathology: A Forgotten General?

ABSTRACT@#Orofacial clefts (OFC) are one of the most common birth defects that affects the lip, palate, or lip and palate of an infant. The deterioration of clefts is multifactorial involving multiple genes, various interactions from environmental factor and most forgotten, mitochondrial abnormality. The aim of this review is to highlight the importance of mitochondrial activity related to non-syndromic OFC deformity. Despite its important role in cells, the study on mitochondrial activity in cleft pathology was scarce and almost forgotten compared to other genetic investigations. This systematic review was completed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist. The literature search was done via the following databases: Google Scholar, Pubmed and Scopus with a total of nine studies of mitochondrial abnormalities were included. We hypothesise that mitochondria play an important role in early craniofacial development. A decreased in its function or activity may result in cleft lip formation. Hence, we would like to shed light on the remarkable role of mitochondria activity in the pathogenesis of non-syndromic OFC.

Association study between haplotypes of WNT signaling pathway genes and nonsyndromic oral clefts among Chinese Han populations / 北京大学学报(医学版)

OBJECTIVE@#To explore whether WNT signaling pathway genes were associated with non-syndromic oral clefts (NSOC) based on haplotypes analyses among 1 008 Chinese NSOC case-parent trios.@*METHODS@#The genome-wide association study (GWAS) data of 806 Chinese non-syndromic cleft lip with or without cleft palate (NSCL/P) trios and 202 Chinese non-syndromic cleft palate (NSCP) case-parent trios were drawn from the International Consortium to Identify Genes and Interactions Controlling Oral Clefts (ICOCs) study GWAS data set, whose Chinese study population were recruited from four provinces in China, namely Taiwan, Shandong, Hubei, and Sichuan provinces. The process of DNA genotyping was conducted by the Center for Inherited Disease Research in the Johns Hopkins University, using Illumina Human610-Quad v.1_B Bead Chip. The method of sliding windows was used to determine the haplotypes for analyses, including 2 SNPs haplotypes and 3 SNPs haplotypes. Haplotypes with a frequency lower than 1% were excluded for further analyses. To further assess the association between haplotypes and NSOC risks, and the transmission disequilibrium test (TDT) was performed. The Bonferroni method was adopted to correct multiple tests in the study, with which the threshold of statistical significance level was set as P < 0.05 divided by the number of tests, e.g P < 3.47×10-4 in the current stu-dy. All the statistical analyses were performed by using plink (v1.07).@*RESULTS@#After quality control, a total of 144 single nucleotide polymorphisms (SNPs) mapped in seven genes in WNT signaling pathway were included for the analyses among the 806 Chinese NSCL/P trios and 202 Chinese NSCP trios. A total of 1 042 haplotypes with frequency higher than 1% were included for NSCL/P analyses and another 1 057 haplotypes with frequency higher than 1% were included for NSCP analyses. Results from the TDT analyses showed that a total of 69 haplotypes were nominally associated with the NSCL/P risk among Chinese (P < 0.05). Another 34 haplotypes showed nominal significant association with the NSCP risk among Chinese (P < 0.05). However, none of these haplotypes reached pre-defined statistical significance level after Bonferroni correction (P>3.47×10-4).@*CONCLUSION@#This study failed to observe any statistically significant associations between haplotypes of seven WNT signaling pathway genes and the risk of NSOC among Chinese. Further studies are warranted to replicate the findings here.

Exploring the association between de novo mutations and non-syndromic cleft lip with or without palate based on whole exome sequencing of case-parent trios / 北京大学学报(医学版)

OBJECTIVE@#To explore the association between de novo mutations (DNM) and non-syndromic cleft lip with or without palate (NSCL/P) using case-parent trio design.@*METHODS@#Whole-exome sequencing was conducted for twenty-two NSCL/P trios and Genome Analysis ToolKit (GATK) was used to identify DNM by comparing the alleles of the cases and their parents. Information of predictable functions was annotated to the locus with SnpEff. Enrichment analysis for DNM was conducted to test the difference between the actual number and the expected number of DNM, and to explore whether there were genes with more DNM than expected. NSCL/P-related genes indicated by previous studies with solid evidence were selected by literature reviewing. Protein-protein interactions analysis was conducted among the genes with protein-altering DNM and NSCL/P-related genes. R package "denovolyzeR" was used for the enrichment analysis (Bonferroni correction: P=0.05/n, n is the number of genes in the whole genome range). Protein-protein interactions among genes with DNM and genes with solid evidence on the risk factors of NSCL/P were predicted depending on the information provided by STRING database.@*RESULTS@#A total of 339 908 SNPs were qualified for the subsequent analysis after quality control. The number of high confident DNM identified by GATK was 345. Among those DNM, forty-four DNM were missense mutations, one DNM was nonsense mutation, two DNM were splicing site mutations, twenty DNM were synonymous mutations and others were located in intron or intergenic regions. The results of enrichment analysis showed that the number of protein-altering DNM on the exome regions was larger than expected (P < 0.05), and five genes (KRTCAP2, HMCN2, ANKRD36C, ADGRL2 and DIPK2A) had more DNM than expected (P < 0.05/(2×19 618)). Protein-protein interaction analysis was conducted among forty-six genes with protein-altering DNM and thirteen genes associated with NSCL/P selected by literature reviewing. Six pairs of interactions occurred between the genes with DNM and known NSCL/P-related genes. The score measuring the confidence level of the predicted interaction between RGPD4 and SUMO1 was 0.868, which was higher than the scores for other pairs of genes.@*CONCLUSION@#Our study provided novel insights into the development of NSCL/P and demonstrated that functional analyses of genes carrying DNM were warranted to understand the genetic architecture of complex diseases.

Atraso de escolaridade e dificuldade de socialização de pacientes com fissura labiopalatina não sindrômica / Scholar delay and socialization dificulty of patients with non syndromic cleft lip and palate

Dentre as principais consequências da fissura labial e/ou palatina não sindrômica (FL/ PNS) estão dificuldades com fonação e autoestima, a primeira uma questão funcional e a segunda um problema social derivado não raro de contextos de bullying que, dentre outros, podem levar o indivíduo à evasão escolar. O objetivo deste estudo foi avaliar o atraso de escolaridade e a dificuldade de socialização de pacientes com FL/PNS quando comparados a uma população não afetada da mesma faixa etária de 7 a 20 anos, atendidos na Universidade José do Rosário Vellano ­UNIFENAS, campus de Alfenas. Os sujeitos foram agrupados em duas categorias de indivíduos, o grupo caso composto por indivíduos com FL/PNS em tratamento no Centro Pró-Sorriso da UNIFENAS; e o grupo controle composto por indivíduos sem FL/PNS em tratamento nas clínicas de Odontopediatria e Integrada da UNIFENAS. Os resultados demonstraram que a proporção de pacientes com FL/PNS atrasados na escola foi de quase 5 vezes maior que o número de pacientes sem fissuras (p<0,01). Constatou-se que a presença da FL/PNS pode ser o ponto de partida para outros contribuintes, com interferências psicológicas e/ou sociais, interferindo negativamente no processo de socialização (bullying) do paciente (p=0,0018). Portanto devem ser tratadas com abordagem multidisciplinar, incluindo diversos profissionais, dentre eles pedagogos, psicólogos e odontólogos(AU)

Among the main consequences of Non Syndromic Cleft Lip and Palate (NSCLP) are the difficulties with phonation and self estime, the first being a functional issue na the later being social that is derived from, not rarely, bullying contexts, that among other things, may lead na individual to school evasion. The objective of this study was to avaluate the levels of scholarity of patients with NSCLP when compared to a non affected population of the same age in individuals from 7 to 20 years old, attended the Pediatric and Integrated Pediatric Clinic of UNIFENAS, Alfenas campus. The subjects were grouped into two categories of individuals, the case group was composed of individuals with FL/PNS with treatment at the ProSmile center at UNIFENAS. The control group was composed of individuals without FL/PNS in treatment at the clinics of pediatric and integrated denistry at UNIFENAS. The results demonstrated the number of patients with FL/PNS that presented scholar delay were almost 5 times the number of patients that didn't present FL/PNS (p<0,01). The presence of NFL/PNS may be the starting point for other contributors with psychological and/or social interferences, interfering negatively with the socialization process (bullying) of the patient (p=0,0018). They should be treated with a multidisciplinary manner, including multiple professionals, among them pedagogues, psychologist and dentist(AU)

Research progress on MAFB gene polymorphism and nonsyndromic cleft lip and palate / 口腔疾病防治

@#Nonsyndromic cleft lip with/without cleft palate is a common congenital birth defect of the maxillofacial region. The pathogenic mechanism is related to the interaction of genes and environmental factors. At present, there are many studies on genes, and genome-wide association analysis has found that the new susceptibility gene v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) is associated with the development of nonsyndromic cleft lip with/without cleft palate. This paper reviews the research progress on the correlation between single nucletide polymorphism(SNPs) in MAFB and nonsyndromic cleft lip with/without cleft palate. The results of this review reveal how the MAFB gene is expressed and differentiated in various cell types and plays an important role in maintaining the development of various organs, such as the brain, pancreas, and parathyroid glands. The MAFB gene is significantly associated with the occurrence of nonsyndromic cleft lip with/without cleft palate in the Asian population. rs13041247, rs11696257, rs17820943 and other teratopoietic single nucleotide loci are the most commonly studied teratopoietic single nucleotide loci, and the research conclusions on the correlation between SNPs in MAFB genes are obviously different in different populations. The interaction between the MAFB gene and other susceptibility genes leads to the occurrence of nonsyndromic cleft lip with/without cleft palate; nevertheless, more in-depth research is needed on specific mechanisms and approaches based on the relationship between these two factors.

IRF6 polymorphisms in Brazilian patients with non-syndromic cleft lip with or without palate / Polimorfismos do gene IRF6 em pacientes brasileiros com fenda labial não sindrômica com ou sem fenda palatina

Abstract Introduction: Non-syndromic orofacial clefts have a complex etiology due to the contribution from both genetic and environmental risk factors, as well as the interaction between them. Among the more than 15 susceptibility loci for non-syndromic orofacial clefts with considerable statistical and biological support, the IRF6 is the most validated gene by the majority of studies. Nonetheless, in genetically heterogeneous populations such as Brazilian, the confirmation of association between non-syndromic orofacial clefts and IRF6 common variants is not a consolidated fact and unrecognized IRF6 variants are poorly investigated. Objective: The aim of this study was to investigate the association of IRF6 polymorphisms with non-syndromic orofacial clefts development in a population from northeast Brazil. Methods: Blood samples of 186 non-syndromic orofacial clefts patients and 182 controls from Rio Grande do Norte, Brazil, were obtained to analyze IRF6 polymorphisms (rs2235371, rs642961, rs2236907, rs861019, and rs1044516) by real-time polymerase chain reaction. Non-syndromic orofacial clefts patients were classified in cleft lip and palate, cleft palate only and cleft lip only groups. Results: The genotype and allele frequencies of single nucleotide polymorphism rs2235371 in IRF6 showed significant differences in patients with cleft palate when compared to the controls, whereas no association was shown between rs642961, rs2236907, rs861019, and rs1044516 and non-syndromic orofacial clefts. Conclusion: The association found between rs2235371 and isolated cleft palate should be interpreted with caution due to the low number of individuals investigated, and more studies with larger sample size are needed to confirm these association. In addition, there is a lack of association of the rs642961, rs2236907 and rs861019 polymorphisms with non-syndromic orofacial clefts susceptibility.

Resumo Introdução: As fendas orofaciais não sindrômicas possuem uma etiologia complexa devido à contribuição de fatores de risco genéticos e ambientais, assim como a interação entre eles. Dentre os mais de 15loci de susceptibilidade para as fendas orofaciais não sindrômicas com considerável suporte estatístico e biológico, o IRF6 é o gene mais validado pela maioria dos estudos. Apesar disso, em populações geneticamente heterogêneas como a brasileira, a confirmação da associação entre as fendas orofaciais não sindrômicas e as variantes mais comuns do IRF6 ainda não é um fato consolidado e outras variantes não tão conhecidas IRF6 são pouco investigadas. Objetivo: O objetivo deste estudo foi investigar a associação de variados polimorfismos do IRF6 com o desenvolvimento das fendas orofaciais não sindrômicas em uma população do nordeste do Brasil. Método: Amostras de sangue de 186 pacientes com fendas orofaciais não sindrômicas e 182 controles do estado do Rio Grande do Norte, Brasil, foram obtidas para analisar os polimorfismos do IRF6 (rs2235371, rs642961, rs2236907, rs861019 e rs1044516) por reação em cadeia da polimerase em tempo real. Os pacientes com fendas orofaciais não sindrômicas foram classificados em fenda labiopalatina, fenda palatina isolada e fenda labial isolada. Resultados: As frequências genotípica e alélica do polimorfismo de único nucleotídeo rs2235371 no IRF6 mostraram-se significativamente diferentes em pacientes com fenda palatina isolada quando comparadas às dos controles, enquanto que nenhuma associação foi encontrada entre rs642961, rs2236907, rs861019 e rs1044516 e risco para o desenvolvimento das fendas orofaciais não sindrômicas. Conclusão: A associação encontrada entre rs2235371 e fenda palatina isolada deve ser interpretada com cautela devido ao baixo número de indivíduos investigados, sendo necessários mais estudos com um tamanho amostral maior para confirmar essa associação. Além disso, não foram encontradas associações significativas entre os demais polimorfismos do IRF6 rs642961, rs2236907, rs861019 e rs1044516 e a susceptibilidade às fendas orofaciais não sindrômicas.

A Novel Heterozygous Missense Variant (c.667G>T;p.Gly223Cys) in USH1C That Interferes With Cadherin-Related 23 and Harmonin Interaction Causes Autosomal Dominant Nonsyndromic Hearing Loss

BACKGROUND: Pathogenic variants of USH1C, encoding a PDZ-domain-containing protein called harmonin, have been known to cause autosomal recessive syndromic or nonsyndromic hearing loss (NSHL). We identified a causative gene in a large Korean family with NSHL showing a typical pattern of autosomal dominant (AD) inheritance.METHODS: Exome sequencing was performed for five affected and three unaffected individuals in this family. Following identification of a candidate gene variant, segregation analysis and functional studies, including circular dichroism and biolayer interferometry experiments, were performed.RESULTS: A novel USH1C heterozygous missense variant (c.667G>T;p.Gly223Cys) was shown to segregate with the NSHL phenotype in this family. This variant affects an amino acid residue located in the highly conserved carboxylate-binding loop of the harmonin PDZ2 domain and is predicted to disturb the interaction with cadherin-related 23 (cdh23). The affinity of the variant PDZ2 domain for a biotinylated synthetic peptide containing the PDZ-binding motif of cdh23 was approximately 16-fold lower than that of the wild-type PDZ2 domain and that this inaccessibility of the binding site was caused by a conformational change in the variant PDZ2 domain.CONCLUSIONS: A heterozygous variant of USH1C that interferes with the interaction between cdh23 and harmonin causes novel AD-NSHL.

Research progress on pathogenic genes and molecular mechanisms of nonsyndromic tooth agenesis / 口腔疾病防治

@#Tooth agenesis is a common tooth number deficiency that occurs in the tooth-forming process or earlier period of tooth germ development and has a serious impact on the maxillofacial development, aesthetics and masticatory function of patients. According to the presence or absence of systemic symptoms, tooth agenesis can be divided into syndromic tooth agenesis and nonsyndromic tooth agenesis. In recent years, the discovery of new related genes, new mutation sites and related molecular mechanisms has become a major direction of gene research. This article will review the current research progress of the signaling pathways related to nonsyndromic tooth agenesis, such as the WNT/beta-catenin pathway, TGF-β/BMP pathway, PAX9, MSX1, and the EDA/EDAR/NF-κb pathway, and their molecular mechanisms. The interaction between Pax9 activating the Wnt/β-catenin and TGF-β/BMP pathways, MSX1 activating the TGF-β/BMP pathway, and Wnt activating the EDA/EDAR/NF-κb pathway was also found, which provides a new theoretical basis for the prevention and treatment of tooth agenesis. The molecular mechanism of nonsyndromic tooth agenesis is rarely studied; thus, the exploration of its mechanism will become one of the main research directions in the future.

Association between platelet-derived growth factor-C single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate in Western Chinese population / 华西口腔医学杂志

OBJECTIVE@#To explore the association between two single nucleotide polymorphisms (SNPs), namely, rs4691383 and rs7667857, in the platelet-derived growth factor-C (PDGF-C) gene, the genotypes, environmental exposure factors, and nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Western Chinese population.@*METHODS@#A total of 268 case-parent trios were selected, and two SNPs (rs4691383 andrs7667857) were genotyped by using polymerase chain reaction and restriction enzyme fragment length polymorphic method and direct sequencing method. Hardy-Weinberg equilibrium, linkage disequilibrium test, transmission disequilibrium test, and haplotype analysis were conducted to analyze the data. Meanwhile, the questionnaires on the epidemiology of cleft lip and palate filled by the included samples were collected, and the interaction between the genotypes of the two SNPs and environmental exposure factors was assessed by conditional logistic regression.@*RESULTS@#The A allele at rs4691383 and the G allele at rs7667857 of PDGF-C gene were over-transmitted for NSCL/P (P0.05).@*CONCLUSIONS@#The rs4691383 and rs7667857 at PDGF-C gene are closely related to the occurrence of NSCL/P in Western Chinese population. However, the interaction between environmental exposure factors and PDGF-C genotypes is not obvious in the occurrence of NSCL/P.

Association between the JAG2 gene polymorphism and the occurrence of nonsyndromic cleft lip with or without cleft palate in northwest Chinese population / 中华医学遗传学杂志

Objective@#To assess the association of JAG2 gene single nucleotide polymorphisms with the occurrence of nonsyndromic cleft lip with or without cleft palate (NSCLP) among northwest Chinese population.@*Methods@#A case-control study was carried out on 301 NSCLP patients and 304 healthy controls. An iMLDR™ genotyping technique was used to detect three single nucleotide polymorphisms (SNPs) [rs741859 (T/C), rs11621316 (A/G) and rs1057744(C/T)] of the JAG2 gene. Allelic and genotypic frequencies and haplotypic distribution among the two groups were compared.@*Results@#A significant difference was found in the frequency of C and T alleles for rs741859 between the two groups. The CT genotype of rs741859 could significantly reduce the risk for NSCLP to 65% (P < 0.05) and the risk for cleft lip with or without cleft palate (CL/P) to 62% (P < 0.05). rs11621316 and rs1057744 are in the same linkage disequilibrium (LD) region with a high degree of linkage (r2 > 0.8), whose distribution difference between the two groups was not statistically significant (P > 0.05).@*Conclusion@#The CT genotype of the JAG2 gene rs741859 may confer a protective effect for NSCLP among northwest Chinese population.

Evaluating the effect of WNT pathway genes considering interactions on the risk of non-syndromic oral clefts among Chinese populations / 北京大学学报(医学版)

OBJECTIVE@#In this study, we used genome-wide association study (GWAS) data to explore whether WNT pathway genes were associated with non-syndromic oral clefts (NSOC) considering gene-gene interaction and gene-environment interaction.@*METHODS@#We conducted the analysis using 806 non-syndromic cleft lip with or without cleft palate (NSCL/P) case-parent trios and 202 non-syndromic cleft palate (NSCP) case-parent trios among Chinese populations selected from an international consortium established for a GWAS of non-syndromic oral clefts. Genotype data and maternal environmental exposures were collected through DNA samples and questionnaires. Conditional Logistic regression models were adopted to explore gene-gene interaction and gene-environment in teraction using trio package in R software. The threshold of significance level was set as 3.47×10-4 using Bonferroni correction.@*RESULTS@#A total of 144 single nucleotide polymorphisms (SNPs) in seven genes passed the quality control process in NSCL/P trios and NSCP trios, respectively. Totally six pairs of SNPs interactions showed statistically significant SNP-SNP interaction (P < 3.47×10-4) after Bonferroni correction, which were rs7618735 (WNT5A) and rs10848543 (WNT5B), rs631948 (WNT11) and rs556874 (WNT5A), and rs631948 (WNT11) and rs472631 (WNT5A) among NSCL/P trios; rs589149 (WNT11) and rs4765834 (WNT5B), rs1402704 (WNT11) and rs358792 (WNT5A), and rs1402704 (WNT11) and rs358793 (WNT5A) among NSCP trios, respectively. In addition, no significant result was found for gene-environment interaction analysis in both of the NSCL/P trios and NSCP trios.@*CONCLUSION@#Though this study failed to detect significant association based on gene-environment interactions of seven WNT pathway genes and the risk of NSOC, WNT pathway genes may influence the risk of NSOC through potential gene-gene interaction.

Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios / 北京大学学报(医学版)

OBJECTIVE@#Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios.@*METHODS@#We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (<i>P</i> < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction.@*RESULTS@#A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10-4).@*CONCLUSION@#Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.

Research progress in environmental factors of nonsyndromic orofacial clefts / 中华整形外科杂志

Nonsyndromic orofacial clefts (NSOC) is a common but complicated congenital malformation, resulted from complex interplay of genetic and environmental factors. In this study, certain environmental factors was demonstrated, including drug, supplementation intake, occupational exposure, environmental pollution and psychosocial factor, to be associated with increasing risk of NSOC.

Study regarding the parent-of-origin effect of WNT pathway genes on non-syndromic cleft lip with or without cleft palate among the Chinese population / 中华流行病学杂志

Objective@#Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with its genetic evidence widely explored. This study explored the potential the parent-of-origin (PoO) effect of WNT pathway on the risks of NSCL/P, using a case-parent trio design.@*Methods@#Data on the single nucleotide polymorphism (SNP) of WNT genes were selected from a genome-wide association study (GWAS). A total of 806 Chinese non-syndromic cleft lip patients, with or without cleft palate (NSCL/P) case-parent trios, were gathered from an international consortium. PoO effect of WNT pathway genes and its haplotypes were explored by log-linear models. Additional Wald tests were performed to assess: a) the heterogeneity of PoO effect between different maternal exposures, b) the interaction between PoO effect, c) maternal exposure to environmental tobacco smoke (ETS), and d) multivitamin supplementation during pregnancy. The threshold for statistical significance was adjusted as 3.47×10-4, according to Bonferroni correction.@*Results@#After quality control, a total of 144 SNPs within seven genes were included for analyses, among which 8 SNPs were of potential PoO effect (P<0.05). However, none of them achieved the statistical significance after Bonferroni correction. The haplotype rs4074668-rs12725747 (T-A) on WNT9A showed significant PoO effect, based on the haplotype test for PoO (P=2.74×10-4). In addition, no statistically significant interaction was found in further exploration of this haplotype under environmental exposures as ETS or multivitamin supplementation.@*Conclusions@#Genes in the WNT pathway may influence the NSCL/P risks through the potential PoO effect. Particularly, the haplotype rs4074668-rs12725747 (T-A) on WNT9A presented significant PoO effect on NSCL/P, statistically. From this current study, findings on WNT pathway related risks among the NSCL/P, need to be further validated by independent samples in the future.

Association of EPHA3 gene polymorphism and folic acid with the occurrence of non-syndromic cleft lip with or without cleft palate / 中华整形外科杂志

Objective@#To study the mutual effect of EPHA3 gene polymorphism, folic acid intake in early pregnancy, and the occurrence of non-syndromic cleft lip with or without cleft palate, so as to provide the oretical basis for a etiological study on non-syndromic cleft lip with or without cleft palate.@*Methods@#A total of 195 patients and 170 controls were included.The candidate site rs7650466 was genotyped by Snapshot technique.The correlation with folic acid intake in early pregnancy was analyzed.@*Result@#The rs7650466 T allele was highly associated with the pathogenesis of non-syndromic cleft lip with or without cleft palate(OR=0.2472, 95%CI=0.1567-0.3899, P=1.851×10-9). The T allele had protective effects.Folic acid intake in early pregnancy, and its interaction with EPHA3 gene, were associated with the pathogenesis of this disease(P<0.05).@*Conclusions@#EPHA3 gene, folic acid intake during the first trimester, and theinteractionsare associated with the pathogenesis of non-syndromic cleft lip with or without cleft palate.

Screening and functional analysis of GATA-6 mutations in patients with nonsyndromic conotruncal defects / 中华实用儿科临床杂志

Objective@#To explore the molecular and genetic mechanism of transcription factor GATA-6 in nonsyndromic conotruncal defect (CTD) in order to provide evidence for early prevention and inheritance consultation of CTD.@*Methods@#A total of 32 cases of patients with nonsyndromic CTD and 100 healthy individuals were enrolled in the study.A total of 7 exons and bilateral partial intron-exon boundaries of GATA-6 were amplified by means of polymerase chain reaction (PCR). The PCR products were purified and directly sequenced by using an ABI Genetic Analyzer 3100 Automatic DNA sequence equipment.The acquired GATA-6 gene sequence was compared with standard gene sequence published in National Center for Biotechnology Information database, as well as the healthy control group to observe the GATA-6 gene mutations.The mutations were introduced into pcDNA3.1(+ ) by site-directed mutagenesis PCR on the basis of pcDNA3.1(+ )-GATA-6 in order to generate the GATA6-G245R mutant constructs.Wild type GATA-6, GATA-6-G245R and atrial natriuretic factor-luciferase(ANF-luciferase) were cotransfected into HEK 293T cells in vitro, and the CMV-LacZ were cotransfected as internal reference.Luciferase and galactosidase activity were measured by using luminometer 24 h after transfection and detected in the downstream ANF-luciferase reporter gene.@*Results@#A heterozygous missense mutation in the GATA-6 gene was identified in a patient with double outlets of the right ventricle.The mutation was located in Gly245Arg(G245R) in exon 2 of GATA-6.The mutation of pcDNA3.1(+ )-GATA-6 expression vectors were successfully constructed.Through the detection of luciferase reporter gene activity, it was found that GATA-6-G245R and wild-type GATA-6 decreased by 41.3%, and the comparison between them was statistically significant (P<0.001).@*Conclusions@#Transcription factor GATA-6 gene mutation is associated with the occurrence of nonsyndromic CTD.Transcription factor GATA-6 gene may be susceptible gene in human nonsyndromic CTD.