1
|
Lin Y, Shi J, Shi B, Jia Z. MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese. Cleft Palate Craniofac J 2023; 60:1625-1631. [PMID: 36120833 DOI: 10.1177/10556656221125392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE The role of MMP16 in lip development is unclear. This study aimed to identify nonsyndromic cleft lip with or without palate (NSCL ± P) susceptible loci of MMP16 in western Han Chinese. DESIGN We performed targeted sequencing around MMP16 combined with a 2-phase association analysis on common variants. Phase 2 association analysis was performed with NSCL ± P specific subphenotypes (NSCL and NSCLP). Then we used rare variants burden analysis and genotyping, accompanied by motif analysis. SETTING This study was completed in a tertiary medical center. PATIENTS, PARTICIPANTS Phase 1 targeted sequencing included 159 patients with NSCL ± P and 542 normal controls; phase 2 included 1626 patients with NSCL ± P (1047 NSCL and 579 NSCLP) and 2255 normal controls. INTERVENTIONS Venous blood samples were collected from patients and used to extract DNA. MAIN OUTCOME MEASURES After Bonferroni correction, phase 1 significant threshold of p-value was 4.28 × 10-5 (0.05/1167 single nucleotide polymorphisms [SNPs]), and phase 2 was .00025 (0.05/200 SNPs). Burden analysis significant threshold p-value was .05. RESULTS Common variants phase 1 association analysis identified 11 statistically significant SNPs (lowest p = 1.90 × 10-9, odds ratio (OR) = 0.27, 95% CI: 0.17-0.44), phase 2 replication identified 16 SNPs in NSCL ± P (lowest p = 6.26 × 10-6, OR = 0.77, 95% CI: 0.69-0.86) and 9 in NSCL (lowest p = 8.44 × 10-5, OR = 0.76, 95% CI: 0.66-0.87). Rare variants burden analysis showed no significant results, genotyping results showed they were maternally inherited. CONCLUSIONS Our study identified MMP16 susceptible SNPs in NSCL ± P and NSCL, emphasizing its potential role in lip development. Our study also highlighted the importance to perform association analysis with subphenotypes divided.
Collapse
Affiliation(s)
- Yansong Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
2
|
Rs9891446 in NTN1 is associated with right-side cleft lip in Han Chinese Population. Arch Oral Biol 2022; 141:105485. [DOI: 10.1016/j.archoralbio.2022.105485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/31/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022]
|
3
|
Yin B, Shi JY, Shi B, Zheng Q, Jia ZL. Association Between SNPs in 1q32.2 and NSCL ± P in Han Chinese Population. Cleft Palate Craniofac J 2021; 59:1520-1526. [PMID: 34730443 DOI: 10.1177/10556656211052837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Non-syndromic cleft lip with or without cleft palate (NSCL ± P) is one of the most common birth malformations. Currently, numerous susceptibility SNPs have been reported by GWA studies, however, the replications of them among NSCL ± P from Han Chinese were very limited. DESIGN In this study, we selected 16 SNPs around 1q32.2 based on the published GWA studies and replicated them among 302 trios with NSCL ± P from Han Chinese Population. The genotypic data was analyzed with FBAT, PLINK and R package. SETTING The study was conducted in a tertiary medical center. PATIENTS, PARTICIPANTS 302 patients with CL ± P and their parents. MAIN OUTCOME MEASURES To ascertain the genetic variants in 1q32.2 in patients with CL ± P in Han Chinese Population. INTERVENTIONS Blood samples were collected. RESULTS We found T allele (Z = 4.26, p = 0.00002) and T/T homozygotes (Z = 4.4, p = 0.000011) at rs12063989 was significantly over-transmitted among non-syndromic cleft lip with or without cleft palate (NSCL ± P). CONCLUSIONS We found rs12063989 exhibited significant association with the occurrence of NSCL ± P, which would provide new evidence for the future study in the etiology of NSCL ± P.
Collapse
Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| |
Collapse
|
4
|
Yin B, Shi JY, Lin YS, Shi B, Jia ZL. SNPs at TP63 gene was specifically associated with right-side cleft lip in Han Chinese population. Oral Dis 2020; 27:559-566. [PMID: 32687624 DOI: 10.1111/odi.13566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Non-syndromic cleft lip with or without palate is one of the most common birth malformations. TP63 and GREM1 were recently reported to be associated with NSCL/P. However, there were few studies focused on their associations in non-syndromic cleft lip only (NSCLO). DESIGN Initial screening and replication in large cohorts were used to locate the susceptible SNPs of TP63 and GREM1. Firstly, variations were screened among 192 NSCLO cases by the Sanger sequencing. Then, we selected five associated SNPs in initial screening phase and replicated among 1,006 NSCLO cases and 1,823 normal controls. RESULTS Initial chi-square test showed that rs7653848, rs7624324, rs6790167, and rs1345186 in TP63 and rs2280738 in GREM1 achieved statistical significance (p < .05); the subsequent replication analysis showed that rs1345186 was specifically significant in right-side cleft lip (RCL; p = .017, OR = 1.33, and 95% CI: 1.05-1.69). CONCLUSION This study firstly used the subphenotype of cleft lip samples to verify the association between TP63 and GREM1, which indicated that TP63 is a promising susceptible gene for RCL in Chinese population. And further confirmed the different etiology in the right-sided cleft lip, left-sided cleft lip, and bilateral cleft lip of NSCLO. This will give new reference for the future research and genetic counseling.
Collapse
Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
5
|
Xu Y, Xie B, Shi J, Li J, Zhou C, Lu W, Xu F, He F. Distinct Expression of miR-378 in Nonsyndromic Cleft Lip and/or Cleft Palate: A Cogitation of Skewed Sex Ratio in Prevalence. Cleft Palate Craniofac J 2020; 58:61-71. [PMID: 32580581 DOI: 10.1177/1055665620935364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip and/or cleft palate (NSCL/P) is an isolated phenotype of orofacial clefts with skewed sex ratio in prevalence. This study aims to identify differentially expressed genes (DEGs) and microRNAs (DEMs) of NSCL/P by integrated bioinformatics analysis, revealing mechanisms for sexual dimorphism in prevalence. MATERIALS AND METHODS First, we downloaded the expression profile data from Gene Expression Omnibus database to identify DEGs and DEMs. Second, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses performed DEGs' functions. Then, clustered DEGs were identified through protein-protein interaction networks. Combining clustered DEGs with key genes searched in GeneCards enlarged NSCL/P-related genes. Moreover, the genes were linked by transcription factors (TFs). Subsequently, connected by the above TFs, DEMs and genes were used to establish the miRNA-TF-messenger RNA (mRNA) regulatory networks. RESULTS The DEGs in sex-ignored group, female-only group, and male-only group were obtained, respectively. Among the DEMs, miR-378 was downregulated in females but upregulated in males. In female-only group, the miRNA-TF-mRNA regulatory networks showed miR-378-SP1-POLE2/CDK6/EZR regulatory axis was found to be key candidates of NSCL/P. CONCLUSIONS Our findings suggest that different expression of miR-378 is consistent with the skewed sex ratio in the prevalence of NSCL/P.
Collapse
Affiliation(s)
- Yuzi Xu
- Department of Oral Implantology and Prosthodontics, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China
| | - Binbin Xie
- Department of Medical Oncology, 56660Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jue Shi
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China.,Department of Oral and Maxillofacial Surgery, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China
| | - Jia Li
- Department of Oral Implantology and Prosthodontics, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China
| | - Chuan Zhou
- Department of Oral Implantology and Prosthodontics, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China
| | - Wei Lu
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China.,Department of Periodontics, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China
| | - Fengqin Xu
- The First Affiliated Hospital of Kangda College of Nanjing Medical University, The First People's Hospital of Lianyungang, The Affiliated Lianyungang Hospital of Xuzhou Medical University, Lianyungang, China
| | - Fuming He
- Department of Oral Implantology and Prosthodontics, The Affiliated Stomatology Hospital, School of Medicine, 12377Zhejiang University, Hangzhou, China.,Key Laboratory of Oral Biomedical Research of Zhejiang Province, School of Stomatology, 12377Zhejiang University, Hangzhou, China
| |
Collapse
|
6
|
Jiang S, Shi JY, Lin YS, Duan SJ, Chen X, Jiao JJ, Shen W, Jin X, You M, Wang M, Shi B, Jia ZL. NTN1
gene was risk to non-syndromic cleft lip only among Han Chinese population. Oral Dis 2018; 25:535-542. [PMID: 30506619 DOI: 10.1111/odi.13009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/30/2018] [Accepted: 11/22/2018] [Indexed: 02/05/2023]
Affiliation(s)
- ShuYuan Jiang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry; University of California; Los Angeles California
| | - Yan-Song Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Shi-Jun Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Xieli Chen
- Beijing Smile Angel Children’s Hospital; Beijing China
| | | | - Wei Shen
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Xiaoju Jin
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Miao You
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Moyao Wang
- Beijing Smile Angel Children’s Hospital; Beijing China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology; Sichuan University; Chengdu China
| |
Collapse
|
7
|
Zhang BH, Huang N, Shi JY, Shi B, Jia ZL. Homozygote C/C at rs12543318 was risk factor for non-syndromic cleft lip only from Western Han Chinese population. J Oral Pathol Med 2018; 47:620-626. [PMID: 29683526 DOI: 10.1111/jop.12719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 02/05/2023]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a complex disorder, and it results from both of the genetic modifiers and environmental factors, with genetic modifiers contributes to it more than environmental factors. GWASs made great progress in identifying the candidate genes for NSCL/P, but the findings need to be replicated in other populations. In this study, we selected eleven SNPs from recent GWASs and GWAS meta-analysis to investigate their associations among 308 NSCL/P trios (134 non-syndromic cleft lip only (NSCLO) trios and 174 non-syndromic cleft lip with cleft palate (NSCLP) trios) from Han Chinese population. All SNPs were genotyped using SNPscan method and analyzed the data with FBAT, PLINK, and R package. Allelic TDT analysis showed that allele A at rs12543318 was associated with NSCLO trios (P = .0032, OR = 0.57, 95% CI: 0.39-0.83), and parent-of-origin effect analysis indicated that allele A at rs12543318 was significantly maternally undertransmitted among NSCLO (P = .0046), which implied the potential influence of genomic imprinting; global TDT further confirmed this association. Individual genotypic TDT showed homozygote C/C at rs12543318 was overtransmitted among NSCLO (Z = 3.79, P = .00015) and NSCL/P groups (Z = 3.83, P = .00013), which indicated that it could increase the risk to have cleft babies. Our findings indicated that rs12543318 was associated with NSCLO from Western Han Chinese population, which will give new scientific evidence for later researches in the etiology of NSOCs.
Collapse
Affiliation(s)
- Bi-He Zhang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ning Huang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
8
|
Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
Collapse
Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
9
|
Third molar agenesis as a potential marker for craniofacial deformities. Arch Oral Biol 2018; 88:19-23. [PMID: 29358133 DOI: 10.1016/j.archoralbio.2018.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/05/2018] [Accepted: 01/16/2018] [Indexed: 11/23/2022]
Abstract
The identification of clinical patterns of tooth agenesis in individuals born with craniofacial deformities may be a useful tool for risk determination of these defects. We hypothesize that specific craniofacial deformities are associated with third molar agenesis. OBJECTIVE The aim of this study was to identify if third molar agenesis could have a relation with other craniofacial structure alterations, such as cleft lip and palate, skeletal malocclusion, or specific growth patterns in humans. DESIGN Data were obtained from 550 individuals ascertained as part of studies aiming to identify genetic contributions to oral clefts. 831 dental records of patients aged over eight years seeking orthodontic treatment were also included. SN-GoGn angle were used to classify the growth pattern (hypo-divergent, normal and hyper-divergent), and the ANB angle was used to verify the skeletal malocclusion pattern (Class I, II and III). Panoramic radiographs were used to determine third molar agenesis. RESULTS A high frequency of third molar agenesis among individuals born with cleft lip with or without cleft palate (55%), as well as among their relatives (93.5%) was found. Third molar agenesis was not associated to skeletal malocclusion or growth pattern. CONCLUSION It appears that third molar agenesis is associated with the disturbances that lead to cleft lip and palate.
Collapse
|
10
|
A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts. PLoS One 2017; 12:e0183772. [PMID: 28877219 PMCID: PMC5587310 DOI: 10.1371/journal.pone.0183772] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/10/2017] [Indexed: 11/19/2022] Open
Abstract
Background GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO) and excess of males with cleft lip with or without cleft palate (CL/P). Methods Genotypes for 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European isolated cleft triads were available from a previously published GWAS. The R-package HAPLIN enables genome-wide–level analyses as well as statistical power simulations for a range of biologic scenarios. We analyzed isolated CL/P and isolated CPO for each ethnicity in HAPLIN, using a sliding-window approach to haplotype analysis and two different statistical models, with and without X-inactivation in females. Results There was a larger number of associations in the Asian versus the European sample, and similar to previous reports that have analyzed the same GWAS dataset using different methods, we identified associations with EFNB1/PJA1 and DMD. In addition, new associations were detected with several other genes, among which KLHL4, TBX22, CPXCR1 and BCOR were noteworthy because of their roles in clefting syndromes. A few of the associations were only detected by one particular X-inactivation model, whereas a few others were only detected in one sex. Discussion/Conclusion We found new support for the involvement of X-linked variants in isolated clefts. The associations were specific for ethnicity, sex and model parameterization, highlighting the need for flexible tools that are capable of detecting and estimating such effects. Further efforts are needed to verify and elucidate the potential roles of EFNB1/PJA1, KLHL4, TBX22, CPXCR1 and BCOR in isolated clefts.
Collapse
|
11
|
Fernandez N, Escobar R, Zarante I. Craniofacial anomalies associated with hypospadias. Description of a hospital based population in South America. Int Braz J Urol 2017; 42:793-7. [PMID: 27564292 PMCID: PMC5006777 DOI: 10.1590/s1677-5538.ibju.2015.0568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 01/26/2016] [Indexed: 12/03/2022] Open
Abstract
Introduction: Hypospadias is a congenital abnormality of the penis, in which there is incomplete development of the distal urethra. There are numerous reports showing an increase of prevalence of hypospadias. Association of craniofacial malformations in patients diagnosed with hypospadias is rare. The aim of this study is to describe the association between hypospadias and craniofacial congenital anomalies. Materials and Methods: A retrospective review of the Latin-American collaborative study of congenital malformations (ECLAMC) data was performed between January 1982 and December 2011. We included children diagnosed with associated hypospadias and among them we selected those that were associated with any craniofacial congenital anomaly. Results: Global prevalence was 11.3 per 10.000 newborns. In this population a total of 809 patients with 1117 associated anomalies were identified. On average there were 1.7 anomalies per patient. Facial anomalies were present in 13.2%. The most commonly major facial anomaly associated to hypospadias was cleft lip/palate with 52 cases. We identified that 18% have an association with other anomalies, and found an association between craniofacial anomalies and hypospadias in 0.59 cases/10.000 newborns. Discussion: Hypospadias is the most common congenital anomaly affecting the genitals. Its association with other anomalies is rare. It has been reported that other malformations occur in 29.3% of the cases with hypospadias. The more proximal the meatus, the higher the risk for having another associated anomaly. Conclusion: Associated hypospadias are rare, and it is important to identify the concurrent occurrence of craniofacial anomalies to better treat patients that might need a multidisciplinary approach.
Collapse
Affiliation(s)
- Nicolas Fernandez
- Hospital Universitario San Ignacio Pontificia Universidad Javeriana - Urología - Genética Bogota, Colombia
| | - Rebeca Escobar
- Universidad del Rosario - Epidemiología, Bogotá, Colombia
| | - Ignacio Zarante
- Hospital Universitario San Ignacio Pontificia Universidad Javeriana - Genética, Bogotá, Colombia
| |
Collapse
|
12
|
Vieira-Machado CD, de Carvalho FM, Santana da Silva LC, Dos Santos SE, Martins C, Poletta FA, Mereb JC, Vieira AR, Castilla EE, Orioli IM. Analysis of the genetic ancestry of patients with oral clefts from South American admixed populations. Eur J Oral Sci 2016; 124:406-11. [PMID: 27105611 DOI: 10.1111/eos.12275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 12/30/2022]
Abstract
Increased susceptibility to cleft lip, with or without cleft palate (CL±P) has been observed in South America, as related to Amerindian ancestry, using epidemiological data, uniparental markers, and blood groups. In this study, it was evaluated whether this increased risk remains when Amerindian ancestry is estimated using autosomal markers and considered in the predictive model. Ancestry was estimated through genotyping 62 insertion and deletion (INDEL) markers in sample sets of patients with CL±P, patients with cleft palate (CP), and controls, from Patagonia in southern Argentina and Belém in northern Brazil. The Amerindian ancestry in patients from Patagonia with CL±P was greater than in controls although it did not reach statistical significance. The European ancestry in patients with CL±P from Belém and in patients with CP from Belém and Patagonia was higher than in controls and statistically significant for patients with CP who were from Belém. This high contribution of European genetic ancestry among patients with CP who were from Belém has not been previously observed in American populations. Our results do not corroborate the currently accepted risks for CL±P and CP estimated by epidemiological studies in the North American populations and probably reflect the higher admixture found in South American ethnic groups when compared with the same ethnic groups from the North American populations.
Collapse
Affiliation(s)
- Camilla D Vieira-Machado
- ECLAMC at Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro.,INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro
| | - Flavia M de Carvalho
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at LEMC (Laboratory of Congenital Malformations Epidemiology), Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro
| | - Luiz C Santana da Silva
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,Institute of Biological Sciences, Federal University of Pará, Belém, Pará
| | | | - Claudia Martins
- Speech Therapy Division, Ophir Loyola Hospital, Belém, Pará, Brazil
| | - Fernando A Poletta
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation), Buenos Aires
| | - Juan C Mereb
- (In memoriam) ECLAMC at Hospital Zonal El Bolsón, El Bolsón, Argentina
| | - Alexandre R Vieira
- Department of Oral Biology and Pediatric Dentistry, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.,Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eduardo E Castilla
- INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro.,ECLAMC at LEMC (Laboratory of Congenital Malformations Epidemiology), Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro.,ECLAMC at CEMIC (Center for Medical Education and Clinical Research) and CONICET (National Council for Scientific and Technical Investigation), Buenos Aires
| | - Iêda M Orioli
- ECLAMC at Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro.,INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro
| |
Collapse
|