Genetic contribution for non-syndromic cleft lip with or without cleft palate (NS CL/P) in different regions of Brazil and implications for association studies

2011 ◽  
Vol 155 (7) ◽  
pp. 1581-1587 ◽  
Author(s):  
Luciano A. Brito ◽  
Lucas A. Cruz ◽  
Kátia M. Rocha ◽  
Ligia K. Barbara ◽  
Camila B.F. Silva ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Cleft Lip ◽  
Association Studies ◽  
Genetic Contribution

scholarly journals Investigation of candidate genes of non-syndromic cleft lip with or without cleft palate, using both case–control and family-based association studies

Medicine ◽  
2019 ◽  
Vol 98 (26) ◽  
pp. e16170 ◽  
Author(s):  
Xing Ge ◽  
Jia-Wei Hong ◽  
Jun-Yu Shen ◽  
Zheng Li ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Candidate Genes ◽  
Cleft Lip ◽  
Association Studies ◽  
Case Control ◽  
Family Based

scholarly journals Exclusion of candidate genes from a role in cleft lip with or without cleft palate: linkage and association studies.

1993 ◽  
Vol 30 (9) ◽  
pp. 773-778 ◽  
Author(s):  
G M Vintiner ◽  
K K Lo ◽  
S E Holder ◽  
R M Winter ◽  
S Malcolm
Keyword(s):  
Cleft Palate ◽  
Candidate Genes ◽  
Cleft Lip ◽  
Association Studies

Investigation of dominant and recessive inheritance models in genome-wide association studies data of nonsyndromic cleft lip with or without cleft palate

2017 ◽  
Vol 110 (4) ◽  
pp. 336-341 ◽  
Author(s):  
Anne C. Böhmer ◽  
Lina Gölz ◽  
Thomas Kreusch ◽  
Franz-Josef Kramer ◽  
Bernd Pötzsch ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Cleft Lip ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Recessive Inheritance ◽  
Genome Wide

scholarly journals Genetic Association Studies of Cleft Lip and/or Palate with Hypodontia outside the Cleft Region

2003 ◽  
Vol 40 (3) ◽  
pp. 274-279 ◽  
Author(s):  
Rebecca L. Slayton ◽  
Laura Williams ◽  
Jeffrey C. Murray ◽  
James J. Wheeler ◽  
Andrew C. Lidral ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Candidate Genes ◽  
Cleft Lip ◽  
Transforming Growth Factor ◽  
Cleft Lip And Palate ◽  
Association Studies ◽  
Polymorphism Analysis ◽  
Missing Teeth ◽  
Orofacial Clefting ◽  
Genotype Information

Objective The purpose of this study was to determine whether the candidate genes previously studied in subjects with cleft lip, cleft palate, or both are associated with hypodontia outside the region of the cleft. Subjects One hundred twenty subjects from the Iowa Craniofacial Anomalies Research Center were selected based on the availability of both dental records and genotype information. Method The type of orofacial clefting and type and location of dental anomalies (missing teeth, supernumerary teeth, or peg laterals) were assessed by dental chart review and radiographic examination. Genotype analysis of candidate genes was performed using polymerase chain reaction/single-strand conformation polymorphism analysis. Results The prevalence of hypodontia in this sample was 47.5%, with 30.0% of subjects having missing teeth outside the cleft. There was a positive association between subjects with cleft lip or cleft lip and palate who had hypodontia outside the cleft region (compared with noncleft controls) and both muscle segment homeo box homolog 1 (MSX1) (p = .029) and transforming growth factor beta 3 (TGFB3) (p = .024). It was not possible in this analysis to determine whether this association was specifically associated with orofacial clefting combined with hypodontia or whether it was due primarily to the clefting phenotype. Conclusions In this sample, there was a significantly greater incidence of hypodontia outside the cleft region in subjects with cleft lip and palate, compared with cleft lip only or cleft palate only. Cleft lip and/or palate with hypodontia outside the cleft region was positively associated with both TGFB3 and MSX1, compared with noncleft controls.

scholarly journals Association studies of low-frequency coding variants in nonsyndromic cleft lip with or without cleft palate

2017 ◽  
Vol 173 (6) ◽  
pp. 1531-1538 ◽  
Author(s):  
Elizabeth J. Leslie ◽  
Jenna C. Carlson ◽  
John R. Shaffer ◽  
Carmen J. Buxó ◽  
Eduardo E. Castilla ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Cleft Lip ◽  
Association Studies ◽  
Low Frequency ◽  
Frequency Coding ◽  
Coding Variants

scholarly journals Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)

2021 ◽  
pp. 105566562110363
Author(s):  
Lord J. J. Gowans ◽  
Carissa L. Comnick ◽  
Peter A. Mossey ◽  
Mekonen A. Eshete ◽  
Wasiu L. Adeyemo ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Cleft Lip ◽  
Association Studies ◽  
African Ancestry ◽  
Parental Origin ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
A Genome ◽  
Parent Of Origin ◽  
Origin Effects

Objective Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene–environment interactions, stochastic factors, gene–gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset. Methods The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P. Results We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16. Conclusion Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.

scholarly journals Role of ARHGAP29 nucleotide variants in the etiology of non-syndromic cleft lip with or without cleft palate.

2020 ◽  
Vol 89 (2) ◽  
pp. e414
Author(s):  
Justyna Dąbrowska ◽  
Barbara Biedziak ◽  
Agnieszka Lasota ◽  
Paweł P. Jagodziński ◽  
Adrianna Mostowska
Keyword(s):  
Cleft Palate ◽  
Candidate Gene ◽  
Cleft Lip ◽  
Association Studies ◽  
Missense Variant ◽  
P Value ◽  
Genome Wide Association Studies ◽  
Polish Population ◽  
Increased Risk ◽  
Strong Candidate

Aim. Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common birth defect of complex and heterogeneous aetiology. Genome-wide association studies (GWAS) of nsCL/P have identified an association for the 1p22.1 chromosomal region, in which ARHGAP29 was suggested as a candidate gene. Thus, the current study aimed to determine the contribution of the common and rare ARHGAP29 nucleotide variants to the risk of nsCL/P in the Polish population. Material and Methods. In total,197 common nucleotide variants (SNVs) and 22 missense variants located within the ARHGAP29 locus at chromosome 1p22.1 were genotyped by SNV microarray. The study was conducted in 269 individuals with nsCL/P and 569 healthy individuals. Results. Statistical analysis revealed that 31 common nucleotide variants located at the ARHGAP29 locus were significantly associated with the increased risk of nsCL/P. The strongest individual SNV was rs2391467 with a p-value = 2.49E-06 (OR = 1.64, 95%CI: 1.34–2.02). Besides, one potentially deleterious missense variant (rs140877322, p. Arg348Leu) was identified in a single patient with nsCLP. Conclusion. These findings confirm ARHGAP29 as a strong candidate gene for nsCL/P, with both common and rare nucleotide variants of this gene involved in the aetiology of nsCL/P in the Polish population.

scholarly journals Association between 20q12 rs13041247 polymorphism and risk of nonsyndromic cleft lip with or without cleft palate: a meta-analysis

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Liheng Huang ◽  
Xinglong Liang ◽  
Yangzhan Ou ◽  
Shijie Tang ◽  
Yunpu He
Keyword(s):  
Cleft Palate ◽  
Cleft Lip ◽  
Association Studies ◽  
Meta Analysis ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies ◽  
Chromosomal Locus ◽  
Asian Ethnicity ◽  
Study Population

Abstract Background Previous genome-wide association studies have identified a link between the rs13041247 single nucleotide polymorphisms (SNPs) in the chromosome 20q12 locus and the development of the congenital malformation known as nonsyndromic cleft lip with or without cleft palate (NSCL/P). The present meta-analysis was therefore designed to formally assess the relationship between rs13041247 and NSCL/P. Methods We searched Embase, Web of Science, PubMed, the China National Knowledge Internet (CNKI), and the China Wanfang database in order to identify relevant published through 25 June 2019. This allowed us to identify 13 studies incorporating 4914 patients and 5981 controls for whom rs13041247 genotyping had been conducted, with STATA 12.0 then being used to conduct a meta-analysis of these pooled results. The I2 statistic was used to compare heterogeneity among studies. Results In total this analysis incorporated 13 case-control studies. No association between the rs13041247 polymorphism and NSCL/P risk was detected in individuals of Asian ethnicity (C vs T: OR = 0.847, 95% CI = 0.702–1.021; CC vs TT: OR = 0.725, 95% CI = 0.494–1.063; CC vs CT: OR = 0.837, 95% CI = 0.657–1.067; CT + TT vs CC: OR = 1.265, 95% CI = 0.951–1.684; CC + CT vs TT: OR = 0.805, 95% CI = 0.630–1.029) or Caucasian ethnicity (C vs T: OR = 0.936, 95% CI = 0.786–1.114; CC vs TT: OR = 0.988, 95% CI = 0.674–1.446; CC vs CT: OR = 1.197, 95% CI = 0.816–1.757; CT + TT vs CC: OR = 0.918, 95% CI = 0.639–1.318; CC + CT vs TT: OR = 0.855, 95% CI = 0.677–1.081). However, an overall analysis of all participants in these studies revealed the rs13041247 C allele, the CT genotype, and the CC + CT model to be linked to a reduced NSCL/P risk (C vs T: OR = 0.897, 95% CI: 0.723–1.114, P = 0.048; CT vs TT: OR = 0.839, 95% CI: 0.734–0.959, P = 0.01; CC + CT vs TT: OR = 0.824, 95% CI: 0.701–0.968, P = 0.019). Conclusion These results suggest that the rs13041247 SNP located at the 20q12 chromosomal locus is associated with NSCL/P risk in an overall pooled study population, although this association was not significant in East Asian or Caucasian populations.

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