Linkage Disequilibrium between MSX1 and Non-syndromic Cleft Lip/Palate in                the Chilean Population

Non-syndromic cleft lip/palate (NSCLP) is a complex genetic trait. Linkage and association studies have suggested that a clefting locus could be located on chromosome 4p. Sixty Chilean families were recruited for this study; from these, we used unrelated trios to evaluate the possible linkage disequilibrium between MSX1 and NSCLP. An intragenic marker, MSX1-CA, and an extragenic marker, D4S432 at a distance of 0.8 cM from MSX1, were analyzed by means of polymerase chain-reaction with fluorescent-labeled forward primers, followed by electrophoresis on a laser-fluorescent sequencer. We carried out a transmission/disequilibrium test (TDT) for multiple alleles to evaluate the presence of linkage disequilibrium. Results showed a preferential transmission of the 169-bp allele of MSX1 (p = 0.03). Although there was no preferential transmission for the D4S432 marker, the overall extended TDT (ETDT) showed a significant result (p = 0.01). The authors’ findings support the hypothesis of the contribution of MSX1 in the etiology of NSCLP in the Chilean population.

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No Evidence for Linkage and Association between 4q Microsatellite Markers and Nonsyndromic Cleft Lip and Palate in Chilean Case-Parents Trios

The Cleft Palate-Craniofacial Journal ◽

10.1597/03-160.1 ◽

2005 ◽

Vol 42 (3) ◽

pp. 267-271 ◽

Cited By ~ 4

Author(s):

Rafael Blanco ◽

José Suazo ◽

JoséLuis Santos ◽

Hernán Carreño ◽

Hernán Palomino ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Microsatellite Markers ◽

Cleft Lip ◽

Cleft Lip And Palate ◽

Association Studies ◽

Statistical Significance ◽

P Value ◽

Genetic Trait ◽

Multiple Alleles ◽

Cleft Lip Palate

Objective Nonsyndromic cleft lip/palate (NSCLP) has the characteristics of a complex genetic trait. Linkage and association studies have suggested that one or more clefting loci may be located on chromosome 4q. The goal of this study was to evaluate the possible linkage and association due to linkage disequilibrium between five microsatellite markers located on 4q28 to 4q33 and NSCLP, using the case-parent trio design. Subjects and Methods A total of 56 Chilean families (32 simplex and 24 multiplex) were recruited. Microsatellite markers were analyzed using polymerase chain reaction with fluorescent-labeled forward primers, followed by electrophoresis on a laser-fluorescent sequencer. Case-parents trios were ascertained to assess linkage and linkage disequilibrium through a multistage procedure. Transmission disequilibrium tests for multiple alleles were carried out to assess the statistical significance of 4q28 to 4q33 microsatellite markers. Results Only weak evidence for linkage was obtained for the FGA marker (asymptotic uncorrected p value = .08 and empirical p value = .05). Only the FGA and UCP1 markers were selected for association analysis in trios, with unrelated cases achieving a nearly significant result for the UCP1 marker (asymptotic uncorrected p value = .07 and empirical p value = .19). Conclusion Though the FGA and UCP1 markers showed nearly significant p values for linkage and association, respectively, the results of the present study provided insufficient evidence of the existence of a major susceptibility locus in the 4q region that was analyzed in the present study.

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Linkage disequilibrium betweenIRF6variants and nonsyndromic cleft lip/palate in the Chilean population

American Journal of Medical Genetics Part A ◽

10.1002/ajmg.a.32494 ◽

2008 ◽

Vol 146A (20) ◽

pp. 2706-2708 ◽

Cited By ~ 8

Author(s):

José Suazo ◽

José Luis Santos ◽

Lilian Jara ◽

Rafael Blanco

Keyword(s):

Linkage Disequilibrium ◽

Cleft Lip ◽

Cleft Lip Palate ◽

Chilean Population

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MSX1, PAX9, and TGFA Contribute to Tooth Agenesis in Humans

Journal of Dental Research ◽

10.1177/154405910408300913 ◽

2004 ◽

Vol 83 (9) ◽

pp. 723-727 ◽

Cited By ~ 89

Author(s):

A.R. Vieira ◽

R. Meira ◽

A. Modesto ◽

J.C. Murray

Keyword(s):

Dna Sequence ◽

Cleft Lip ◽

Dna Analysis ◽

Ethnically Diverse ◽

Tooth Agenesis ◽

Single Strand Conformational Polymorphism ◽

Coding Regions ◽

Cleft Lip Palate ◽

Transmission Distortion ◽

Polymerase Chain

In this study, we sought to determine the association between tooth agenesis and DNA sequence variation in the genes MSX1 and PAX9 in an ethnically diverse human population. Since cleft lip/palate is also associated with both tooth agenesis and the gene TGFA, we included TGFA in the analysis as well. Cheek swab samples were obtained for DNA analysis from 116 case/parent trios. Probands had at least one developmentally missing tooth, excluding third molars. Genotyping was performed by single-strand conformational polymorphism or kinetic polymerase chain-reaction assays. Transmission distortion of the marker alleles and DNA sequence analysis was performed. Results showed that tooth agenesis is associated with markers of the genes MSX1 and TGFA. No mutations were found in MSX1 or PAX9 coding regions. There were statistically significant data suggesting that MSX1 interacts with PAX9. These findings suggest that MSX1, PAX9, and TGFA play a role in isolated dental agenesis.

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Association between 10 Microsatellite Markers and Nonsyndromic Cleft Lip Palate in the Chilean Population

The Cleft Palate-Craniofacial Journal ◽

10.1597/02-147 ◽

2004 ◽

Vol 41 (2) ◽

pp. 163-167 ◽

Cited By ~ 13

Author(s):

Rafael Blanco ◽

José Suazo ◽

JoséLuis Santos ◽

Mónica Paredes ◽

Hsiao Sung ◽

...

Keyword(s):

Cleft Lip ◽

Statistical Significance ◽

Positive Family History ◽

Case Control ◽

University Hospital ◽

Control Group ◽

Exact Test ◽

Rehabilitation Centers ◽

Cleft Lip Palate ◽

Chilean Population

Objective The objective of this case-control study was to evaluate the possible association between nonsyndromic cleft lip/palate (NSCLP) and 10 genetic markers in four chromosomal regions in the admixed Spanish-Amerindian Chilean population. Setting Study participants included 56 patients with NSCLP identified and interviewed for positive family history during the course of clinical examinations at different rehabilitation centers in the cities of Santiago and Talca, Chile. A control group of 59 normal individuals without known familial antecedents of clefting was obtained from blood bank donors of the University Hospital, University of Chile. Cases and controls belonged to low- to low-middle socioeconomic strata. Results Ten markers from chromosome 4p, 4q, 6p, 17q, and 19q were assessed (MSX1, D4S175, D4S192, F13A1, EDN1, D6S89, D6S105, D6S109, D17S579, BCL3). Four of them showed significant deviations from Hardy-Weinberg expectations in controls, according to the exact test (D4S192, BCL3, F13A1, and D6S89). The case-control comparison by means of the CLUMP program showed significant differences only in BCL3, and D6S109 almost reached statistical significance. Conclusions Most of the genetic regions with positive results in Caucasian populations may not be involved in NSCLP in Chile, regardless of the positive evidence for the candidate region on chromosome 19. Similar findings have been reported recently in the Chinese population.

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Screening of IRF6 Variants in Patients Subjected to Genetic Association Studies for Nonsyndromic Cleft Lip/Palate

The Cleft Palate-Craniofacial Journal ◽

10.1177/1055665620980238 ◽

2020 ◽

pp. 105566562098023

Author(s):

José A. Velázquez-Aragón ◽

Ariadna González-del Angel ◽

Miguel A. Alcántara-Ortigoza ◽

Miriam E. Reyna-Fabián ◽

Bernardette Estandia-Ortega

Keyword(s):

Association Study ◽

Cleft Lip ◽

Diagnostic Yield ◽

Association Studies ◽

Tertiary Care ◽

Case Series ◽

Case Control ◽

Retrospective Case ◽

Cleft Lip Palate ◽

Control Association

Objective: To screen for interferon regulatory factor 6 (IRF6) pathogenic variants in patients clinically diagnosed with nonsyndromic cleft lip palate (NSCL/P) and establish the proportion of misdiagnosed Van der Woude syndrome (VWS) cases, which could have biased previous NSCL/P case–control association studies. Design: Retrospective case series. Setting: Tertiary care children’s hospital. Participants: One hundred seventy-two unrelated Mexican patients with NSCL/P, 128 of whom had previously been included in a NSCL/P case–control association study. Main Outcomes Measurements: Sanger sequencing of the 9 IRF6 exons were performed, all variants respect with sequence reference were reported and classified for their pathogenic significance according to the American College of Medical Genetics and Genomics guidelines. Results: Seven percent of cases were familial. No pathogenic variant was identified in IRF6. We identified 12 previously reported benign variants; their frequencies did not significantly differ from those reported for individuals of Mexican ancestry. Three of them were uncommon intronic variants not reported in ClinVar. The rs2235371 and rs2235375 variants, which were previously analyzed in a NSCL/P case–control association study (containing 132 patients, 128 of whom were analyzed herein) did not show discordant association results comparing to the 370 controls from the previous study. Conclusions: The misdiagnosis of IRF6-related VWS as NSCL/P appears to be infrequent in our sample, suggesting that mutational screening of IRF6 would have a low diagnostic yield in patients with NSCL/P. The absence of IRF6 pathogenic alleles could be related to the application of an exhaustive clinical evaluation that discarded the syndromic forms and/or the low proportion of familial cases included.

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Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate

American Journal of Medical Genetics Part A ◽

10.1002/ajmg.a.33482 ◽

2010 ◽

Vol 152A (7) ◽

pp. 1701-1710 ◽

Cited By ~ 18

Author(s):

Ariadne Letra ◽

Renato Menezes ◽

Manika Govil ◽

Renata F. Fonseca ◽

Toby McHenry ◽

...

Keyword(s):

Cleft Lip ◽

Chromosome Region ◽

Association Studies ◽

Cleft Lip Palate

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Parent-of-origin effects for MSX1 in a Chilean population with nonsyndromic cleft lip/palate

American Journal of Medical Genetics Part A ◽

10.1002/ajmg.a.33528 ◽

2010 ◽

Vol 152A (8) ◽

pp. 2011-2016 ◽

Cited By ~ 16

Author(s):

José Suazo ◽

José Luis Santos ◽

Lilian Jara ◽

Rafael Blanco

Keyword(s):

Cleft Lip ◽

Cleft Lip Palate ◽

Parent Of Origin ◽

Origin Effects ◽

Chilean Population

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Risk variants in BMP4 promoters for nonsyndromic cleft lip/palate in a Chilean population

BMC Medical Genetics ◽

10.1186/1471-2350-12-163 ◽

2011 ◽

Vol 12 (1) ◽

Cited By ~ 21

Author(s):

José Suazo ◽

Julio C Tapia ◽

José Luis Santos ◽

Víctor G Castro ◽

Alicia Colombo ◽

...

Keyword(s):

Cleft Lip ◽

Risk Variants ◽

Cleft Lip Palate ◽

Chilean Population

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Whole-genome Sequencing Reveals De-novo Mutations Associated with Nonsyndromic Cleft Lip/Palate

10.21203/rs.3.rs-1064924/v1 ◽

2021 ◽

Author(s):

Waheed Awotoye ◽

Peter A. Mossey ◽

Jacqueline B. Hetmanski ◽

Lord Jephthah Joojo Gowans ◽

Mekonen A. Eshete ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Cleft Lip ◽

De Novo ◽

Association Studies ◽

Whole Genome ◽

Loss Of Function ◽

De Novo Mutations ◽

Pathogenic Variants ◽

Cleft Lip Palate

Abstract The majority (85%) of nonsyndromic cleft lip with or without cleft palate (nsCL/P) cases occur sporadically, suggesting a role for de novo mutations (DNMs) in the etiology of nsCL/P. To identify high impact DNMs that contribute to the risk of nsCL/P, we conducted whole genome sequencing (WGS) analyses in 130 African case-parent trios (affected probands and unaffected parents). We identified 162 high confidence protein-altering DNMs that contribute to the risk of nsCL/P. These include novel loss-of-function DNMs in the ACTL6A, ARHGAP10, MINK1, TMEM5 and TTN genes; as well as missense variants in ACAN, DHRS3, DLX6, EPHB2, FKBP10, KMT2D, RECQL4, SEMA3C, SEMA4D, SHH, TP63, and TULP4. Experimental evidence showed that ACAN, DHRS3, DLX6, EPHB2, FKBP10, KMT2D, MINK1, RECQL4, SEMA3C, SEMA4D, SHH, TP63, and TTN genes contribute to facial development and mutations in these genes could contribute to CL/P. Association studies have identified TULP4 as a potential cleft candidate gene, while ARHGAP10 interacts with CTNNB1 to control WNT signaling. DLX6, EPHB2, SEMA3C and SEMA4D harbor novel damaging DNMs that may affect their role in neural crest migration and palatal development. This discovery of pathogenic DNMs also confirms the power of WGS analysis of trios in the discovery of potential pathogenic variants.

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