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1.
Genet Epidemiol ; 43(6): 704-716, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31172578

RESUMO

Phenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes-cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a "cleft map" of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 [CP], WNT5A [CLP]), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.

2.
Am J Med Genet A ; 179(3): 467-474, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30582786

RESUMO

Genome-wide scans have shown that common risk alleles for orofacial clefts (OFC) tend to be located in noncoding regulatory elements and cumulatively explain only part of the heritability of OFCs. Low-frequency variants may account for some of the "missing" heritability. Therefore, we scanned low-frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP-Seq studies in craniofacial tissues or cell lines contained multiple low-frequency (0.01-1%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low-frequency variants across each enhancer region with CL/P and CP. We discovered a significant association between CP and a branchial arch enhancer near FOXP1 (mm60; p-value = .0002). Additionally, we observed a suggestive association between CL/P and a forebrain enhancer near FOXE1 (hs1717; p-value = .001). These findings suggest that low-frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.

3.
Genet Epidemiol ; 42(7): 664-672, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30277614

RESUMO

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans and is notable for its apparent sexual dimorphism where approximately twice as many males are affected as females. The sources of this disparity are largely unknown, but interactions between genetic and sex effects are likely contributors. We examined gene-by-sex (G × S) interactions in a worldwide sample of 2,142 NSCL/P cases and 1,700 controls recruited from 13 countries. First, we performed genome-wide joint tests of the genetic (G) and G × S effects genome-wide using logistic regression assuming an additive genetic model and adjusting for 18 principal components of ancestry. We further interrogated loci with suggestive results from the joint test ( p < 1.00 × 10 -5 ) by examining the G × S effects from the same model. Out of the 133 loci with suggestive results ( p < 1.00 × 10 -5 ) for the joint test, we observed one genome-wide significant G × S effect in the 10q21 locus (rs72804706; p = 6.69 × 10 -9 ; OR = 2.62 CI [1.89, 3.62]) and 16 suggestive G × S effects. At the intergenic 10q21 locus, the risk of NSCL/P is estimated to increase with additional copies of the minor allele for females, but the opposite effect for males. Our observation that the impact of genetic variants on NSCL/P risk differs for males and females may further our understanding of the genetic architecture of NSCL/P and the sex differences underlying clefts and other birth defects.


Assuntos
Alelos , Encéfalo/anormalidades , Fenda Labial/genética , Fissura Palatina/genética , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Caracteres Sexuais , Estudos de Casos e Controles , Epistasia Genética , Feminino , Frequência do Gene/genética , Loci Gênicos , Humanos , Masculino , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Fatores de Risco
4.
Sci Rep ; 8(1): 8470, 2018 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-29855589

RESUMO

Velopharyngeal dysfunction (VPD) occurs when the muscular soft palate (velum) and lateral pharyngeal walls are physically unable to separate the oral and nasal cavities during speech production leading to hypernasality and abnormal speech reduction. Because VPD is often associated with overt or submucous cleft palate, it could be present as a subclinical phenotype in families with a history of orofacial clefting. A key assumption to this model is that the overt and subclinical manifestations of the orofacial cleft phenotype exist on a continuum and therefore share common etiological factors. We performed a genome-wide association study in 976 unaffected relatives of isolated CP probands, 54 of whom had VPD. Five loci were significantly (p < 5 × 10-8) associated with VPD: 3q29, 9p21.1, 12q21.31, 16p12.3 and 16p13.3. An additional 15 loci showing suggestive evidence of association with VPD were observed. Several genes known to be involved in orofacial clefting and craniofacial development are located in these regions, such as TFRC, PCYT1A, BNC2 and FREM1. Although further research is necessary, this could be an indication for a potential shared genetic architecture between VPD and cleft palate, and supporting the hypothesis that VPD is a subclinical phenotype of orofacial clefting.

5.
Genet Epidemiol ; 41(8): 887-897, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-29124805

RESUMO

Orofacial clefts (OFCs) are common, complex birth defects with extremely heterogeneous phenotypic presentations. Two common subtypes-cleft lip alone (CL) and CL plus cleft palate (CLP)-are typically grouped into a single phenotype for genetic analysis (i.e., CL with or without cleft palate, CL/P). However, mounting evidence suggests there may be unique underlying pathophysiology and/or genetic modifiers influencing expression of these two phenotypes. To this end, we performed a genome-wide scan for genetic modifiers by directly comparing 450 CL cases with 1,692 CLP cases from 18 recruitment sites across 13 countries from North America, Central or South America, Asia, Europe, and Africa. We identified a region on 16q21 that is strongly associated with different cleft type (P = 5.611 × 10-8 ). We also identified significant evidence of gene-gene interactions between this modifier locus and two recognized CL/P risk loci: 8q21 and 9q22 (FOXE1) (P = 0.012 and 0.023, respectively). Single nucleotide polymorphism (SNPs) in the 16q21 modifier locus demonstrated significant association with CL over CLP. The marker alleles on 16q21 that increased risk for CL were found at highest frequencies among individuals with a family history of CL (P = 0.003). Our results demonstrate the existence of modifiers for which type of OFC develops and suggest plausible elements responsible for phenotypic heterogeneity, further elucidating the complex genetic architecture of OFCs.


Assuntos
Encéfalo/anormalidades , Cromossomos Humanos Par 16 , Fenda Labial/genética , Fissura Palatina/genética , Alelos , Encéfalo/patologia , Fenda Labial/patologia , Fissura Palatina/patologia , Grupos de Populações Continentais/genética , Feminino , Fatores de Transcrição Forkhead/genética , Loci Gênicos , Estudo de Associação Genômica Ampla , Humanos , Masculino , Fenótipo , Polimorfismo de Nucleotídeo Único , Fatores de Risco
6.
Am J Med Genet A ; 173(6): 1531-1538, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28425186

RESUMO

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a group of common human birth defects with complex etiology. Although genome-wide association studies have successfully identified a number of risk loci, these loci only account for about 20% of the heritability of orofacial clefts. The "missing" heritability may be found in rare variants, copy number variants, or interactions. In this study, we investigated the role of low-frequency variants genotyped in 1995 cases and 1626 controls on the Illumina HumanCore + Exome chip. We performed two statistical tests, Sequence Kernel Association Test (SKAT) and Combined Multivariate and Collapsing (CMC) method using two minor allele frequency cutoffs (1% and 5%). We found that a burden of low-frequency coding variants in N4BP2, CDSN, PRTG, and AHRR were associated with increased risk of NSCL/P. Low-frequency variants in other genes were associated with decreased risk of NSCL/P. These results demonstrate that low-frequency variants contribute to the genetic etiology of NSCL/P.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Encéfalo/anormalidades , Fenda Labial/genética , Fissura Palatina/genética , Enzimas Reparadoras do DNA/genética , Glicoproteínas/genética , Proteínas de Membrana/genética , Proteínas Repressoras/genética , Alelos , Encéfalo/fisiopatologia , Fenda Labial/fisiopatologia , Fissura Palatina/fisiopatologia , Grupo com Ancestrais do Continente Europeu/genética , Exoma/genética , Frequência do Gene , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco
7.
Hum Genet ; 136(3): 275-286, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-28054174

RESUMO

Nonsyndromic orofacial clefts (OFCs) are a heterogeneous group of common craniofacial birth defects with complex etiologies that include genetic and environmental risk factors. OFCs are commonly categorized as cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which have historically been analyzed as distinct entities. Genes for both CL/P and CP have been identified via multiple genome-wide linkage and association studies (GWAS); however, altogether, known variants account for a minority of the estimated heritability in risk to these craniofacial birth defects. We performed genome-wide meta-analyses of CL/P, CP, and all OFCs across two large, multiethnic studies. We then performed population-specific meta-analyses in sub-samples of Asian and European ancestry. In addition to observing associations with known variants, we identified a novel genome-wide significant association between SNPs located in an intronic TP63 enhancer and CL/P (p = 1.16 × 10-8). Several novel loci with compelling candidate genes approached genome-wide significance on 4q21.1 (SHROOM3), 12q13.13 (KRT18), and 8p21 (NRG1). In the analysis of all OFCs combined, SNPs near FOXE1 reached genome-wide significance (p = 1.33 × 10-9). Our results support the highly heterogeneous nature of OFCs and illustrate the utility of meta-analysis for discovering new genetic risk factors.


Assuntos
Fenda Labial/genética , Fissura Palatina/genética , Fatores de Transcrição Forkhead/genética , Estudo de Associação Genômica Ampla , Fatores de Transcrição/genética , Proteínas Supressoras de Tumor/genética , Mapeamento Cromossômico , Humanos , Polimorfismo de Nucleotídeo Único
8.
Hum Mol Genet ; 25(13): 2862-2872, 2016 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-27033726

RESUMO

Orofacial clefts (OFCs), which include non-syndromic cleft lip with or without cleft palate (CL/P), are among the most common birth defects in humans, affecting approximately 1 in 700 newborns. CL/P is phenotypically heterogeneous and has a complex etiology caused by genetic and environmental factors. Previous genome-wide association studies (GWASs) have identified at least 15 risk loci for CL/P. As these loci do not account for all of the genetic variance of CL/P, we hypothesized the existence of additional risk loci. We conducted a multiethnic GWAS in 6480 participants (823 unrelated cases, 1700 unrelated controls and 1319 case-parent trios) with European, Asian, African and Central and South American ancestry. Our GWAS revealed novel associations on 2p24 near FAM49A, a gene of unknown function (P = 4.22 × 10-8), and 19q13 near RHPN2, a gene involved in organizing the actin cytoskeleton (P = 4.17 × 10-8). Other regions reaching genome-wide significance were 1p36 (PAX7), 1p22 (ARHGAP29), 1q32 (IRF6), 8q24 and 17p13 (NTN1), all reported in previous GWASs. Stratification by ancestry group revealed a novel association with a region on 17q23 (P = 2.92 × 10-8) among individuals with European ancestry. This region included several promising candidates including TANC2, an oncogene required for development, and DCAF7, a scaffolding protein required for craniofacial development. In the Central and South American ancestry group, significant associations with loci previously identified in Asian or European ancestry groups reflected their admixed ancestry. In summary, we have identified novel CL/P risk loci and suggest new genes involved in craniofacial development, confirming the highly heterogeneous etiology of OFCs.


Assuntos
Fenda Labial/genética , Fissura Palatina/genética , Grupo com Ancestrais do Continente Africano/genética , Grupo com Ancestrais do Continente Asiático/genética , Cromossomos Humanos Par 17/genética , Cromossomos Humanos Par 19/genética , Cromossomos Humanos Par 2/genética , Grupos Étnicos , Grupo com Ancestrais do Continente Europeu/genética , Feminino , Loci Gênicos , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Masculino , Polimorfismo de Nucleotídeo Único/genética , Fatores de Risco
9.
Am J Hum Genet ; 98(4): 744-54, 2016 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-27018472

RESUMO

Cleft palate (CP) is a common birth defect occurring in 1 in 2,500 live births. Approximately half of infants with CP have a syndromic form, exhibiting other physical and cognitive disabilities. The other half have nonsyndromic CP, and to date, few genes associated with risk for nonsyndromic CP have been characterized. To identify such risk factors, we performed a genome-wide association study of this disorder. We discovered a genome-wide significant association with a missense variant in GRHL3 (p.Thr454Met [c.1361C>T]; rs41268753; p = 4.08 × 10(-9)) and replicated the result in an independent sample of case and control subjects. In both the discovery and replication samples, rs41268753 conferred increased risk for CP (OR = 8.3, 95% CI 4.1-16.8; OR = 2.16, 95% CI 1.43-3.27, respectively). In luciferase transactivation assays, p.Thr454Met had about one-third of the activity of wild-type GRHL3, and in zebrafish embryos, perturbed periderm development. We conclude that this mutation is an etiologic variant for nonsyndromic CP and is one of few functional variants identified to date for nonsyndromic orofacial clefting. This finding advances our understanding of the genetic basis of craniofacial development and might ultimately lead to improvements in recurrence risk prediction, treatment, and prognosis.


Assuntos
Fissura Palatina/genética , Proteínas de Ligação a DNA/genética , Polimorfismo de Nucleotídeo Único , Fatores de Transcrição/genética , Animais , Estudos de Casos e Controles , Fissura Palatina/diagnóstico , Modelos Animais de Doenças , Grupos Étnicos/genética , Loci Gênicos , Estudo de Associação Genômica Ampla , Técnicas de Genotipagem , Humanos , Mutação de Sentido Incorreto , Fatores de Risco , Peixe-Zebra/embriologia , Peixe-Zebra/genética
10.
BMC Cancer ; 11: 324, 2011 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-21801414

RESUMO

BACKGROUND: Oral cancer incidence is high on the Island of Puerto Rico (PR), particularly among males. As part of a larger study conducted in PR, we evaluated smoking and drinking as risk factors for oral potentially malignant disorders (OPMDs). METHODS: Persons diagnosed with either an OPMD (n = 86) [oral epithelial dysplasia (OED), oral hyperkeratosis/epithelial hyperplasia without OED] or a benign oral tissue condition (n = 155) were identified through PR pathology laboratories. Subjects were interviewed using a standardized, structured questionnaire that obtained information, including detailed histories of smoking and drinking. Odds ratios (ORs) for smoking and drinking in relation to having an OPMD, relative to persons with a benign oral tissue condition, were obtained using logistic regression and adjusted for age, gender, education, fruit/vegetable intake and smoking or drinking. RESULTS: For persons with an OPMD and relative to individuals with a benign oral tissue condition, the adjusted OR for current smoking was 4.32 (95% CI: 1.99-9.38), while for former smokers, the ORadj was 1.47 (95% CI: 0.67-3.21), each ORadj relative to never smokers. With regard to drinking, no adjusted ORs approached statistical significance, and few point estimates exceeded 1.0, whether consumption was defined in terms of ever, current, level (drinks/week), or beverage type. CONCLUSIONS: In this study, conducted in Puerto Rico, current smoking was a substantial risk factor for OPMDs while former smokers had a considerably reduced risk compared to current smokers. There was little evidence suggesting that alcohol consumption was positively associated with OPMD risk.


Assuntos
Consumo de Bebidas Alcoólicas/epidemiologia , Doenças da Boca/epidemiologia , Lesões Pré-Cancerosas/epidemiologia , Fumar/epidemiologia , Adulto , Idoso , Estudos de Casos e Controles , Dieta , Feminino , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Neoplasias Bucais/epidemiologia , Razão de Chances , Porto Rico/epidemiologia , Fatores de Risco , Inquéritos e Questionários
11.
BMC Public Health ; 11: 391, 2011 May 26.
Artigo em Inglês | MEDLINE | ID: mdl-21612663

RESUMO

BACKGROUND: In Puerto Rico, relative to the United States, a disparity exists in detecting oral precancers and early cancers. To identify factors leading to the deficit in early detection, we obtained the perspectives of San Juan healthcare practitioners whose practice could be involved in the detection of such oral lesions. METHODS: Key informant (KI) interviews were conducted with ten clinicians practicing in or around San Juan, Puerto Rico. We then triangulated our KI interview findings with other data sources, including recent literature on oral cancer detection from various geographic areas, current curricula at the University of Puerto Rico Schools of Medicine and Dental Medicine, as well as local health insurance regulations. RESULTS: Key informant-identified factors that likely contribute to the detection deficit include: many practitioners are deficient in knowledge regarding oral cancer and precancer; oral cancer screening examinations are limited regarding which patients receive them and the elements included. In Puerto Rico, specialists generally perform oral biopsies, and patient referral can be delayed by various factors, including government-subsidized health insurance, often referred to as Reforma. Reforma-based issues include often inadequate clinician knowledge regarding Reforma requirements/provisions, diagnostic delays related to Reforma bureaucracy, and among primary physicians, a perceived financial disincentive in referring Reforma patients. CONCLUSIONS: Addressing these issues may be useful in reducing the deficit in detecting oral precancers and early oral cancer in Puerto Rico.


Assuntos
Diagnóstico Precoce , Pessoal de Saúde/psicologia , Neoplasias Bucais/diagnóstico , Biópsia , Feminino , Pessoal de Saúde/educação , Humanos , Entrevistas como Assunto , Masculino , Porto Rico , Classe Social
12.
Cancer Detect Prev ; 32(5-6): 424-30, 2009.
Artigo em Inglês | MEDLINE | ID: mdl-19250772

RESUMO

BACKGROUND: Intraoral lesions clinically suspicious for cancer/precancer should be biopsied and diagnosed histopathologically. We evaluated whether the frequency of oral cancer (OC) cases diagnosed in Puerto Rico (PR) is disproportionately high relative to the frequency of persons with histopathologic diagnoses that would have appeared clinically suspicious for OC/precancer at biopsy. METHODS: All pathology reports for oral (ICD-O-3 C01-C06) soft tissue biopsies generated during 1/2004-5/2005 by seven PR and two New York City (NYC) pathology laboratories were reviewed. The analysis was restricted to persons diagnosed with invasive oral squamous cell carcinoma (OSCC), epithelial dysplasia, or hyperkeratosis/epithelial hyperplasia (HK/EH), i.e., diagnoses associated with lesions clinically suspicious for OC/precancer. The OC relative frequency measured the percentage of persons diagnosed with OSCC among persons with OSCC, dysplasia, or HK/EH. OC relative frequencies for PR and NYC laboratories were compared. RESULTS: Overall, the OC relative frequency was 67% in PR and 40% and 4% in the NYC general and oral pathology laboratories, respectively (each p<0.001). In PR, the OC relative frequency was highest for males (80%). When OC relative frequencies were stratified by pathology laboratory type (general/oral) and compared across PR and NYC, age/gender-specific OC relative frequencies were always higher in PR; however, differences were consistently statistically significant for males only. CONCLUSION: A disparity in the OC relative frequency exists in PR vs. NYC indicating a shortfall in biopsying potentially precancerous oral lesions in PR. PR residents with intraoral lesions suspicious for oral cancer/precancer are most likely to be biopsied only after developing an invasive OC.


Assuntos
Biópsia/estatística & dados numéricos , Carcinoma de Células Escamosas/patologia , Laboratórios/normas , Neoplasias Bucais/patologia , Lesões Pré-Cancerosas/patologia , Neoplasias de Tecidos Moles/patologia , Fatores Etários , Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/epidemiologia , Transformação Celular Neoplásica/patologia , Células Epiteliais/patologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias Bucais/diagnóstico , Neoplasias Bucais/epidemiologia , Cidade de Nova Iorque/epidemiologia , Lesões Pré-Cancerosas/diagnóstico , Lesões Pré-Cancerosas/epidemiologia , Porto Rico/epidemiologia , Fatores Sexuais , Neoplasias de Tecidos Moles/diagnóstico , Neoplasias de Tecidos Moles/epidemiologia
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