Genome-wide DNA methylation analysis of a cohort of 41 patients affected by Oculo-auriculo-vertebral spectrum (OAVS).
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638638 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Oculo-auriculo-vertebral spectrum (OAVS; OMIM 164210) is a rare developmental disorder originating from abnormal development of the first and second branchial arch. The clinical phenotype is extremely heterogeneous with ear anomalies, hemifacial microsomia, ocular defects, and vertebral malformations being the main features. MYT1, AMIGO2 and ZYG11B gene variants having been reported in a few OAVS patients, but the etiology of the disease remains largely unknown. A multifactorial origin of the OAVS has been proposed, including the involvement of environmental or epigenetic mechanisms. To identify the epigenetic mechanisms contributing to OAVS, we evaluated the DNA-methylation profile of 41 affected patients by using a BeadChip 450K genome-wide approach. The analysis was first carried out at a group level by comparing the OAVS group methylation profile to the control group (n=48) revealing a slight epigenetic variation in a number of genes implicated in biological processes involving basic chromatin dynamics such as DNA packaging, chromatin assembly, protein-DNA organization, and gene silencing in patients compared to controls . A subsequent analysis focused on searching for Stochastic Epigenetic Variations (SEV) in individual profiles identified an increased number of SEV in OAVS patients compared to controls. Although no recurrent deregulated enriched region was evidenced, isolated patients harboring suggestive epigenetic variations, including changes in imprinted domains, were identified. The recognition of a different DNA methylation pattern in OAVS patients and the identification of isolated patients with suggestive epigenetic variations provide consistent evidences for the contribution of epigenetic mechanisms to the etiology of this complex and heterogeneous disorder.
2021-02-04 | GSE152204 | GEO
Project description:Oculo-auriculo-vertebral-spectrum (OAVS; OMIM 164210) is a rare disorder originating from abnormal development of the first and second branchial arch. The clinical phenotype is extremely heterogeneous with ear anomalies, hemifacial microsomia, ocular defects, and vertebral malformations being the main features. MYT1, AMIGO2, and ZYG11B gene variants were reported in a few OAVS patients, but the etiology remains largely unknown. A multifactorial origin has been proposed, including the involvement of environmental and epigenetic mechanisms. To identify the epigenetic mechanisms contributing to OAVS, we evaluated the DNA-methylation profiles of 41 OAVS unrelated affected individuals by using a genome-wide microarray-based methylation approach. The analysis was first carried out comparing OAVS patients with controls at the group level. It revealed a moderate epigenetic variation in a large number of genes implicated in basic chromatin dynamics such as DNA packaging and protein-DNA organization. The alternative analysis in individual profiles based on the searching for Stochastic Epigenetic Variants (SEV) identified an increased number of SEVs in OAVS patients compared to controls. Although no recurrent deregulated enriched regions were found, isolated patients harboring suggestive epigenetic deregulations were identified. The recognition of a different DNA methylation pattern in the OAVS cohort and the identification of isolated patients with suggestive epigenetic variations provide consistent evidence for the contribution of epigenetic mechanisms to the etiology of this complex and heterogeneous disorder.
| S-EPMC7866060 | biostudies-literature
Project description:Oculo-facio-cardio-dental syndrome (OFCD) is a rare genetic disorder characterized by teeth with extremely long roots (radiculomegaly), and craniofacial, eye and cardiac abnormalities. The mutation of the transcriptional co-repressor BCOR has been identified as being responsible for oculo-facio-cardio-dental (OFCD) syndrome. Mesenchymal stem cells (MSCs) is isolated from the root apical papilla of an OFCD patient. Gene expression profiling is performed and compared between mutant MSCs and wild type MSCs. Total RNA were extracted from normal MSCs (MSCWT) and mutant MSCs (MSCO).
2009-07-23 | E-GEOD-15214 | biostudies-arrayexpress
Project description:Oculo-facio-cardio-dental syndrome (OFCD) is a rare genetic disorder characterized by teeth with extremely long roots (radiculomegaly), and craniofacial, eye and cardiac abnormalities. The mutation of the transcriptional co-repressor BCOR has been identified as being responsible for oculo-facio-cardio-dental (OFCD) syndrome. Mesenchymal stem cells (MSCs) is isolated from the root apical papilla of an OFCD patient. Gene expression profiling is performed and compared between mutant MSCs and wild type MSCs.
2009-07-23 | GSE15214 | GEO
Project description:Mice were obtained from in house breeding of C57BL/6J and C57BL/6J-Chr 1A/Na breeding pairs (Jackson Laboratories, USA). To produce F1 hybrids, C57BL/6J females were mated with C57BL/6J-Chr 1A/Na males. The F1 hybrids were intercrossed, producing 82 F2 progeny (41 males and 41 females). Microarray analysis was performed on six pairs of affected and non-affected male animals from the F2 progeny selected on the basis of their motor activity levels (average daily levels of distance moved over a 3 days recording: 768±74 cm/hr (affected) versus 1765±175 cm/hr (non-affected)(p<0.0001).
2006-12-31 | E-UMCU-22 | biostudies-arrayexpress
Project description:Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family. Keywords: control study: target detection and specificity 2 lab strains of adenovirus (type 40 and 41) were extracted directly from ATCC samples. Viral DNA was was extracted and labeled with Cy3 and Cy5 dyes for Adenovirus type 40 and 41 respectively.
2010-05-26 | E-GEOD-10569 | biostudies-arrayexpress
Project description:Background and purposeCranial nerve abnormalities might be observed in hemifacial microsomia and microtia (oculo-auriculo-vertebral spectrum), but the rate, features, and relationship with functional impairment or phenotype severity have not yet been defined. This study aimed at investigating absence/asymmetry, abnormal origin, morphology and course of cranial nerves, and presence/asymmetry of the foramen ovale and inferior alveolar nerve canal in a cohort of oculo-auriculo-vertebral spectrum patients.Materials and methodsTwenty-nine patients with oculo-auriculo-vertebral spectrum (mean age, 7 years; age range, 0.2-31 years; 12 females) underwent brain MR imaging, CT, and neurologic evaluation; 19 patients had a more severe phenotype (Goldenhar syndrome).ResultsCranial nerve abnormalities were detected only in patients with Goldenhar syndrome (17/19, bilaterally in 8) and were involved the second (4/19), third (1/18), fifth (11/19), sixth (8/16), seventh (11/18), and eighth (8/18) cranial nerves. Multiple cranial nerve abnormalities were common (11/17). Eleven patients showed bone foramina abnormalities. Trigeminal and facial nerve dysfunctions were common (44% and 58%, respectively), especially in patients with Goldenhar syndrome. Trigeminal abnormalities showed a good correlation with ipsilateral dysfunction (P = .018), which further increased when bone foramina abnormalities were included. The facial nerve showed a trend toward correlation with ipsilateral dysfunction (P = .081). Diplopia was found only in patients with Goldenhar syndrome and was associated with third and sixth cranial nerve abnormalities (P = .006).ConclusionsAmong patients with oculo-auriculo-vertebral spectrum, cranial nerve morphologic abnormalities are common, correlate with phenotype severity, and often entail a functional impairment. The spectrum of cranial nerve abnormalities appears wider than simple hypo-/aplasia and includes an anomalous cisternal course and partial/complete fusion of diverse cranial nerves.
| S-EPMC7965278 | biostudies-literature
Project description:Co-hybridization of Adenovirus type 40 and 41 to test probe specificity for closely related viral targets. ATCC strains of Adenovirus type 40 and 41 were hybridized to the array as a control run and a proof of concept. Degree of cross hybridization between polio nucleic acid and non-adenovirus 40 and 41 probes was evaluated. Specificity of the probe design was determined between closely related members of the same virus family. Keywords: control study: target detection and specificity
2008-02-28 | GSE10569 | GEO
Project description:Sinorhizobium meliloti 41 Resequencing
| PRJNA501436 | ENA