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Application of CGH-array and SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE62440 | GEO | 2014/10/17

SECONDARY ACCESSION(S): PRJNA264094

REPOSITORIES: GEO

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Application of array-CGH for the detection of genomic rearrangements responsible for syndromic mental retardation of unknown cause

2014-05-22 | GSE57899 | GEO

Application of CGH-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

Project description:Developmental delay/intellectual disability (DD/ID)affects 2% of our population. However, most patients are often left without aspecific diagnosis,with the corresponding consequences for the patients and their families. The application of microarray technology in the study of patients with DD/ID allows whole-genome analysis with a high resolutionand performance. Here we present the results of four cases included in a series of 246 patients with DD/ID, as part of the screening of the genetic causes responsible for their phenotype.

2014-10-17 | GSE62439 | GEO

Application of SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

Project description:Developmental delay/intellectual disability (DD/ID)affects 2% of our population. However, mostpatients are often leftwithout aspecific diagnosis,with thecorresponding consequences for the patientsand their families. The application of microarray technology in the study of patients with DD/ID allows whole-genome analysis with a high resolutionand performance. Here we present the results of a case included in a series of 246 patients with DD/ID, as part of the screening of the genetic causes responsible for their phenotype.

2014-10-17 | GSE62438 | GEO

Application of array-CGH for the detection of genomic rearrangements responsible for syndromic mental retardation of unknown cause

Project description:Here we describe an interstitial pure duplication of 19p13.3 that was initially considered as a de novo alteration, in a patient with intellectual disability studied by array-CGH. The finding of the same chromosomal alteration in a first-degree cousin of this patient led us to investigate the presence of insertional translocations. An intrachromosomal insertional translocation was found in at least three generations. Three intellectually disabled patients with the same duplication and multiples abortions among translocation carrier family members were found. A review of other published cases has allowed us to find three other cases with a similar pure duplication and some clinical findings present in all patients as intrauterine growth retardation, microcephaly, motor and speech delay, moderate to severe intellectual disability and dysmorphic features. These findings allow us to suggest the existence of a new microduplication syndrome in chromosomal region 19p13.3. Whole genome array-CGH was performed on Agilent oligo-chip 44K (human genome CGH microarray G4410B from Agilent Technologies, Palo Alto, CA) as recommended. The patientsM-bM-^@M-^Y DNA samples were tested against a pool of 10 sex-matched normal DNA samples, all of them (patients and normal controls) from our geographical area. Scanned images were quantified using Agilent Feature Extraction Software (v9.0). The results were analyzed using Agilent Genomic Workbench software. Annotations have been obtained from UCSC (http://genome.ucsc.edu) based on human genome build GRCh37/hg19.

2014-05-22 | E-GEOD-57899 | biostudies-arrayexpress

Application of SNP-array for the detection of genomic rearrangements responsible for sindromic mental retardation of unknown cause

Project description:Developmental delay/intellectual disability (DD/ID)affects 2% of our population. However, mostpatients are often leftwithout aspecific diagnosis,with thecorresponding consequences for the patientsand their families. The application of microarray technology in the study of patients with DD/ID allows whole-genome analysis with a high resolutionand performance. Here we present the results of a case included in a series of 246 patients with DD/ID, as part of the screening of the genetic causes responsible for their phenotype. SNP-array was performed on Genome-Wide Human SNP_6 (Affymetrix) as recommended by the manufacter. Analysis was performed with Affymetrix reference profile 'GenomeWideSNP_6.hapmap270.na31.r1.a5.ref'.

2014-10-17 | E-GEOD-62438 | biostudies-arrayexpress

Use of array CGH in the diagnosis of patients with mental retardation

Project description:This series represent the data set belonging to the publication by de Vries et al. Diagnostic genome profiling in mental retardation. American Journal of Human Genetics, vol 77: 606-616 (2005). In this study 100 patients with unexplained mental retardation were analyzed for DNA copy-number changes using a tiling-resolution genomewide microarray containing 32,447 BACs. Keywords: CGH

2005-09-16 | GSE3191 | GEO

Chromosomal copy number changes in patients with non-syndromic X linked mental retardation detected by array CGH.

Project description:Several studies have shown that array based comparative genomic hybridisation (CGH) is a powerful tool for the detection of copy number changes in the genome of individuals with a congenital disorder. In this study, 40 patients with non-specific X linked mental retardation were analysed with full coverage, X chromosomal, bacterial artificial chromosome arrays. Copy number changes were validated by multiplex ligation dependent probe amplification as a fast method to detect duplications and deletions in patient and control DNA. This approach has the capacity to detect copy number changes as small as 100 kb. We identified three causative duplications: one family with a 7 Mb duplication in Xp22.2 and two families with a 500 kb duplication in Xq28 encompassing the MECP2 gene. In addition, we detected four regions with copy number changes that were frequently identified in our group of patients and therefore most likely represent genomic polymorphisms. These results confirm the power of array CGH as a diagnostic tool, but also emphasise the necessity to perform proper validation experiments by an independent technique.

| S-EPMC2563232 | biostudies-literature

High-resolution SNP array analysis of patients with developmental disorder and normal array CGH results.

Project description:BACKGROUND: Diagnostic analysis of patients with developmental disorders has improved over recent years largely due to the use of microarray technology. Array methods that facilitate copy number analysis have enabled the diagnosis of up to 20% more patients with previously normal karyotyping results. A substantial number of patients remain undiagnosed, however. METHODS AND RESULTS: Using the Genome-Wide Human SNP array 6.0, we analyzed 35 patients with a developmental disorder of unknown cause and normal array comparative genomic hybridization (array CGH) results, in order to characterize previously undefined genomic aberrations. We detected no seemingly pathogenic copy number aberrations. Most of the vast amount of data produced by the array was polymorphic and non-informative. Filtering of this data, based on copy number variant (CNV) population frequencies as well as phenotypically relevant genes, enabled pinpointing regions of allelic homozygosity that included candidate genes correlating to the phenotypic features in four patients, but results could not be confirmed. CONCLUSIONS: In this study, the use of an ultra high-resolution SNP array did not contribute to further diagnose patients with developmental disorders of unknown cause. The statistical power of these results is limited by the small size of the patient cohort, and interpretation of these negative results can only be applied to the patients studied here. We present the results of our study and the recurrence of clustered allelic homozygosity present in this material, as detected by the SNP 6.0 array.

| S-EPMC3523000 | biostudies-literature

Microarray CGH (aCGH) analysis of a patient with Mental Retardation (MR)

Project description:Background: Mental Retardation occurs with the prevalence of 2%-3% of general population. Molecular karyotyping by 1-Mb resolution microarray revealed that pathological genomic imbalances were found in 14%-20% of MR. Aim: The aim of this study is to find the submicroscopic rearrangements in patient with MR using the custom BAC microarray (probe spacing at 0.75 Mb throughout the human genome). Conclusion: We identified approximate 2.0-Mb deletion on 9q33.3-q34.11 in a female with MR (Patient 1). Keywords: array CGH

2008-05-11 | GSE10077 | GEO

Mental Retardation Patients

Project description:Profiling the genomic profiles of mental retardation patients. 13 mental retardation patients were selected for detection of genomic aberrations.

2009-12-16 | GSE19457 | GEO

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