Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

16p13 aberrations predispose to autism and MR

ABSTRACT: Autism and mental retardation (MR) are often associated, suggesting that these conditions are etiologically related. Recently, array-based comparative genomic hybridization (array CGH) has identified submicroscopic deletions and duplications as a common cause of MR. This prompted us to search for such genomic imbalances in autism and related disorders. Here we describe a 1.5 Mb duplication on chromosome 16p13.1, found in four autistic male patients from three families and several variably affected and unaffected relatives. A deletion of the same interval was identified in three unrelated patients with MR and other clinical abnormalities. Duplications and deletions of this interval have not been described before, neither as copy number variants in the Database of Genomic Variants nor in >600 individuals from other cohorts examined by high resolution array CGH in our laboratory. Thus, this is the first description of a recurrent genomic imbalance predisposing to autism and/or MR. Keywords: array CGH

ORGANISM(S): Homo sapiens

PROVIDER: GSE6225 | GEO | 2007/05/22

SECONDARY ACCESSION(S): PRJNA97585

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

X chromosome-specific Array-CGH of XLMR patient

Project description:Mental retardation (MR) is a non-progressive cognitive impairment affecting 2 to 3% of the Western population. So far, point mutations and subtle deletions and insertions have been shown to represent only a proportion (<40%) of genetic causes underlying X-linked mental retardation (XLMR). We have screened a subset of 300 presumable X-linked families by X chromosome-specific array-CGH and identified 6 families with overlapping microduplications at Xp11.22 containing two candidate genes; both of which showed overexpression in the affected individuals. Array-CGH data revealed aberrant Cy5/Cy3 log2 ratios for different but overlapping sets of clones indicating varying sizes of these duplications in the different families. X chromosome-specific array-CGH performed for probands of families A, FAM3, B, MRX17, C, MRX31, and D, A057, revealing the duplications at Xp11.22. DNA from two unrelated MR patients were differentially labeled and co-hybridized onto the X-array. The patients with duplications were hybridized in Cy5 against unrelated MR patients, named Pat XY1-6, in the Cy3 channel.

2010-06-25 | E-GEOD-9143 | biostudies-arrayexpress

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

X chromosome-specific Array-CGH of XLMR patient

2008-02-20 | GSE9143 | GEO

Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation.

2007-03-12 | GSE7226 | GEO

Transcription profiling of human children with mental retardation and immediate family members

Project description:The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically-detectable chromosomal abnormalities are the most frequent recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy number variants. We studied 100 children with idiopathic mental retardation and their parents using the Affymetrix GeneChipÂ® Mapping 100K Assay and found de novo duplications as small as 1.1 Mb in three cases, de novo deletions as small as 178 kb in eight cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy number variants as conventional cytogenetic analysis in people with mental retardation. Experiment Overall Design: Using the Affymetrix GeneChipÂ® Mapping 100K Assay we studied 100 trios that each included one child with idiopathic mental retardation (MR) and both of his/her unaffected biological parents. We also tested 10 unaffected siblings of the MR children from 10 of the above families. In addition, we analyzed 7 trios (child and both unaffected biological parents) as positive controls with previously identified chromosomal aberrations. Experiment Overall Design: Within each sample ID the four digit number refers to a family. Following this four digit family number, 'c' indicates child with MR, 'm' means unaffected mother, 'f' means unaffected father and 's' means unaffected sibling.

2008-06-21 | E-GEOD-7226 | biostudies-arrayexpress

Identification of Candidate Genes for Sporadic Amyotrophic Lateral Sclerosis by Array Comparative Genomic Hybridisation

Project description:Background: Amyotrophic lateral sclerosis (ALS) is a devastating disorder of the central nervous system that leads to progressive loss of upper and lower motor neurons. Most cases are sporadic and of unknown aetiology. In this study, we screened 71 patients with sporadic ALS for the presence of DNA copy number variations, in order to identify novel candidate disease genes. Methods: We have used sub-megabase resolution BAC array comparative genomic hybridisation to detect genomic imbalances in our ALS patient cohort. In order to distinguish phenotypically neutral copy number variations occurring frequently in the normal population from disease-associated aberrations, we screened our results against both the Database of Genomic Variants and a reference data set of approximately 700 normal individuals and probands with other disorders analysed in our laboratory. Aberrations with potential relevance for disease aetiology were verified by oligo array CGH. Findings: In 71 patients with sporadic ALS, we identified a total of six duplications and seven deletions that scored above our threshold. Twelve of these thirteen variations were smaller than 1Mb. Seven were observed exclusively in ALS patients and thus likely play causal roles in the disorder. Analysis of these regions highlighted, for example, the SLC1A7 (EAAT5) glutamate transporter and the kinesin family member KIF9 as good positional and functional candidate genes for ALS. Interpretation: Non-polymorphic sub-microscopic duplications and deletions observable by array CGH are frequent in patients with sporadic ALS. Analysis of such aberrations serves as an excellent starting point in deciphering the aetiology of this complex disease. Keywords: array CGH

2008-12-25 | GSE7950 | GEO

Identification of Candidate Genes for Sporadic Amyotrophic Lateral Sclerosis by Array Comparative Genomic Hybridisation

2008-12-24 | E-GEOD-7950 | biostudies-arrayexpress

Array-based comparative genomic hybridization study of human embryonic stem cell lines

Project description:G-banding of human embryonic stem cells (hESC) has proved their predisposition to aneuploidy of chromosomes 12, 17 and X. Now, using array-based comparative genomic hybridization, we find that hESC also accumulate other recurrent chromosomal abnormalities, such as duplications of stemness genes, submicroscopic instability of 20q11.21 and the appearance of a derivative chromosome 18. Keywords: comparative genomic hybridization, genomic integrity of human embryonic stem cells

2008-11-04 | GSE13422 | GEO

Large inverted duplications form via a hairpin mechanism

Project description:Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted repeats are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “hairpin” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the hairpin. We also find evidence of short insertions and inversions at inverted duplication junctions, consistent with a DNA replication-based CNV mechanism. This process can give rise to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes High resolution array CGH; two-color experiment, clinical patient vs. normal control gDNA; sex mis-matched

2013-04-03 | E-GEOD-45395 | biostudies-arrayexpress

Detection of de novo and homozygous copy number variants in 99 autism simplex trios

Project description:Comparison of whole genome exome array CGH to a commercial SNP array for detection of de novo and homozygous copy number variants in 99 autism simplex trios. Will update once manuscript is prepared.

2011-04-30 | GSE23765 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data