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SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

ABSTRACT: Array CGH analysis in order to determine the size of atypical NF1 deletions under investigation 12 atypical NF1 deletions were investigated with the custom array CGH

ORGANISM(S): Homo sapiens

SUBMITTER: Julia Vogt

PROVIDER: E-GEOD-57859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

Project description:Array CGH analysis in order to determine the size of atypical NF1 deletions under investigation

2014-05-29 | GSE57859 | GEO

Atypical neurofibromas in neurofibromatosis type 1 are premalignant tumors

Project description:Agilent oligonucleotide 244k microarray CGH analysis of NF1-related atypical neurofibromas and high grade MPNSTs

2011-09-30 | E-MEXP-3052 | biostudies-arrayexpress

Copy number variation between BJ cells and BJ-derived iPS cells

Project description:Copy number variation analysis between BJ cells and BJ cells derived iPS cells which were established by using non-transmissible measles virus vector DNA derived from BJ cell and iPS cells were extracted and analysis using CGH array

2016-06-22 | E-GEOD-79604 | biostudies-arrayexpress

Human esophageal dysplasia (16 cases) vs. esophageal squamous cell carcinoma (59 cases)

Project description:Our aim is to identify frequent genomic aberrations both in ESCC and esophageal dysplasia, and to discover important copy number-driving genes and microRNAs in ESCC. We carried out array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR and immunohistochemistry (IHC). Integrated analysis was performed to identify genes or microRNAs with copy number-expression correlations. Two group experiment, esophageal dysplasia vs. esophageal squamous cell carcinoma. Biological replicates: 16 dysplasias vs. 59 carcinomas

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aCGH: Human SUM149-Luc triple-negative Inflammatory Breast Cancer cell line versus its metabolically adaptable variants MA1 and MA2

Project description:CGH array of MA1 and MA2 variant cells as compared to the parental SUM149-Luc breast cancer cell line. The MA1 and MA2 variants were isolated based on the ability of rare cancer cells to survive and grow without adding glutamine in culture medium. To gain insight into the characteristic of metabolically adaptable MA cells that enables them to survive severe metabolic challenge, i.e., prolonged lack of glutamine and other challenges [Singh et al., PLoS ONE 7: e36510, 2012], we analyzed CGH array to compare these cells with the parental SUM149-Luc (luciferase-transfected) cells. We analyzed two independently selected cell populations, one from 0.5 million parental cells (designated MA1) and one from 1 million parental cells (designated MA2). Comparing the MA1 and MA2 variants to the common parental SUM149-Luc cell line. One sample each.

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Molecular characterization of two unrelated patients ABCB4 deletions

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Detection of non-coding deletion CNVs upstream to FOXF1 [Agilent-030795]

Project description:Genomic copy number analysis in patients with ACD/MPV. An unanticipated and tremendous amount of the non-coding sequences of the human genome are transcribed. Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and their functions remain enigmatic. We demonstrate that deletions of lncRNA genes cause a lethal lung developmental disorder, Alveolar Capillary Dysplasia with Misalignment of Pulmonary Veins (ACD/MPV), with parent of origin effects. We identify non-coding overlapping deletions 250 kb upstream to FOXF1 in nine patients with ACD/MPV that arose de novo specifically on the maternally inherited chromosome and delete a fetal lung-specific EST, part of an lncRNA. These deletions define distant cis-regulatory region that harbors a differentially methylated CpG island, binds GLI2 depending on the methylation status of this CpG island, and physically interacts with and up-regulates the FOXF1 promoter, consistent with the absence of the fetal lung-transcribed lncRNA perturbing FOXF1 regulation. LncRNA-mediated chromatin interactions may be responsible for position effect phenomenon and potentially cause many disorders of human development.potentially cause many disorders of human development. CNVs were identified by array CGH with custom-designed 16q24.1 region specific (1Mb flanking FOXF1) 44K oligonucleotide microarrays (Agilent technologies) in 3 patients with ACD.

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Project description:To allow accute charaterization of NF1 locus constitutional microdeletion in 70 NF1 patients, a custom array CGH was developped. Goal was to obtain genomic rearrangements fine characterization in order to perform genotype-phenotype correlation in NF1 microdeleted patients. To serve as a reference group in our genotype-phenotype correlation study in NF1 microdeletion patients, non-deleted NF1 patients (i.e. patients with an intragenic NF1 mutation) were also selected from our database. A total of 389 NF1 patients were included in the reference group of non-deleted patients. Multiple logistic regression was performed to test the association of each clinical feature individually with the type of constitutional NF1 mutation (intragenic mutation vs. microdeletion). The phenotypic traits of the 389 reference patients are available in the "GSE19730_control_patient_characteristics.txt" supplementary file on the Series record. NF1 locus microdeletions characterization vs reference sample (pool of six normal control DNAs)

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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

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