Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Affymetrix SNP 6.0 profiles of 10 Human B-NHL lines

ABSTRACT: B-cell Non Hodgkin Lymphoma are a heterogenous group chracterized by a variety of genetic changes, including translocations, deletions and amplifications. Here we analyzed 10 B-NHL lines by Affymetrix SNP 6.0 to detect copy number changes. Specifically, we aim to identify cell lines suitable for testing the consequences of acute reintroduction of candidate tumor suppressor genes as they harbor deletions which include the candidate gene(s). 10 BNHL cell lines were grown in standard cell culture conditions. Genomic DNA was exptracted from frozen pellets and analyzed for copy number variations with Affymetrix SNP 6.0 Arrays

ORGANISM(S): Homo sapiens

SUBMITTER: Claudio Scuoppo

PROVIDER: E-GEOD-36967 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Affymetrix SNP 6.0 profiles of 10 Human B-NHL lines

Project description:B-cell Non Hodgkin Lymphoma are a heterogenous group chracterized by a variety of genetic changes, including translocations, deletions and amplifications. Here we analyzed 10 B-NHL lines by Affymetrix SNP 6.0 to detect copy number changes. Specifically, we aim to identify cell lines suitable for testing the consequences of acute reintroduction of candidate tumor suppressor genes as they harbor deletions which include the candidate gene(s).

2012-04-03 | GSE36967 | GEO

Affymetrix SNP 6.0 array data from neuroendocrine primary tumor and its metastasis

Project description:Reports on common mutations in neuroendocrine tumors (NET) are rare and clonality of NET metastases has not been investigated in this tumor entity yet. We selected a NET and a the corresponding lymph node and liver metastases as well as the derivative cell lines to screen for somatic mutations in the primary NET and to track the fate of genetic changes (by Affymetrix SNP 6.0 micorarray and targeted resequencing by 454 GS FLX) and during metastasis and in vitro progression. using Affymetrix SNP 6.0 Arrays. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.

2012-07-16 | E-GEOD-39371 | biostudies-arrayexpress

A framework for identification of actionable cancer genome dependencies in small cell lung cancer

Project description:We analyzed copy numbers of 60 SCLC cell lines using 6.0 SNP-arrays. For a subgroup of 36 cell lines, previously published copy number data was utilized. CEL and SEG files are included for all cell lines, for which copy number data were not publicly available.

2012-09-21 | GSE40142 | GEO

Elimination of mitochondrial DNA variants by nuclear genome transfer in human oocytes.

Project description:Nuclear genome exchange between different oocytes results in efficient development and stem cell derivation. No differences in homozgyous CNVs were found between swaPS and pES lines. No differences in total copy number variations were found between the swaPS and pES lines. DNA was isolated from cultured cells. Affymetrix SNP arrays were used in accordance with the manufacturer's instructions. Copy number analysis was performed using NEXUS 6.0.

2013-01-01 | E-GEOD-42271 | biostudies-arrayexpress

High-resolution mapping of copy-number alterations with massively parallel sequencing

Project description:In order to benchmark the reproducibility of Affymetrix Genome-Wide Human SNP Array 6.0 for detecting copy-number alterations, we performed replicate hybridizations of 3 tumor cell lines and 2 paired normal cell lines obtained from the American Type Culture Collection (ATCC). We calculated copy numbers at each SNP probeset by a custom copy-number pipeline (PMID: 18772890). For each cell line, copy number data from replicate arrays are supplied in the accompanying matrix files. For each SNP probeset, we calculated the median copy number across replicate arrays. We compared the copy-number alterations detected by Circular Binary Segmentation segmentation of these arrays with statistical analyses of short sequence reads obtained from the Illumina/Solexa 1G GenomeAnalyzer. Shotgun sequencing results can be found in the NCBI Short Read Archive, accession number SRP000246 Keywords: disease state analysis

2008-11-14 | GSE13372 | GEO

Identification of candidate predisposing copy number variants in familial and early-onset colorectal cancer patients

Project description:In the majority of colorectal cancers (CRC) under clinical suspicion for a hereditary cause, the disease-causing genetic factors are still to be discovered. In order to identify such genetic factors we stringently selected a discovery cohort of 41 CRC index patients with microsatellite-stable tumors. All patients were below 40 years of age at diagnosis and/or exhibited an overt family history. We employed genome-wide copy number profiling using high-resolution SNP-based array CGH on germline DNA, which resulted in the identification of novel copy number variants (CNVs) in 6 patients (15%) encompassing, among others, the cadherin gene CDH18, the bone morphogenetic protein antagonist family gene GREM1, and the breakpoint cluster region gene BCR. In addition, two genomic deletions were encountered encompassing two microRNA genes, hsa-mir-491/KIAA1797 and hsa-mir-646/AK309218. None of these CNVs has previously been reported in relation to CRC predisposition in humans, nor were they encountered in large control cohorts (>1,600 unaffected individuals). Since several of these newly identified candidate genes may be functionally linked to CRC development, our results illustrate the potential of this approach for the identification of novel candidate genes involved in CRC predisposition. Copy number detection was performed using CNAG2.0 software for 250k SNP arrays and using the Affymetrix Genotyping Console v2.1 software for SNP 6.0 arrays, Reference genomes are included in this data set. Germline genomic DNA from 41 patients with early-onset microsatellite stable colorectal cancer was hybridized on Affymetrix Nsp/6.0 SNP-based arrays according to manufacturer's procedures.

2010-11-01 | E-GEOD-13429 | biostudies-arrayexpress

Affymetrix SNP6.0 on Ollier disease-related tumors

Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.

2011-08-26 | GSE22984 | GEO

Affymetrix SNP array data for 4 MYC-negative B-cell lymphoma cases and 2 B-cell lymphoma cell lines (SU-DHL-5 and HT)

Project description:Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from blood samples and cell lines Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 MYC-negative B-cell lymphoma and 2 B-cell lymphoma cell lines

2014-01-10 | E-GEOD-47507 | biostudies-arrayexpress

Genomic exploration of monozygotic twins discordant (MZD) for schizophrenia uncovers de novo mutations (DNM) and reveals candidate genes

Project description:We examined six pairs of monozygotic twins discordant (MZD) for schizophrenia and identified copy number variation (CNV) and single nucleotide polymorphism (SNP) differences between affected and unaffected co-twins using the Affymetrix Genome Wide SNP 6.0.

2011-11-11 | GSE33598 | GEO

A framework for identification of actionable cancer genome dependencies in small cell lung cancer

2012-09-21 | E-GEOD-40142 | biostudies-arrayexpress