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Series GSE42624 Query DataSets for GSE42624
Status Public on Nov 30, 2012
Title GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in meningioma tumors
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Cytogenetic profiles of 50 meningiomas using high-density GeneChip Mapping 500K set and Genome-Wide Human SNP 6.0 Array in the tumor tissues and in the peripheral blood of the same patients. A total of two hundred 500k arrays (100 tumor samples and 100 blood samples) and 14 SNP6.0 arrays (7 tumour samples and 7 peripheral blood samples) were studied to explore the most common recurrent chromosomal abnormalities (gains and losses) in meningiomas. Our results confirm that del(22q) (52%) and del(1p) (16%) (common deleted regions: 22q11.21-22q13.3. and 1p31.2-p36.33) are the most frequent abnormalities. Additionally, recurrent monosomy 14 (8%), del(6p) (10%), del(7p) (10%) and del(19p) (6%) were also observed, while copy number variation (CNV) patterns consistent with recurrent chromosome gains, gene amplification was absent or rare. Based on their overall SNP profiles meningiomas could be classified into: i) diploid cases, ii) meningiomas with a single chromosome change (e.g. monosomy 22/del(22q) and iii) tumours with ≥2 altered chromosomes.
 
Overall design 500K SNP mapping set array and Genome-Wide Human SNP 6.0 Array were used to profile 50 meningiomas with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair. In seven tumors, both types of arrays were assessed.
 
Contributor(s) Tabernero MD, Orfao JA
Citation(s) 22371336, 24536048
Submission date Nov 29, 2012
Last update date Nov 27, 2018
Contact name MariaDolores Tabernero
E-mail(s) taberner@usal.es
Fax 0034-923-264795
Organization name Hospital Universitario de Salamanca y Centro del Cáncer
Lab Unidad de Investigación
Street address Paseo San Vicente 58-182
City Salamanca
ZIP/Postal code 37007
Country Spain
 
Platforms (3)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (214)
GSM1045896 Sample#1 Blood DNA_NSP
GSM1045897 Sample#1 Blood DNA_STY
GSM1045898 Sample#1 Tumor DNA _NSP
Relations
BioProject PRJNA182380

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE42624_RAW.tar 6.4 Gb (http)(custom) TAR (of CEL, CHP)
GSE42624_SNP6_SNPcn_probes_14_meningioma_arrays.txt.gz 3.9 Mb (ftp)(http) TXT
GSE42624_SNP6_probes_CN_14_meningioma_arrays.txt.gz 2.7 Mb (ftp)(http) TXT
GSE42624_nsp100_copynumer_dat_meningioma_arrays.txt.gz 29.5 Mb (ftp)(http) TXT
GSE42624_sty100_copynumber_data_meningioma_arrays.txt.gz 22.3 Mb (ftp)(http) TXT
Processed data are available on Series record
Processed data provided as supplementary file
Processed data included within Sample table

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