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Series GSE7822 Query DataSets for GSE7822
Status Public on Nov 02, 2007
Title A comparison of DNA copy number profiling platforms using a panel of melanoma cell lines
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Genome variation profiling by SNP array
Summary The accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes. Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have emerged as a cornerstone technology in the genomic era. The diversity of commercially-available platforms prompted a systematic comparison of five copy number profiling assays for their ability to detect 2-fold copy number gain and loss (4n or 1n, respectively) as well as focal high-amplitude CNAs. Here, using a collection of established human melanoma cell lines, we defined the reproducibility, absolute signals, signal:noise, false-positive and false-negative rates for each of the five assays against ground-truth defined by Spectral Karyotyping (SKY), in addition to comparing the concordance of CNAs detection by two high-resolution Agilent and Affymetrix microarray platforms. Our analyses concluded that the Agilent’s 60mer oligo-microarray with probe design optimized for genomic hybridization offers the highest sensitivity and specificity [area under Receiver Operator Characteristic (ROC) curve >0.99] while Affymetrix’s SNP microarray appears to offer better detection of CNAs in gene-poor region. Availability of these comparison results should guide study design decisions and facilitate further computational development.
Keywords: comparative genomic hybridization
 
Overall design We generated copy number profiles of a defined set of tumor cell lines on five oligo-microarray-based assays of three platforms (Agilent, Affymetrix and NimbleGen) and determined the reproducibility, signal and noise as well as sensitivity and specificity of each in detecting two-fold signals based on SKY-defined aberrations as ground-truth for comparison. In addition, high-density microarray assays from Agilent and Affymetrix platforms were further compared for definition of CNAs in an independent dataset using published analytical approaches. All arrays were run from the same DNA harvest from respective cell lines. Each array was run according to the protocol of the manufacturer.
 
Contributor(s) Greshock JD, Feng B, Weber BL, Chin L
Citation(s) 17968032, 19671800
Submission date May 16, 2007
Last update date Dec 22, 2017
Contact name Joel Greshock
Organization name GlaxoSmithKline
Department Translational Medicine, Oncology
Street address 2301 Renaissance Blvd.
City King of Prussia
State/province PA
ZIP/Postal code 19406
Country USA
 
Platforms (8)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
GPL2879 Agilent-013282 Human Genome CGH Microarray 44B (Feature number version)
Samples (151)
GSM187938 Germline DNA derived from normal individual (AFFY100KHINDIIIREF12)
GSM187939 Germline DNA derived from normal individual (AFFY100KHINDIIIREF11)
GSM187940 Germline DNA derived from normal individual (AFFY100KHINDIIIREF10)
Relations
BioProject PRJNA100055

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
GSE7822_RAW.tar 4.3 Gb (http)(custom) TAR (of CEL, TXT)
GSE7822_Readme.txt 162 b (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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