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Series GSE212051 Query DataSets for GSE212051
Status Public on Aug 25, 2023
Title Evaluation of somatic copy number variation detection by NGS techonologies and bioinformatics tools
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary We have benchmarked the performance of cancer CNV calling by six most recent software tools on their detection accuracy, sensitivity, and reproducibility. We also explored the consistency of CNV calling across different orthogonal technologies, including optical mapping and microarrays. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we established a high-confidence CNV call set for the reference sample.
Overall design Three replicate preparations of the tumor cell line HCC1395 were compared to three replicate preparations of its matched normal control cell line HCC1395BL using the Illumina Infinium CytoSNP-850K BeadChip.
Contributor(s) Jaeger E, Xiao W
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Submission date Aug 25, 2022
Last update date Aug 25, 2023
Contact name Wenming Xiao
Organization name Center for Drug Evaluation and Research, FDA
Department Office of New Drugs
Street address 10903 New Hampshire Avenue
City Silver Spring
State/province MD
ZIP/Postal code 20993
Country USA
Platforms (1)
GPL31039 IIllumina Infinium human CytoSNP-850K iScan BeadChip
Samples (6)
GSM6508475 HCC1395-rep1
GSM6508476 HCC1395BL-rep1
GSM6508477 HCC1395-rep2
BioProject PRJNA873703

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
GSE212051_RAW.tar 169.4 Mb (http)(custom) TAR (of IDAT)
GSE212051_processed_genotype_calls.txt.gz 94.0 Mb (ftp)(http) TXT
GSE212051_signal_intensties.txt.gz 65.7 Mb (ftp)(http) TXT
Processed data are available on Series record

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