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| 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
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| 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.
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| 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.
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| Contributor(s) |
Jaeger E, Xiao W |
| Citation missing |
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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
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| Department |
Office of New Drugs
|
| Street address |
10903 New Hampshire Avenue
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| City |
Silver Spring |
| State/province |
MD |
| ZIP/Postal code |
20993 |
| Country |
USA |
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| Platforms (1) |
| GPL31039 |
IIllumina Infinium human CytoSNP-850K iScan BeadChip |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA873703 |
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