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| Status |
Public on Nov 17, 2023 |
| Title |
Increased HRD score in cisplatin resistant penile cancer cells |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
HRD Score was generated from a penile carcinoma cell line resistant to 5FU and CDDP as well as cross resistant cell line.
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| Overall design |
Array-based genome-wide copy-number analysis was conducted using OncoScan FFPE Microarrays (Affymetrix, Santa Clara, California, USA). For the assay, an input amount of 79.2 ng DNA was used. The OncoScan® assay utilizes the molecular inversion probe technology (MIP), which is optimized for highly degraded FFPE samples, for the identification of copy number (CN) alterations, loss of heterozygosity (LOH) and somatic mutations (SMs). MIP probes in the OncoScan® assay capture the alleles of over 220,000 SNPs within ~900 cancer genes. Furthermore, the MIP probes also enable detection of 74 frequently tested somatic mutations in nine genes implicated in cancer (BRAF, KRAS, EGFR, IDH1, IDH2, PTEN, PIK3CA, NRAS and TP53). The molecular inversion probe processing was done according to the OncoScan FFPE Assay Kit Protocol (Affymetrix, Santa Clara, California, USA). At the end of the hybridization period, arrays were stained and washed using the GeneChip® Fluidics Station 450 and loaded into the GeneChip® Scanner 3000 7G (Affymetrix, Santa Clara, California, USA) where array fluorescence intensity was scanned to generate array images (DAT file). Array fluorescence intensity (CEL) files were automatically generated from DAT files by the Affymetrix® GeneChip® Command Console® (AGCC) Software version 4.0. Resulting data files (CEL files) were processed and viewed by using Chromosome Analysis Suite (ChAS) software version 4.2.0.80.
Copy number analysis of Affymetrix 100K and 500K SNP arrays was performed for penile carcinoma cell lines from one patient resistant against 5FU and CDDP as well as both agents.
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| Contributor(s) |
Winkelmann R, Doering C |
| Citation missing |
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| Submission date |
Nov 25, 2022 |
| Last update date |
Nov 18, 2023 |
| Contact name |
Ria Winkelmann |
| E-mail(s) |
winkelmann@em.uni-frankfurt.de
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| Organization name |
Dr. Senckenberg Institute of Pathology Frankfurt am Main
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| Street address |
Theodor-Stern-Kai 7
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| City |
Frankfurt am Main |
| ZIP/Postal code |
60596 |
| Country |
Germany |
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| Platforms (1) |
| GPL18602 |
[OncoScan] Affymetrix OncoScan FFPE Assay |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA905440 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE218782_RAW.tar |
123.3 Mb |
(http)(custom) |
TAR (of CEL, OSCHP) |
| Processed data provided as supplementary file |
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