|
| Status |
Public on Dec 01, 2021 |
| Title |
T27: Colon tumor from patient 27 |
| Sample type |
genomic |
| |
|
| Source name |
FFPE tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Colon cancer
tissue: FFPE tumor
|
| Treatment protocol |
All patients were first-line treated with surgery, and none of them received adjuvant chemotherapy.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from each formalin-fixed paraffin-embedded (FFPE) tumor samples using the QIAmp DNA FFPE kit (Qiagen, Hilden, Germany) and then quantified using Qubit fluorometer assay (Thermo Fisher Scientific, MA, USA)
|
| Label |
Biotin
|
| Label protocol |
Affymetrix OncoScan FFPE Assay kit for staining with Biotin.
|
| |
|
| Hybridization protocol |
Affymetrix OncoScan™ FFPE Assay kit
|
| Scan protocol |
Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.
|
| Description |
Hybridized to Affymetrix Oncoscan SNP array for profiling copy-number alterations in tumor samples
|
| Data processing |
raw SNP-array fluorescence intensity data (CEL files) were processed using SNP-FASST2 segmentation algorithm from Nexus Copy Number software version 9.0 (BioDiscovery, El Segundo, CA, USA) , achieving an estimate of the mean log2-ratio and B-allele frequency (BAF) values for each genome region. Major and minor allele numbers of each segment were inferred utilizing ASCAT R package version 2.5. For a chromosome region to be considered as carrying a CN gain or loss, log2-ratio cut-offs were set on 0.18 and -0.18, respectively; and to be considered to have a loss of heterozygosity (LOH), BAF threshold was set on 0.3. Chromosomal regions showing a non-altered log2-ratio and BAF <0.3 were classified as copy-number neutral LOH (CNN-LOH).
Probe set values in OSCHP files include intensity values (column ‘Log2Ratio’) and frequency of the alternative allele (BAF) for each array-probe.
|
| |
|
| Submission date |
Apr 09, 2021 |
| Last update date |
Dec 02, 2021 |
| Contact name |
Sara Lahoz |
| E-mail(s) |
saralahoz93@gmail.com, salahoz@clinic.cat
|
| Organization name |
Institut D'Investigacions Sanitàries August Pi i Sunyer
|
| Street address |
Carrer del Rosselló, 149
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21558 |
| Series (2) |
| GSE171777 |
Affymetrix OncoScan SNP arrays for profiling copy-number alterations (CNAs) and loss-of-heterozygosity (LOH) in colon cancer |
| GSE172191 |
Intratumor genomic heterogeneity in stage II colon cancer |
|
