|
| Status |
Public on Jul 31, 2014 |
| Title |
Patient 9 in group SynSa1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
histosubtype: synovial sarcoma
age at diagnosis [years]: 33
gender: Male
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche).
|
| Label |
Cy5
|
| Label protocol |
1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to manufacturer's recommendations. Male and female Megapool Reference DNA (catalog no. EA-100M and EA-100F) (KREATECH Diagnostics) were used for the aCGH experiments.
|
| |
|
| Channel 2 |
| Source name |
Reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Pooled genomic DNA from 100 healthy individuals
|
| Treatment protocol |
not applicable
|
| Growth protocol |
not applicable
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche).
|
| Label |
Cy3
|
| Label protocol |
1ug of genomic DNA was labeled using Cy5 dye, and 1ug reference female DNA was labeled using Cy3 dye, according to manufacturer's recommendations. Male and female Megapool Reference DNA (catalog no. EA-100M and EA-100F) (KREATECH Diagnostics) were used for the aCGH experiments.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were hybridized to SurePrint G3 Human CGH 4x180K whole-genome microarrays (G4449A) (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.
|
| Scan protocol |
The microarray slides were scanned using the Agilent G2565A DNA Microarray Scanner (Agilent Technologies, SantaClara, CA, USA).
|
| Description |
aCGH profile in primary tumor sample
|
| Data processing |
Image analysis was done using the Feature Extraction V10.10.1.1 software (Agilent Technologies, SantaClara, CA, USA). aCGH data were analyzed using Agilent Genomic Workbench 7.0.4.0. software (Agilent Technologies, SantaClara, CA, USA). The ADM-2 algorithm was applied to identify DNA copy number aberrations (CNAs). Aberration Filter: ( Minimum Number of Probes for Amplification >= 500 AND Minimum Avg. Absolute Log Ratio for Amplification >= 0.25 ) OR ( Minimum Number of Probes for Deletion >= 500 AND Minimum Avg. Absolute Log Ratio for Deletion >= 0.25 )
Normalized log2 ratio (Cy5/Cy3), ADM-2 alogrithm, threshold 6.0, calculated by the Agilent Genomic Workbench 7.0.4.0. software.
|
| |
|
| Submission date |
Jan 17, 2014 |
| Last update date |
Jul 31, 2014 |
| Contact name |
Joanna Przybyl |
| E-mail(s) |
jprzybyl@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Department of Pathology
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE54183 |
Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features [aCGH] |
| GSE54188 |
Metastatic potential is determined early in synovial sarcoma development and reflected by tumor molecular features |
|
