|
| Status |
Public on Aug 01, 2017 |
| Title |
HGSC_JH1066 |
| Sample type |
genomic |
| |
|
| Source name |
primary ovarian tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
stic: No
age: 59
path.stage: IIIC
surgical.outcome: Optimal
diagnosis.of.record: Ovarian Ca
diagnosis.after.path.re.review: Ovarian Ca
platinumfreeinterval.mos..: 53.8
platinumstatus: Sensitive
recurrence: N
pfs.mos..: 58.6
os.mos..: 58.6
vitalstatus: Alive
race: OTHER
tcga_subtype_dif: 0.026
tcga_subtype_imr: 0.173
tcga_subtype_mes: -0.102
tcga_subtype_pro: -0.08
tissue: primary tumor tissue from high grade serous ovarian tumors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.). DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.
|
| Label |
NA
|
| Label protocol |
Total genomic DNA (500 ng) was collected from all 96 samples included in the study, and digested with Nsp I and Sty I restriction enzymes and ligated to adaptors.
|
| |
|
| Hybridization protocol |
The amplified DNA is then fragmented, labeled, and hybridized to a SNP Array 6.0 containing more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation.
|
| Scan protocol |
All 96 samples were assayed at once, in a single batch
|
| Data processing |
The Affy Power Tools (APT) copy number workflow was used to preprocess the SNP arrays and derive log R ratios representing relative copy number abundance. A standard HapMap reference included in the APT toolbox was used to represent a diploid genome. Circular binary segmentation (CBS) as implemented in the DNAcopy (Seshan VE and Olshen A. DNAcopy: DNA copy number data analysis. R package version 1.42.0) package from Bioconductor, using standard settings
The GISTIC2.0 algorithm was applied to the segmented data via the Genome Pattern online tool suite, using default settings, to make gene level copy number calls and identify significantly, copy number altered regions
|
| |
|
| Submission date |
Jul 31, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
leslie cope |
| E-mail(s) |
cope@jhu.edu
|
| Organization name |
leslie cope
|
| Street address |
550 N. Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21209 |
| Country |
USA |
| |
|
| Platform ID |
GPL6801 |
| Series (2) |
| GSE102085 |
Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [CNV] |
| GSE102094 |
Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma |
|
