|
| Status |
Public on Jun 01, 2020 |
| Title |
OC08_ADN0162 |
| Sample type |
genomic |
| |
|
| Source name |
tumor sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ovarian cancer biopsy
|
| Treatment protocol |
none
|
| Growth protocol |
DNA extract from tumor biopsies
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using Macherey-Nagel NucleoSpin® Tissue kit
|
| Label |
Biotin
|
| Label protocol |
as per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Data processing |
CytoScan HD SNP-arrays (Affymetrix, ThermoFisher Scientific) data were processed using the GAP methodology to obtain absolute copy number (CN) profiles (Popova et al, Genome Biol., 2009, doi:10.1186/gb-2009-10-11-r128), including DNA structural rearrangements and chromosome number. The DNA index was calculated as the averaged CN and tumor ploidy of tumors was set as near-diploid (DNA index <1.3) or near-tetraploid (DNA index >1.3). HRD was detected based on the number of Large-scale State Transitions (LSTs) as described previously 47. Briefly, LST was defined as a chromosomal breakpoint (change in CN or major allele counts) between adjacent regions of at least 10 Mb. The number of LSTs was calculated after smoothing and filtering out CN variant regions < 3 Mb in size based on two ploidy-specific cut-offs (15 and 20 LSTs per genome in near-diploid and near-tetraploid tumors respectively). Tumors were classified as HRD (equal or above the cut-off) or HR Proficient (HRP) (below the cut-off)
The matrix table contains the log2 intensity data by probe
|
| |
|
| Submission date |
Jun 03, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
OUMOU GOUNDIAM |
| E-mail(s) |
oumou.goundiam@curie.fr
|
| Organization name |
INSTITUT CURIE
|
| Street address |
26 RUE D'ULM
|
| City |
PARIS |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL16131 |
| Series (1) |
| GSE132088 |
Genomic alteration analysis in ovarian cancers |
|
