|
| Status |
Public on Dec 07, 2011 |
| Title |
Neuroblastoma 279 (INES-320) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Tumor DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: neuroblastoma
tumor stage: localized, unresectable
gender: male
age at diagnosis (months): 10
tumor localization: abdominal (ADR)
metastases: no
bone marrow metastasis: no
liver metastasis: yes
cutaneous metastasis: no
cns metastasis: no
bone metastasis: no
relapse/progression: yes
time from diagnosis to event or last follow-up (months): 13
patient status: alive
time from diagnosis to death or last follow up (months): 69
genomic profile: numerical chromosome alteration (NCA)
1p status (1=1p deletion; 0=normal; 9=silent): 0
11q status (1=11q deletion; 0=normal; 9=silent): 0
17q status (1=17q gain; 0=normal; 9=silent): 0
2p status (1=2p gain; 0=normal; 9=silent): 0
3p status (1=3p deletion; 0=normal; 9=silent): 0
4p status (1=4p deletion; 0=normal; 9=silent): 0
|
| Treatment protocol |
Samples of neuroblastoma obtained at diagnosis were flash frozen and stored at –80°C. All tumor samples contained >50% cancer cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAs were extracted from frozen tumors using a standard phenol-chloroform procedure.
|
| Label |
Cy5
|
| Label protocol |
After digestion with DPNII (Ozyme, Saint Quentin en Yvelines, France) and column purification (Qiaquick PCR purification kit; Qiagen, Courtaboeuf, France), tumor DNAs were labeled by the random priming method (Bioprime DNA labelling system; Invitrogen, Cergy-Pontoise, France) with Cyanine-5 (Perkin-Elmer, Wellesley, MA). Using the same procedure, control DNAs were with Cyanine-3.
|
| |
|
| Channel 2 |
| Source name |
Normal reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
disease state: healthy
|
| Treatment protocol |
Samples of neuroblastoma obtained at diagnosis were flash frozen and stored at –80°C. All tumor samples contained >50% cancer cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNAs were extracted from frozen tumors using a standard phenol-chloroform procedure.
|
| Label |
Cy3
|
| Label protocol |
After digestion with DPNII (Ozyme, Saint Quentin en Yvelines, France) and column purification (Qiaquick PCR purification kit; Qiagen, Courtaboeuf, France), tumor DNAs were labeled by the random priming method (Bioprime DNA labelling system; Invitrogen, Cergy-Pontoise, France) with Cyanine-5 (Perkin-Elmer, Wellesley, MA). Using the same procedure, control DNAs were with Cyanine-3.
|
| |
|
| |
| Hybridization protocol |
After ethanol-coprecipitation with Human Cot-1 DNA (Invitrogen, Cergy-Pontoise, France), resuspension in hybridization buffer (50% formamide), denaturation at 95°C for 10 minutes and prehybridization at 37°C for 90 minutes, probes were cohybridized on aCGH (BAC/PAC non-commercial arrays: Platform GPL9715) or NimbleGen 4x72K arrays (commercial arrays: GPL8971). The aCGH slide was previously preblocked with a buffer containing 2.6mg succinic anhydride/118ml N-methyl-2-pyrrolidinone/32ml sodium tetraborate decahydrate, pH 8.0 (Sigma-Aldrich, Lyon, France).
|
| Scan protocol |
After washing, arrays were scanned using a 4000B scanner (Axon, Union City, CA). Image analysis was performed first with GenePix software (Axon) (firstly with version 5.1 and then with the 6.0.1.27 when it was available), and ratios of Cy5/Cy3 signals were determined.
|
| Data processing |
Tumors were classified into two groups: those with numerical alterations only or those with any segmental chromosome change. The overall images of the genomic profiles on which the genomic classifications in the manuscript are based are included in 'GSE26494_GenomicProfiles.pdf', which is linked to the Series GSE26494 record as a supplementary file.
|
| |
|
| Submission date |
Jan 14, 2011 |
| Last update date |
Nov 18, 2014 |
| Contact name |
Gudrun Schleiermacher |
| E-mail(s) |
gudrun.schleiermacher@curie.net
|
| Phone |
+33 1 44 32 45 50
|
| Fax |
+33 1 53 10 40 05
|
| Organization name |
Institut Curie
|
| Department |
Department of Pediatric Oncology
|
| Street address |
26 rue d'Ulm
|
| City |
PARIS |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL8971 |
| Series (1) |
| GSE26494 |
array-CGH profiling of human neuroblastoma samples obtained from infants included in the INES99.1, INES99.2 and INES99.3 trials |
|
