|
| Status |
Public on Dec 31, 2012 |
| Title |
Case 6 C1076 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Adenoid cystic cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: adenoid cystic carcinoma
tumor site: Submandibular gland
grade: I
gender: F
|
| Treatment protocol |
Fresh tumor tissue from 40 ACCs were obtained from surgical resection specimens. The tumors were classified as grade I to III according to the histologic classification of salivary gland tumours by WHO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from frozen tumour tissue using the QIAampR DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.
|
| Label |
Cy5
|
| Label protocol |
2.0 µg of genomic tumor DNA and sex-matched reference DNA (Promega p/n G1471) were digested with AluI and Rsa1 for 2 h at 37 1C. Digested tumor and reference DNAs (1.5 mg of each) were labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA), respectively.
|
| |
|
| Channel 2 |
| Source name |
Normal tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
sample type: sex-matched reference DNA (Promega p/n G1471)
|
| Treatment protocol |
Fresh tumor tissue from 40 ACCs were obtained from surgical resection specimens. The tumors were classified as grade I to III according to the histologic classification of salivary gland tumours by WHO.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from frozen tumour tissue using the QIAampR DNA Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer instructions.
|
| Label |
Cy3
|
| Label protocol |
2.0 µg of genomic tumor DNA and sex-matched reference DNA (Promega p/n G1471) were digested with AluI and Rsa1 for 2 h at 37 1C. Digested tumor and reference DNAs (1.5 mg of each) were labeled with Cy3-dUTP and Cy5-dUTP (Perkin-Elmer Life and Analytical Sciences Inc., Wellesley, MA, USA), respectively.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets (Cot-1 DNA and Blocking agent) and hybridization buffer (Agilent oligo aCGH/ChIP-on-Chip Hybridization Kit) were added, the samples were denatured and applied to microarrays (Agilent Human Genome CGH Microarray 244K 60-mer oligonucleotide arrays) as recommended by the manufacturer. The arrays were enclosed in a rotating hybridization oven at 65°C for 40 h. After hybridization, the slides were sequentially washed and dried.
|
| Scan protocol |
The arrays were scanned on an Agilent High-Resolution C Microarray Scanner (G2505B) and the images were quantified using Agilent Feature Extraction Software (v.9.1).
|
| Data processing |
Data analysis was carried out using Nexus Copy Number software v.4.1 (BioDiscovery Inc., El Segundo, CA, USA), which uses the Rank segmentation algorithm to define non-random regions of CNAs across the genome. Sex chromosomes were excluded from the analysis. The significance threshold for segmentation was set to p=1.0E-6 and the thresholds of log2 ratio values for gain and loss were 0.25 and −0.2, respectively; the thresholds for high copy number gain/amplification and homozygous deletion were 1.0 and −1.0, respectively.
|
| |
|
| Submission date |
Jan 03, 2012 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Marta Persson |
| E-mail(s) |
[email protected]
|
| Organization name |
Sahlgrenska Cancer Center
|
| Street address |
Box 425
|
| City |
Gotenburg |
| ZIP/Postal code |
405 90 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE34816 |
Clinically significant copy number alterations and complex rearrangements of MYB and NFIB in adenoid cystic carcinoma of the head and neck |
|
| Relations |
| Reanalyzed by |
GSM4636288 |
