|
| Status |
Public on Feb 01, 2011 |
| Title |
non-BRCA1/2 hereditary breast tumor (BRCAx)_BX435_HB376-14 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
FFPE primary breast tumor material BRCAx family
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tumor: breast canrcinoma
histology: Invasive ductal carcinoma
grade: 1
er ihc: 10-50% positive
pr ihc: 10-50% positive
her2 ihc: <10% positive
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%. Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours. At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)
|
| |
|
| Channel 2 |
| Source name |
genomic DNA from blood from 8 healthy females
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation for arrayCGH was performed as described elsewhere. (20) In short, formalin-fixed paraffin-embedded FFPE tissue of uterine corpus cancer was used. Cases were discarded if the tumor cell percentage was below 70%. Genomic DNA was isolated from 10*10µm thick paraffin slides. Slides were deparaffinized twice in xylene for 5 minutes, rehydrated in 100% (twice), 90%,70% ethanol and stained with hematoxylin. To remove formalin induced cross-links an overnight incubation in 1M NaSCN at 37°C was performed. Slides were subsequently washed in PBS twice for 10 minutes and air-dried. Tumor cells were collected by macro dissection by scraping from the slides and cells were transferred to a tube containing 200 µl ATL buffer (QIAamp® DNA Mini Kit cat 51304, Qiagen), 27 µl Proteinase-K was added and samples were incubated at 55°C while shaken at 450 rmp for at least 40 hours. At intervals of 4, 16 and 24 hours additional 27 µl of Proteinase-K was added (Qiagen kit). Further isolation was done following the manufacturers instructions (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Sample and reference DNA were labeled with the Cy5- or Cy3-conjugates from the Universal Linkages System (ULS; Kreatech biotechnology, Amsterdam, The Netherlands)
|
| |
|
| |
| Hybridization protocol |
hybridization as describe in Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 2007;7:43.
|
| Scan protocol |
ImaGene v6.0 software (BioDiscovery Inc) was used to translate the cy5/cy3 intensity ratios into average of the triplicates log2-ratio.
|
| Description |
-
|
| Data processing |
average of triplicate Log2 ratios after Lowess pintip normalization
|
| |
|
| Submission date |
Oct 19, 2009 |
| Last update date |
Feb 01, 2011 |
| Contact name |
Petra Nederlof |
| E-mail(s) |
[email protected]
|
| Phone |
+31 205122757
|
| Fax |
+31 205122759
|
| URL |
http://www.nki.nl
|
| Organization name |
The Netherlands Cancer Institute
|
| Department |
Pathology
|
| Lab |
Molecular Pathology
|
| Street address |
Plesmanlaan 121
|
| City |
Amsterdam |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL4560 |
| Series (1) |
| GSE18626 |
Comparative genomic hybridization of BRCAX breast tumors |
|
