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| Status |
Public on Feb 19, 2009 |
| Title |
CUMC17 |
| Sample type |
genomic |
| |
|
| Source name |
Renal Cell Carcinoma, Clear Cell Type, DNA from Paraffin Embedded Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
Furhman Nuclear Grade: 3
TNM Stage: pT3a Nx Mx
LymphoVascular Invasion: FALSE
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Deparaffinization followed by Qiagen DNeasy Blood and Tissue kit by manufacturer's instructions
|
| Label |
Biotin
|
| Label protocol |
Custom labeling protocol for FFPE tissue based on Affymetrix Mapping 10K Assay (Lyons-Weiler MA et al, Mol Diagn Pathol, 2008 Mar;17(1):3-13)
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| |
|
| Hybridization protocol |
Affymetrix Mapping 10K Xba 2.0 Assay
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| Scan protocol |
Affymetrix Mapping 10K Xba 2.0 Assay with an Affymetrix GeneChip 3000 7G scanner
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| Description |
RenalCellCarcinoma_ClearCell_FFPE_27
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| Data processing |
Affymetrix GCOS 1.4, GTYPE 4.0 and GDAS 3.0
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| |
|
| Submission date |
Sep 16, 2008 |
| Last update date |
Feb 19, 2009 |
| Contact name |
Federico A Monzon |
| E-mail(s) |
famonzon@tmhs.org
|
| Organization name |
The Methodist Hospital Research Institute
|
| Department |
Pathology
|
| Street address |
6565 Fannin St., MS205
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL2641 |
| Series (2) |
| GSE12808 |
Detection of chromosomal aberrations in renal tumors by virtual karyotyping with SNP microarrays |
| GSE14670 |
Virtual-Karyotyping with SNP microarrays in morphologically challenging renal cell neoplasms |
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| Data table header descriptions |
| ID_REF |
|
| VALUE |
Genotypes: AA, AB, BB, No Call |
| CONFIDENCE |
|
| RAS1 |
Relative allele signal for the data in the first probe group |
| RAS2 |
Relative allele signal for the data in the second probe group |
| P-VALUE AA |
|
| P-VALUE AB |
|
| P-VALUE BB |
|
| P-VALUE NO CALL |
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| Data table |
| ID_REF |
VALUE |
CONFIDENCE |
RAS1 |
RAS2 |
P-VALUE AA |
P-VALUE AB |
P-VALUE BB |
P-VALUE NO CALL |
| AFFX-5Q-123 |
No Call |
17673 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-456 |
No Call |
7980.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-789 |
No Call |
22183.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| AFFX-5Q-ABC |
No Call |
25962.5 |
0 |
0 |
0 |
0 |
0 |
0 |
| SNP_A-1513509 |
BB |
0.258015 |
0.128647 |
0 |
0.128647 |
0 |
0 |
0 |
| SNP_A-1518411 |
BB |
0.316372 |
0.166613 |
0.0444337 |
0.166613 |
0.0444337 |
0 |
0 |
| SNP_A-1511066 |
AA |
0.187601 |
0.962389 |
0.87197 |
0.962389 |
0.87197 |
0 |
0 |
| SNP_A-1517367 |
No Call |
10 |
-2 |
-2 |
-2 |
-2 |
0 |
0 |
| SNP_A-1512567 |
AB |
0.44796 |
0.290389 |
0.566989 |
0.290389 |
0.566989 |
0 |
0 |
| SNP_A-1519604 |
No Call |
1.01173 |
0.0464396 |
0.315789 |
0.0464396 |
0.315789 |
0 |
0 |
| SNP_A-1507932 |
BB |
0.0385167 |
0.00838926 |
0.0235149 |
0.00838926 |
0.0235149 |
0 |
0 |
| SNP_A-1519685 |
No Call |
10 |
-2 |
-2 |
-2 |
-2 |
0 |
0 |
| SNP_A-1516165 |
No Call |
10 |
-2 |
-2 |
-2 |
-2 |
0 |
0 |
| SNP_A-1514890 |
AB |
0.58204 |
0.333862 |
0.387785 |
0.333862 |
0.387785 |
0 |
0 |
| SNP_A-1507580 |
No Call |
1.21172 |
0.421642 |
0 |
0.421642 |
0 |
0 |
0 |
| SNP_A-1510991 |
AA |
0.140691 |
0.994909 |
0.878918 |
0.994909 |
0.878918 |
0 |
0 |
| SNP_A-1516205 |
AA |
0.439637 |
1 |
0.788716 |
1 |
0.788716 |
0 |
0 |
| SNP_A-1512666 |
BB |
0.164968 |
0 |
0.0548926 |
0 |
0.0548926 |
0 |
0 |
| SNP_A-1512740 |
BB |
0.211039 |
0.102201 |
0.0906405 |
0.102201 |
0.0906405 |
0 |
0 |
| SNP_A-1512132 |
AA |
0.0891828 |
0.935753 |
0.954389 |
0.935753 |
0.954389 |
0 |
0 |
Total number of rows: 10208
Table truncated, full table size 607 Kbytes.
| Supplementary file |
Size |
Download |
File type/resource |
| GSM321616.CEL.gz |
2.1 Mb |
(ftp)(http) |
CEL |
| GSM321616.CHP.gz |
111.0 Kb |
(ftp)(http) |
CHP |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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