NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM816595 Query DataSets for GSM816595
Status Public on Feb 06, 2013
Title BLD2_P-44
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics sample type: peripheral blood
cell_type: lymphocyte
patient: P-44
gender: male
age: 62
transplanted organ: kidney
immunosuppressive drugs: azathioprine + prednison
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from SCC and AK samples that contained at least 70% tumor cells, as determined by haematoxylin and eosin stained frozen sections. DNA from the tumor samples was isolated using the Genomic-tips 20/G kit (Qiagen). A salting-out procedure was used to isolate genomic DNA from the peripheral blood samples. DNA was quantified using a Nanodrop (NanoDrop technologies) and evaluated for degradation on agarose gel.
Label C-Bio and A-DNP
Label protocol 400 ng of genomic DNA was labelled according to Illumina's standard protocol
 
Hybridization protocol Hybridizations were performed at the Leiden Genome Technology Center according to the manufacturer's instructions
Scan protocol The beadChips were scanned using the Illumina BeadArray Reader, using the standard Illumina scanning protocol
Data processing Image analysis and quality control (call rate > 98%) was performed in Illumina's BeadStudio Version 3.2 software using the genotyping module. Each BeadChip was self-normalized using information contained within the array. Further analysis and visualization was performed with the Illumina Genome Viewer in Beadstudio. First, tumor data was paired with data from their corresponding normal control. Subsequently, examination of the log R ratio (signal intensity tumor/signal intensity normal control) and B allele frequency (BAF) was analyzed for the presence of copy number variations (CNVs) and/or loss of heterozygosity (LOH) in the tumor samples. By plotting the log R ratio across a chromosome, CNVs could be visualized by an increase or decrease in baseline signal. Secondly, the BAF was plotted across each chromosome to detect regions of LOH in tumor cells. A region with LOH was defined as a stretch of heterozygous SNPs in normal DNA but homozygous in the matched tumor DNA.
Matrix signal (ie, The signal intensities of all SNPs for each sample) is linked as a supplementary file on the Series record.
 
Submission date Oct 13, 2011
Last update date Feb 06, 2013
Contact name Harry Vrieling
E-mail(s) [email protected]
Organization name Leiden University Medical Center
Department Toxicogenetics, S4-P
Lab room T4-34
Street address Einthovenweg 20
City Leiden
ZIP/Postal code 2333 ZC
Country Netherlands
 
Platform ID GPL6982
Series (2)
GSE32969 Genome-wide SNP analysis of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients
GSE32979 Cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

Data table header descriptions
ID_REF
VALUE Gtype (Genotype)
BLD2_P.44.Score
BLD2_P.44.Theta
BLD2_P.44.R
BLD2_P.44.B.Allele.Freq
BLD2_P.44.Log.R.Ratio

Data table
ID_REF VALUE BLD2_P.44.Score BLD2_P.44.Theta BLD2_P.44.R BLD2_P.44.B.Allele.Freq BLD2_P.44.Log.R.Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.299218 0.004745088 2.798934 0 -0.7059745
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.298474 0.02337649 4.133963 0 -0.4378465
MitoA11252G-13273288_B_R_IFB1141661584:0 AA 0.329167 0.02171688 4.13557 0.00363872 -0.4807503
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3187215 0.01704466 4.205319 0.0004931649 -0.5805163
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2514375 0.05291162 3.486396 0.01017069 -0.5764817
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.2877009 0.02240784 3.141471 0.0005943747 -0.6560223
MitoA13106G-13273298_B_R_IFB1141641623:0 BB 0.3484128 0.9846623 1.027907 1 -0.1556806
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2567114 0.02496694 4.621227 0 -0.5427909
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.3457177 0.03443166 0.6558537 0 -0.9580807
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.3183387 0.0159504 2.076878 0 -0.6722136
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.329661 0.01050574 1.340148 0 -0.7586054
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2908708 0.07703391 3.280448 0.02379275 -0.653953
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.319456 0.04744322 2.263097 0.007877715 -0.2543567
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2650885 0.9283873 2.226111 1 -0.2076826
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.3469829 0.01429232 4.448756 0.003079982 -0.5130752
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.2785909 0.02767918 2.128572 0 -0.8883188
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.2527641 0.0746052 4.384098 0.03315174 -0.54804
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3183387 0.02011876 2.85162 0.003708027 -0.6560504
MitoA1738G-13273322_T_F_IFB1141639534:0 AA 0.2923732 0.02347953 3.569962 0.003895637 -0.7783926
MitoA3349G-13273328_T_F_IFB1141711832:0 AA 0.2904017 0.04313711 5.135814 0.0139483 -0.4557947

Total number of rows: 561466

Table truncated, full table size 46535 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap