E-GEOD-14582 - Genotyping of human diagnostic Follicular Lymphoma (FL) patients to assess the prognostic relevance of aUPD reveals regions of acquired UPD at diagnosis of FL are associated with both overall survival and risk of transformation

Status
Submitted on 27 January 2009, released on 9 February 2009, last updated on 1 May 2014
Organism
Homo sapiens
Samples (181)
Array (1)
Protocols (4)
Description
SNP array analysis was performed using the Affymetrix 10K 2.0 Gene-chip array on DNA from 181 diagnostic Follicular Lymphoma (FL) patients to assess the prognostic relevance of aUPD. Genetic abnormalities were detected in 118/181 (65%) patients. Number of abnormalities was predictive of outcome; > 3 abnormalities was associated with inferior overall survival (OS) (p<0.03). Sites of recurrent aUPD were detected on 6p (n=25), 16p (n=22), 12q (n=17), 1p36 (n=14), 10q (n=8) and 6q (n=8). On multivariate analysis aUPD 1p36 correlated with shorter OS (p=0.05). aUPD 16p was predictive of transformation (p=0.03) and correlated with poorer progression free survival (p=0.02). Experiment Overall Design: Genomic DNA from 181 diagnostic FL samples were analysed using Affymetrix 10K 2.0 SNP arrays. Genomic DNA from the blood of ten unrelated Hapmap controls was used as reference for all FL samples. Prevalence and regions of homozygosity were identified.
Experiment types
genotyping by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-14582.idf.txt
Sample and data relationshipE-GEOD-14582.sdrf.txt
Raw data (2)E-GEOD-14582.raw.1.zip, E-GEOD-14582.raw.2.zip
Processed data (1)E-GEOD-14582.processed.1.zip
Array designA-AFFY-65.adf.txt
R ExpressionSetE-GEOD-14582.eSet.r
Links