GSE16125.GPL5175_eset.RdThe current multistep carcinogenesis models of colon cancer do not fully capture the genetic heterogeneity of the disease, which is additionally complicated by the presence of passenger and driver genetic alterations. The aim of this study was to select in the context of this significant heterogeneity additional genes functionally related to colon cancer development. High-throughput copy number and gene expression data of 36 microsatellite stable sporadic colon cancers resected from patients of a single institution characterized for mutations in APC, KRAS, TP53 and loss of 18q were analyzed. Genes whose expression correlated with the underlying copy number pattern were selected, and their association with the above listed mutations and overall survival was evaluated. Gain of 20q was strongly associated with TP53 mutation, and overall survival with alterations on 7p, 8p, 13q, 18q, and 20q. An association with 18q loss and gain of 8q24 was also observed. New candidate genes with a potential role in colon cancer are PLCG1 on 20q, DBC1 on 8q21, and NDGR1 on 8p24. In addition, an unexpected pattern of loss and mutability was found in the region upstream of the KRAS gene. By integrating copy number alterations with gene expression and mutations in colon cancer associated genes, we have developed a strategy that identifies previously known molecular features and additional players in the molecular landscape of colon cancer.Copyright 2009 Wiley-Liss, Inc.
data( GSE16125.GPL5175_eset )
experimentData(eset):
Experiment data
Experimenter name: Reid JF, Gariboldi M, Sokolova V, Capobianco P et al.??Integrative approach for prioritizing cancer genes in sporadic colon cancer.??Genes Chromosomes Cancer??2009 Nov
Laboratory: Reid, Pierotti 2009
Contact information:
Title: Integrative approach for prioritizing cancer genes in sporadic colon cancer.
URL:
PMIDs: 19672874
Abstract: A 225 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) versio
n]
platform_shorttitle:
Affymetrix HuEx-1_0-st
platform_summary:
huex.1.0.st.v2
platform_manufacturer:
Affymetrix
platform_distribution:
commercial
platform_accession:
GPL5175
platform_technology:
in situ oligonucleotide
warnings:
No warnings yet
Preprocessing: default
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: A1CF A2ML1 ... ZYX (10015 total)
varLabels: probeset gene
varMetadata: labelDescription
assayData: 10015 features, 36 samples
Platform type: huex.1.0.st.v2
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
4 observations deleted due to missingness
records n.max n.start events median 0.95LCL 0.95UCL
32.00 32.00 32.00 10.00 6.16 5.26 NA
---------------------------
Available sample meta-data:
---------------------------
alt_sample_name:
Length Class Mode
36 character character
sample_type:
tumor
36
summarystage:
early late NA's
1 27 8
M:
0 1 NA's
14 19 3
Dstage:
B C D NA's
5 8 19 4
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
19.00 61.75 67.50 65.58 71.25 90.00
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
30.0 202.5 390.0 926.2 1658.0 2970.0 4
vital_status:
deceased living NA's
10 22 4
family_history:
n
36
msi:
MSS
36
gender:
f m
20 16
kras:
mutant wt
20 16
tumor_size:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
2.500 4.000 4.000 4.906 5.000 14.000 4
mutation_apc:
n y
8 28
stageall:
1 2 3 4 NA's
1 5 8 19 3
batch:
Length Class Mode
36 character character
preop_drug_treatment:
n
36
uncurated_author_metadata:
Length Class Mode
36 character character