TCGA.COAD_eset.RdTo characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas were found to be hypermutated: three-quarters of these had the expected high microsatellite instability, usually with hypermethylation and MLH1 silencing, and one-quarter had somatic mismatch-repair gene and polymerase ?? (POLE) mutations. Excluding the hypermutated cancers, colon and rectum cancers were found to have considerably similar patterns of genomic alteration. Twenty-four genes were significantly mutated, and in addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9 and FAM123B. Recurrent copy-number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include the fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive colorectal carcinoma and an important role for MYC-directed transcriptional activation and repression.
data( TCGA.COAD_eset )
experimentData(eset):
Experiment data
Experimenter name: Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487:330-337
Laboratory: The Cancer Genome Atlas Network 2012
Contact information:
Title: Comprehensive molecular characterization of human colon and rectal cancer.
URL:
PMIDs: 22810696
Abstract: A 168 word abstract is available. Use 'abstract' method.
Information is available on: preprocessing
notes:
platform_title:
Agilent 244K Custom Gene Expression G4502A-07-3
platform_shorttitle:
Agilent G4502A-07-3
platform_summary:
agilent-014850 whole human genome microarray 4x44k g4112f
platform_manufacturer:
Agilent
platform_distribution:
commercial
platform_accession:
NA
platform_technology:
in situ oligonucleotide
warnings:
No warnings yet
Preprocessing: default
featureData(eset):
An object of class 'AnnotatedDataFrame'
featureNames: 15E1.2 2'-PDE ... ZZZ3 (17814 total)
varLabels: probeset gene
varMetadata: labelDescription
assayData: 17814 features, 130 samples
Platform type: agilent-014850 whole human genome microarray 4x44k g4112f
Overall survival time-to-event summary (in years):
Call: survfit(formula = Surv(time, cens) ~ -1)
124 observations deleted due to missingness
records n.max n.start events median 0.95LCL 0.95UCL
6.00 6.00 6.00 5.00 1.37 1.16 NA
---------------------------
Available sample meta-data:
---------------------------
unique_patient_ID:
Length Class Mode
130 character character
alt_sample_name:
Length Class Mode
130 character character
sample_type:
adjacentnormal tumor
7 123
primarysite:
co NA's
129 1
summarystage:
early late NA's
75 54 1
T:
1 2 3 4
3 27 88 12
N:
0 1 2 NA's
80 22 27 1
M:
0 1 NA's
108 21 1
age_at_initial_pathologic_diagnosis:
Min. 1st Qu. Median Mean 3rd Qu. Max.
36.00 65.00 72.00 70.89 80.00 90.00
days_to_death:
Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
29.0 442.0 500.0 494.5 681.0 774.0 124
vital_status:
deceased living NA's
5 15 110
msi:
MSI MSS NA's
1 4 125
location:
Length Class Mode
130 character character
summarylocation:
l r NA's
59 70 1
gender:
f m
67 63
kras:
mutant wt NA's
2 1 127
stageall:
1 2 3 4 NA's
25 51 30 20 4
ethnicity:
black caucasian NA's
3 17 110
drug_treatment:
n y NA's
2 3 125
preop_drug_treatment:
n y
127 3
fu:
n NA's
31 99
bevacizumab:
n NA's
31 99
irinotecan:
n NA's
31 99
cetuximab:
n NA's
31 99
capecitabine:
n NA's
31 99
dexamethasone:
n NA's
31 99
gcsf:
n NA's
31 99
fudr:
n NA's
31 99
folfiri:
n NA's
31 99
folfox:
n NA's
31 99
leucovorin:
n NA's
31 99
mitomycin:
n y NA's
30 1 99
platin:
n NA's
31 99
panitumumab:
n NA's
31 99
pegfilgrastim:
n NA's
31 99
raltitrexed:
n NA's
31 99
ancillary:
n y NA's
30 1 99
chemotherapy:
y NA's
31 99
moltherapy:
n y NA's
21 10 99
uncurated_author_metadata:
Length Class Mode
130 character character