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The NCI-NHGRI Cancer Genome Atlas (TCGA) Pilot Project
The NCI-NHGRI Cancer Genome Atlas (TCGA) Pilot Project
Genomic Aberrations in GBM from the TCGA pilot project
Subclasses and Targets
Copy Number PlatformsBroad – Affymetrix SNP 6.0
Harvard – Agilent Whole Genome
MSKCC – Agilent Whole Genome, Custom High-density
Stanford – Illumina Infinium SNP
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Example tumor profile, Agilent, MSKCC
Example tumor profile, Agilent, MSKCC
• Example profile, focal CNA events marked by circles
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EGFR
EGFR ampliconEGFR amplicon
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Harvard
MSKCC
High concordance between centersHigh concordance between centers
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Copy number profilingCopy number profiling
• 165 tumors profiled to date
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Subclass Discovery byNon-negative Matrix Factorization (NMF)
Subclass Discovery byNon-negative Matrix Factorization (NMF)
3 kinds of genomic profile found(NMF cluster medians)
2-way 3-way 4-way 5-way
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3-way grouping
+19,+20
-13, -14
+7 -9p -10
Subclass Discovery by NMF3-way grouping
Subclass Discovery by NMF3-way grouping
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+19,+20
-13, -14
Clustering by transcriptomeClustering by transcriptome
• Copy number profiles clustered by matching transcriptome data(Neil Hayes & Katherine Hoadley, UNC)
• Possible overlap of -13/14 and +19/20 subclasses
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3-way grouping
3-way NMF groupsshow no survival difference
3-way NMF groupsshow no survival difference
Survival (weeks)
1
2
3
Group 1Group 2Group 3
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Survival as a function of regional gain and loss
Survival as a function of regional gain and loss
Gain
Loss
better survival / poorer survival
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Overexpressed Skp2 within 5p amplification detected by array-based comparative genomic hybridization is associated with poor prognosis of glioblastomas.Saigusa et al.; Cancer Sci., 2005
+5p
Survival-associated gain/loss:correlation with reported regionsSurvival-associated gain/loss:
correlation with reported regions
Secondary GBMsubclasses
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ARI = “aberration recurrence index”
ARI for 165 tumors
Regions of Interest for CNARegions of Interest for CNA
Derive ROI from copy number profiles by 3 essential features:
1. Amplitude2. Recurrence3. Focality AFI = “aberration focality index”
PDGFRA,KIT
CDK4 MDM2
EGFR
CDKN2ACDKN2B
MDM4
ROI selected for most focally-altered 2% of genome
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226 genes, enriched for “oncogene” CANDID score, p<0.05Top 20 include: EGFR, PDGFRA, KIT, MET, AKT1, AKT3,
PIK3C2B, MDM2, MDM4, CDK4, GLI2Others: GFI1B, PLAG1, RALGDS
MDM4
PDGFRA,KIT
EGFR
MET CDK4 MDM2
GLI2++
+
+
+++
AKT1+
+
Focal amplificationsFocal amplifications
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219 genes, enriched for “tumor suppressor” CANDID score, p<0.013Top 20 include: PTEN, CDKN2A/B/C, NF1, NF2, RB1, PTPRDOthers: PTPRD, WWOX, APAF1, FBXW7, BMPR2
PTENCDKN2ACDKN2B
CDKN2C
+
+
+
++
NF2+
NF1
+
RB1+
PTPRD+
Focal deletionsFocal deletions
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Custom array: 650bp resolution vs whole genome 8,170bp
High-density custom array forintragenic deletions, translocations
High-density custom array forintragenic deletions, translocations
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Custom array: 580bp resolution vs whole genome 10,000bp
High-density custom array forintragenic deletions, translocations
High-density custom array forintragenic deletions, translocations
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Novel TK fusion protein in GBM:KDR-PDGFRA
Novel TK fusion protein in GBM:KDR-PDGFRA
PDGFRA KIT KDRPDGFRA KIT KDR
Ig-like domain: immunoglobulin like domain, S: signal sequence, TM: transmembrane domain,JM: juxtamembrane domain, TK: tyrosine kinase domain, C: criptic exon
KDR-PDGFR-α fusion protein (3,882bp): KDR (1,987bp) + Cryptic exon (38bp) + PDGFRA (1,860bp)
3,879
S 1 2 3 4 5KDR-PDGFRA 6 C TK1 TK2
KDR PDGFRA
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32P-ATP
IB: Myc
IB: actin
Moc
k
KP KD
R-W
T
PR
A-W
T
pMXIG-NIH3T3 cell (p6)Serum Starve O/N
K-P Fusion HRas V12
WT KDR WT PDGFRA
Tatsuya Ozawa
The KP fusion kinase is constitutively phosphorylated and transforming
The KP fusion kinase is constitutively phosphorylated and transforming