OncoGenomics Explorer2
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Transcript of OncoGenomics Explorer2
Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com
OncoGenomics Explorer Taming Big Data
22 March 2012
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Which are the most frequently mutated genes in ovarian serous carcinoma?
Samples from ovarian serous
carcinoma
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TP53, BRCA1 and BRCA2 are the three most frequently mutated genes
TP53 is mutated in almost all tumors
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Mutation of the p53 gene is the key event in the development of high-grade tumors.
Unlike low-grade serous carcinoma, mutations of KRAS, BRAF, or ERBB2 occur very infrequently in
high-grade carcinoma.
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Most high-grade tumors are characterized by TP53 mutations and lack mutations of KRAS,
BRAF, or ERBB2.Vang R., et al., 2009: Ovarian low-grade and high-grade serous carcinoma: pathogenesis, clinicopathologic and molecular biologic features, and diagnostic problems.
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Serous ovarian cancer is also characterized by a low prevalence but statistically recurrent
mutations in a number of other genes, including NF1, RB1 and FAT3.
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Study for example the proportions of point mutations or AA types in NF1...
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...or study the mutations in NF1 in detail with the Gene viewer
Can be zoomed all the way down to sequence level
- The blue boxes represent the exons - Substitutions are shown as red vertical lines, insertions as light blue triangles, and deletions as pink triangles
- The SIFT score predicts whether a mutations will affect protein function
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Is there a correlation between copy number variations of CCNE1 and overall survival of
the patients ?
Select the gene/genes of interest, in this case CCNE1
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Overall survival tends to be lower for patients with CCNE1 amplification
The Cancer Genome Atlas Research Network, 2011: Integrated genomic analyses of ovarian carcinoma
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RAB25 seems to be epigenetically silenced in a subset of HG-OvCa tumors
The Cancer Genome Atlas Research Network, 2011:
Integrated genomic analyses of ovarian
carcinoma
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Genes with correlated CNV and expression include KRAS, POP4 and C19orf2
Wrzeszczynski KO. et al, 2011: Identification of tumor suppressors and
oncogenes from genomic and epigenetic features in ovarian cancer
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Are genes in a region of frequent copy number gain differentially expressed between amplified
and unamplified groups of samples?
Define the two groups to be compared, for example samples with copy number gain vs. samples with normal copy number
Select the genes to be included, for example all genes in chromosome region 3q26
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A volcano plot presenting the results of expression analyses between amplified and
unamplified samples in the 3q26 region
The results are shown as a volcano plot that enables the identification of genes that display high differences in expression that also are statistically significant
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MYNN is a gene that is located in a region of frequent copy number gain on 3q26.2. It is differently expressed
between amplified and unamplified groups
MYNN shows a strong correlation between copy number and expression
Ramakrishna M. et al., 2010: Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis
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In the volcano plot, an interesting group of genes can be selected
Select for example genes with significant p-values and large difference estimates
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A heat map can be drawn of the genes from the defined gene selection and of the samples from the two selected
sample groups
...and examine a summary of clinical covariates
Select an interesting cluster of samples in the heat map...
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Find out how genetic values correlate with clinical reference data...
Study for example how expression values of genes in chromosome region 8p correlate with overall survival
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...or how genetic values correlate with genetic reference data
Study for example how expression values of genes in chromosome region 8p correlate with CNVs of BRCA1
Interesting genes can be selected for
further analysis
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- Find new drug targets- Find new biomarkers- Stratify patient groups- Find clinical correlations
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