OncoGenomics Explorer

March 2012

MediSapiens Ltd
OncoGenomics Explorer – taming Big Data

Which are the most frequently mutated
genes in ovarian serous carcinoma?

Samples from
ovarian serous
carcinoma

Copyright © 2012 MediSapiens Ltd. All rights reserved. • medisapiens.com

TP53, BRCA1 and BRCA2 are the three
most frequently mutated genes

TP53 is mutated in
almost all tumors


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.


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.


Select the aforementioned group of samples from
the Mutation Heat Map and examine a summary
of clinical variables


Results can also be viewed in tabular format and
subsequently be exported for further analysis


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.


Study for example the proportions of
point mutations or AA types in NF1...


...or study the mutations in NF1 in detail
with the Gene viewer
- 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
mutation will affect
protein function

Can be zoomed all
the way down to
sequence level


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


Overall survival tends to be lower for
patients with CCNE1 amplification

The Cancer Genome
Atlas Research
Network, 2011:
Integrated genomic
analyses of ovarian
carcinoma


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


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


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


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


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


In the volcano plot, an interesting group of
genes can be selected

Select for example
genes with
significant p-values
and large
difference
estimates


A heat map can be drawn of the genes from the defined
gene selection and of the samples from the two selected
sample groups

Select an
interesting
cluster of
samples in
the heat
map...

...and examine a summary of
clinical covariates


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


...or how genetic values correlate with
genetic reference data

Study for example Interesting
how expression genes can be
values of genes in selected for
chromosome further analysis
region 8p correlate
with CNVs of
BRCA1


Several different applications with powerful
filter options offer numerous ways to study a
dataset


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