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CASE STUDY
Rapid candidate biomarker discovery with PanHunter
According to the WHO Global Health estimates,
colon and rectum cancers are among the top 10
causes of death in western countries, amounting
to over 900,000 deaths every year, globally. As
with many forms of cancer, early detection and
clear diagnosis are key to apply the right therapy
to achieving full recovery and the best possible
life expectancy. Hence, identifying and linking
molecular markers unambiguously to a specific
type of cancer is a crucial achievement towards
better and affordable point-of-care diagnostics
in preventive medicine, as molecular markers can
detect diseases long before the appearance of
macroscopic symptoms and often also allow for a
more targeted diagnosis.
" The Cancer Genome Atlas " (TCGA) collected
molecular omics data from cancer patients in
combination with clinical information to facilitate
general cancer research including, e.g., candidate
biomarker discovery. For this case study, the patient
cohort for colon adenocarcinoma ('TCGA_COAD')
will be used in PanHunter.
After an initial look at clinical information (e.g.,
the distribution of samples in the cohort), the
next step is the exploration of the molecular data.
PanHunter's New Comparisons app allows to explore
the omics data, in this case transcriptomes, in a
very straightforward way: a very common and easily
accessible visualisation for this kind of exploration is
Figure 7:
Dimensional reduction plot of
the transcriptomics data, based on
the expression data of the 500 most
variant genes. Each dot is representing
one sample/patient.
t-SNE Component 1
Tissue_Definition
Primary_solid_Tumour
Solid_Tissue_Normal
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t-SNE Component 2

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evotec_Nov23_PanOmicsDriven

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