An overview of circulating cell-free DNA (cfDNA) as liquid biopsy biomarkers and the role of circulating tumour DNA (ctDNA) in advancing cancer research and diagnosis through non-invasive tumour mutation profiling

1. The potential of liquid biopsies in
cancer research
2016

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Tumors shed both intact cells (resulting in circulating tumor cells) as well as
cellular components, such as nucleic acids (resulting in cell-free DNA or RNA).
Liquid biopsy: circulating biomarkers
for cancer
Diaz, Jr., L.A. and Bardelli, A. (2014) “Liquid biopsies: genotyping circulating tumor DNA.” Am. Soc. Clin. Oncol. 32, 579.

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Circulating cell-free DNA
can be found under
physiological as well as
pathophysiological
conditions
derives from necrotic
and apoptotic
tissue/cells
is highly fragmented
ctDNA is only a minor
fraction of cfDNA
Origin of circulating cell-free DNA
Crowley et al., 2013

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Applications for liquid biopsy
Non-invasive prenatal diagnostics
Chromosomal aberrations
Sub-chromosomal aberrations
Pathogen detection
Virus
Bacteria
Detection of rejection after transplantation
Cancer diagnostics
Early detection
Treatment selection
Therapy monitoring

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Early detection of cancer is crucial!
Tumour growth and metastasis
Source: American
Cancer Society
stage 5-year survival CRC
5-year survival
breast cancer
0 100% 100%
I 92% 100%
II 63-89% 93%
III 53-89% 72%
IV 11% 22%

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Limitations of tissue biopsy
Biopsy is invasive
May not be feasible based on patient condition
or tumour accessibility
Impractical for periodic monitoring for
progression recurrence
Cancer is a heterogeneous disease
Molecular properties differ within tumours
Primary tumour biopsy may not reflect current
disease condition (clonal evolution)
Surgery is costly
Greater demand due to molecular profiling

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Liquid biopsy for cancer detection
Bettegowda et al 2014.
The opportunity
Circulating tumour DNA (ctDNA) is easy
accessible and can be detected in most
metastatic cancers
The challenge
ctDNA is often only present at
low levels

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cfDNA is highly fragmented
DNA content differs largely (1-100 ng / mL plasma)
Characteristics of cell-free DNA

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Challenges of ctDNA
Crowley et al., 2013
How to discriminate
between ctDNA and
‘normal’ cfDNA?

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Alterations of ctDNA
Crowley et al., 2013
Point mutations
Insertions / Deletions
Copy number
variations
Structural changes or
rearrangements (gene
fusions)
Hypo- and/or
hypermethylation

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Challenges of ctDNA
Crowley et al., 2013
How to discriminate
between ctDNA and
‘normal’ cfDNA?
How to detect very
low levels of ctDNA?
How to quantify the
number of mutant
DNAs in a sample?

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- services for cancer
research
Unbiased discovery
Exome sequencing of
matched samples
from tumour tissue,
cell-free DNA and
blood
ONCOEXOME
Targeted screening
Panel sequencing of
clinically actionable
mutations, including
low frequency
mutations
ONCOPANEL
Monitoring
Frequent detection
of single driver
mutations after
treatment, such as
surgery or therapy
ONCOTARGET

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- services placed on the
cancer treatment timeline
Screening Diagnosis Follow-upTreatment
STAGING SURGERY | CHEMO | RADIATION RECUPERATION
Biopsy
Imaging
Tumour size
Molecular
stratification
Tumour removal
Irradiance
Medication
Monitoring
Diagnosis
Adjuvant treatment decision
Companion diagnostics
Measurement of therapeutic response Follow-up
ONCOEXOME
ONCOPANEL
ONCOTARGET

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Thank you very much for your
attention