Thought Leadership

An introductory guide to biomarkers, precision,

personalised and stratified medicine.

Professor Richard Kennedy

Global VP of Biomarker Development, Almac Diagnostic Services

The application of biomarkers Although most of what is being described in

articles and at conferences is fairly straight
to improve patient outcomes forward, clinicians and scientists as well as the
is now common in clinical regulatory bodies in the US and EU tend to use

trials and is rapidly being what can be seen as fairly obscure terminology.
In this article I have attempted to provide some
adopted into clinical practice. clarity to this evolving field, particularly for those
without a medical or scientific background.
Several of the examples I use are in the area of
cancer medicine, mainly because this has been
at the forefront of biomarker development and
also because I am a Medical Oncologist and
cancer researcher by training. The concepts,
however, are the same for the application of
biomarkers to all human diseases. For more
detailed explanations of concepts covered
here I would recommend the FDA website
that has various useful articles.

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First of all we need to tackle the contentious issue a. Precision medicine: Selection of the best
of personalised medicine versus precision medicine approach to managing a patient based on
versus stratified medicine. I have been on scientific biological measurements (biomarkers).
advisory panels that have spent hours debating For example: a person’s genome is sequenced
these terms with no resolution so it is not surprising or a protein is measured in their blood and a
there is considerable variation as to how they are specific drug is given that is known to work
used. Accepting that some people will disagree I with their unique biology. It can also involve
have found the most useful way to think about repeated monitoring of disease markers to
these as the following: allow tailoring of a treatment to an individual.
For example, a specific cancer related gene
mutation or protein may be detected in blood
and disappear when successful treatment
has been given.

b. Personalised medicine: Selection of the best

approach to managing a specific patient, based
on available biological information about the
patient as well as a patient’s personal
preferences, environmental factors, social
factors and other factors that may affect the
treatment choice. This can be thought of an
extension of precision medicine to a holistic
approach. An example may be the choice of a
prophylactic salpingo-oophorectomy (surgical
removal of fallopian tubes and ovaries) in an
individual who has tested positive for the
BRCA1 or BRCA2 mutation, who has a family
history of ovarian cancer, is aware of the relative
risk of developing ovarian cancer themselves
and has decided to have no pregnancies in
the future.

c. Stratified medicine: Selection of the best

approach to managing a group of patients.
It can be considered a step towards precision
and personalised medicine and is often used
for treatment selection in clinical trials. Stratified
medicine accepts that the treatment selected
has a net effect of benefiting a group of patients
as a whole but may not benefit every individual
within the group. An example may be the use
of the estrogen receptor to select hormone
treatment in breast cancer. The majority (70%)
will benefit, but it is accepted that some will not.

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Biomarkers

These are required for precision, personalised The Oncotype Dx and MammaPrint assays are
and stratified medicine. Again there are multiple examples of prognostic biomarkers used to help
definitions for these, many that are quiet complex. answer this question.
The official FDA definition is here and the European
A predictive biomarker is used to estimate
Medicines Agency (EMA) discusses biomarkers here.
the benefit for a specific treatment. When a
Basically a biomarker is something you measure
predictive biomarker is registered with a regulatory
to let you know if a person is healthy, not healthy,
body (such as the FDA) along with an associated
at risk of becoming unhealthy or if unhealthy is
drug to select appropriate patients it is referred to
responding to a treatment. Biomarkers can be
as a companion diagnostic and is on-label for the
anything that can be measured in a person and
drug. Using the breast cancer example again, HER2
can range from DNA, RNA, Protein, metabolites
overexpression (predictive biomarker positive)
measured from samples such as blood, tumour
indicates potential benefit from trastuzamab
material, urine or saliva to imaging such as digital
(Herceptin) treatment. HER2 overexpression is a
pathology and radiology with special contrast
companion diagnostic on-label for trastuzumab
agents Other examples are blood pressure as a
and the FDA require it is tested prior to prescribing
biomarker for risk of heart disease and blood
this drug. The FDA discuss these definitions and the
sugar and HBA1c as biomarkers for risk of
use of companion diagnostics further here.
diabetes related health problems.

A common point for confusion is where a specific

Biomarkers can be qualitative or quantitative.
intervention such as chemotherapy is shown to
Qualitative biomarkers are either present
have an overall benefit in a high risk population as
or not. For example a KRAS mutation can either
identified by a prognostic biomarker. This does
be measured in a cancer or not. Quantitative
not necessarily mean the biomarker is “predictive”
biomarkers measure something using a continuous
for the treatment. For example, the breast cancer
scale. For example a blood sugar is measured as a
prognostic biomarkers mentioned earlier will
numerical concentration in blood. Tumour mRNA
identify high-risk patients who should be offered
is often measured as a number relative to a control
adjuvant chemotherapy (The low risk patients
mRNA for which the level is known. Quantitative
are unlikely to develop recurrent disease and
biomarkers will usually have associated values
therefore will not need chemotherapy). The actual
which represent “cut-offs” above (or sometime
benefit for chemotherapy used for an individual
below) which is considered abnormal
high-risk patient however is unknown as the
(biomarker positive).
prognostic biomarker does not measure the
A working classification of biomarkers is given in biology that determines sensitivity or resistance
the following table. Each would require an article to chemotherapy. Rather it is designed to predict
to describe them fully, but it is worth discussing the aggressiveness of a tumour and its likelihood
prognostic and predictive biomarkers in more of metastatic spread. This means that the overall
detail as these often cause confusion. response rate is probably less than 50% for standard
adjuvant chemotherapy in the high risk population.
A prognostic biomarker is used to estimate the
Ideally a predictive biomarker that measures
outcome for a patient in the absence of a treatment.
mechanisms of sensitivity or resistance would
For example, if a patient has surgery for breast
be used along with the prognostic biomarker to
cancer how likely are they to be cured without
select the correct chemotherapy for the patient’s
further (adjuvant) chemotherapy?
specific tumour.

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Biomarker Use Examples

Susceptibility Is patient at risk of BRCA1 mutation and risk of breast cancer.

disease? CAG Repeats and Huntington’s Disease.

Diagnostic / Is disease present? D-Dimer measurement and deep venous thrombosis

Biomarker PSA and presence of prostate cancer.

Prognostic Is treatment needed? HBA1C levels and complications of diabetes.

MammaPrint assay and risk of breast cancer recurrence.

Predictive Which treatment? KRAS mutation and cetuximab resistance in colon

cancer. ER and response to tamoxifen in breast cancer.

Pharmacogenomic Is treatment safe? The CYP2C9*3 single nucleotide polymorphism in

germline DNA reduces warfarin metabolism by 90%
increasing the risk of overtreatment and bleeding.

Pharmacodynamic/ Is the treatment as Loss of Ki67 as marker of decreased proliferation

response prescribed working at in cancer. Blood pressure as a response to
a biological level? anti-hypertensives.

Monitoring Is there a change Hepatitis C virus ribonucleic acid (HCV-RNA)

biomarker in the disease with for assessing patients with chronic hepatitis C.
time?

Physiological Is the patient fit for Renal function tests prior to platinum-based
treatment? chemotherapy.

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Biomarker Validation

This again is an area of much confusion with several different terms used. There are, however, two main
aspects to proving a biomarker is fit for purpose that can be summarised as:

I. Analytical validation. This is the proof that the II. Clinical Validation. This is proof that the
biomarker is technically robust (ie it measures biomarker can be used for the clinical purpose
what it is supposed to reliably). This is for which it has been designed. The FDA and
what the Clinical Laboratory Improvement EMA require adequate clinical validation before
Amendments (CLIA) legislation is primarily a biomarker can be routinely used in the clinic.
focussed on in the US. Indeed, in order to be The process usually involves the application
able to use a biomarker for the selection of of the biomarker to a patient population that
patient treatment in many US states, including is entirely different (the validation dataset)
clinical trials, the assay must be compliant with to that used for the purpose of discovery
CLIA biomarker validation requirements. and development (the training dataset).
This typically includes: The true ability of the biomarker to guide
precision medicine can be estimated in terms
a. Accuracy - does the biomarker measure of sensitivity (ability to identify those patients
what it is supposed to? Usually it needs with an adverse outcome and distinct from
to be compared to another measurement “analytical sensitivity” mentioned above) and
technique to demonstrate comparable data. specificity (ability to identify those who do
not have the adverse outcome). Sometimes
b. Precision - does the biomarker give the the validation can be given in terms of a
same result for the same sample every time Hazard Ratio (HR) which is a measure of
it is run or is the technology/process “noisy” the biomarker’s ability to predict the risk of
with a lot of variation? developing an adverse event over time such
as cancer recurrence, stroke, death etc.
c. Analytical Sensitivity - what is the minimum
A P-Value indicates the level of statistical
amount of biological material (eg DNA from
certainty that the biomarker is performing,
blood) that is required to give a reliable result?
with a value of less than 0.05 conventionally
indicating it is working as expected.

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Historically clinical validation has often been Biomarker verification is best reserved for the
poorly performed with the same patient population analysis of a sample set to ensure that a diagnostic
being used for the purposes of discovery and lab can run a commercially available biomarker
clinical validation. accurately and to the manufacturer’s specification.

This approach, rather unsurprisingly, demonstrates the For example, a lab may acquire kits from a vendor
biomarker working very well in this defined group to measure HER2 amplification. They will need to
of patients and is referred to as “overfitting”. The show that they generate comparable results to
problem is that when someone then applies the other labs when analysing a set of verification
overfitted biomarker to a separate group of patients samples before offering the assay to patients.
it can fail due to differences between the
Conclusion
populations the investigators were not aware of.

For example, a centre may collect patient This article has covered some of the main

samples using a specific protocol that is not concepts of biomarker application which will

used elsewhere resulting in any locally developed hopefully orientate those new to the field and

biomarkers only working in that centre. Overfitting provide a working knowledge. There are, of

is avoided by ensuring the clinical validation patient course nuances specific to certain situations

population is entirely different from that used for that are covered elsewhere in more detail.

biomarker discovery. In addition, a third party

should be used to apply the biomarker Please contact Almac Diagnostic Services
independently from the original investigators if you would like to discuss any of the
points raised.
using a pre-specified, locked protocol to
prevent any unintended experimental bias.
Click here to email
One area of confusion is the use of the term
“Biomarker verification” that is sometimes used
interchangeably with the “Biomarker validation”.

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