The omic experiment
Experimental design
Areas that require careful thought include:
• the use of suitable biological samples: the choice
of the sample type to investigate is dependent on
the objectives of the experiment and the
availability of the sample
• the technical/analytical variation: this is the relative
standard deviation of a specific experimental
technique and this needs to be validated
• the biological variation: in humans this can be
very large, therefore it is important to collect
meta-data and, in certain study designs, to match
comparison groups strongly, to ensure that
changes are not due to confounding factors.
A number of factors determine the sample size, but
it has to be such that valid statistical conclusions can
be made. Large numbers of biological specimens are
required to generate the greatest predictive power,
therefore, the collection of clinical data and
biological samples in large biobanks is essential. The
SCOPE (SCreening fOr Pregnancy Endpoints)
study is an example of such a pregnancy-related
biobank (see below and Websites section).
The purpose of the investigation governs what type
of sample should be used. In terms of biomarker
discovery, plasma is the obvious candidate, as the
ultimate goal is usually a blood test.15 However,
biomarkers are likely to occur in low relative
abundance and be massively diluted in the
circulation.15 Rigorous reproducible standard
operating procedures are essential to ensure that
samples are collected, stored and transported in an
identical manner.
Analytical techniques
Sample preparation for omic experiments is imperative
and should be standardised and reproducible.
DNA microarrays have many modes of use, of
which expression profiling is the dominant mode.