Wp mi script_preamp_0613_lr

Scientific article

miRNA biomarker discovery —
overcoming limiting sample material
Karlheinz Semmelmann, Marcus Lewis, Jonathan Shaffer, and Eric Lader
QIAGEN Inc., Frederick, MD, USA

Abstract: microRNAs (miRNAs) exhibit a tightly regulated spatial and temporal pattern of expression
during development and differentiation. Furthermore, miRNAs have been shown to be aberrantly
expressed in cancer and other diseases, and may prove to be excellent diagnostic, theranostic, and
prognostic biomarkers. Often the most valuable and informative samples — such as laser-captured
samples, circulating tumor cells, or extracellular miRNA in body fluids — are the hardest to obtain
in amounts sufficient for detailed miRNome profiling. We present an integrated, PCR-based
system that reduces the amount of sample required for full miRNome profiling by several orders
of magnitude and provides unparalleled reproducibility and precision. This advance enables
detailed miRNA analysis on the smallest of samples and opens up new possibilities for biomarker
development.

Introduction
The discovery of the first miRNA in 1993 (1) provided only a hint

impact on all aspects of biomedical research, from providing a

of the extent to which miRNA function is intertwined in virtually

better understanding of pathway regulation in model systems to

every process in mammalian cells. Once it was discovered that

explaining coordinated gene expression changes in cancer and

miRNAs are widespread in both plant and animal kingdoms

creating new possibilities for molecular diagnostics and nucleic-

and exhibit a complex pattern of expression (2–4), the rise of

acid–based drugs.

the field to scientific prominence seemed inexorable. miRNAs
have been shown to play a critical role in cell fate determination
and in eliciting and maintaining a pre- or post-differentiated

Contents

state. Most miRNA genes are transcribed by RNA Polymerase II

Introduction�� 1

and have regulatory elements as complex as those that regulate
protein-encoding genes (5–7). In fact, many miRNA precursors
are embedded in introns of protein-encoding genes and are
spliced out during mRNA processing as pre-miRNA (5, 8–10).
As we now know that miRNA regulates thousands of genes, it is
not surprising that Croce and others have discovered that many
miRNAs are deregulated in cancer and other diseases, and that
this altered expression can be used to identify and classify subtypes

Circulating, cell-free miRNA �� 2
miRNA profiling techniques and their RNA requirements�� 2
Principle of the miScript PCR System for qRT-PCR�� 2
Preamplification using the miScript PCR System �� 3
Preservation of miRNA expression profile after preamplification_ 5

Preamplification strategies for archival, FFPE tumor samples�� 6
Preamplification strategies for body fluids�� 6

of disease (11). Even more interesting, as well as occurring in

Normalization control for cell-free miRNA�� 8

disease, miRNA deregulation has also been identified in some

Conclusion�� 9

instances as critical to the progression of the cell from a normal

References�� 9

to diseased state. miRNA research has made a significant

Ordering information�� 10

Circulating, cell-free miRNA
The remarkable discovery that stable miRNAs could be found in

Next-generation sequencing (NGS) of RNA, often called

serum and plasma was soon confirmed and extended by many

RNA-seq, is a relatively new technology that takes advantage of

researchers (12, 13). A high level of interest, and hundreds

massively parallel sequencing on a solid support. This technique

of research papers, focused on the possibility that changes

is highly suited to discovery, enabling characterization of SNPs,

in abundance of circulating miRNAs could be adopted as

mutations, processing variants, and novel miRNA species.

noninvasive biomarkers for a variety of indications. Circulating

RNA-seq is generally regarded as a screening technology. In its

miRNA is most certainly not naked miRNA, which would be

current form, RNA-seq characterizes all sequences in a sample

degraded within seconds due to high levels of nucleases in

in a semi-quantitative, but exhaustively thorough, manner.

blood. Several reports have demonstrated that circulating
miRNA derives its stability through several mechanisms. Serum
stability can result from the formation of complexes between
circulating miRNA and specific proteins, such as Ago2 (14–16).
Other studies have found miRNA contained within circulating
exosomes and other microvesicles (17). Fractionation experiments
show that both exosomal and non-exosomal miRNA make up the
total extracellular miRNA repertoire in serum and other body
fluids, although the composition can vary between different
body fluids. While there is no longer any doubt that a stable
population of extracellular miRNAs exist in circulation, nothing
is positively known about their natural function. However, there
are tantalizing hints that circulating miRNAs play a signaling role
in both normal physiology and in promoting metastasis in cancer
(18, 19). Certain types of cancer cells shed high numbers of
exosomes into circulation. In fact, it has been reported that some
cancer cells can selectively shed specific miRNAs to lower their
intracellular concentration. Clearly there are many more exciting
discoveries to be made in miRNA function and regulation.

miRNA profiling techniques and their RNA
requirements
several ways, each of which has advantages and limitations.
Today, the major approaches are hybridization arrays, RNAseq, and qRT-PCR. Screening with hybridization arrays requires
relatively large microgram amounts of RNA and is limited
in both sensitivity and dynamic range. The range of miRNA
expression in a typical cell is several orders of magnitude larger
than the dynamic range of a hybridization array, therefore a
large number of expressed sequences will be undetectable.
Obviously too, it is only possible to detect miRNA species that
have corresponding assays on the array, meaning that this is

2

owing to its combination of low sample amount requirements,
sensitivity, selectivity, and dynamic range. In a single run,
miRNA targets ranging from 10 to 107 copies can be accurately
quantified. Sample requirements for qRT-PCR are much lower
than for RNA-seq or arrays. Without any preamplification,
excellent sensitivity can be achieved with less than 1 ng total
RNA per assay, or approximately 1 µg RNA per 1800 assay
miRNome. Furthermore, using preamplification as described
in this paper, full miRNome screening can be performed, in
technical triplicate, with just 10 ng total RNA. From serum or
plasma, this corresponds to the miRNA content of approximately
1 µl sample. Quantitative preamplification of the miRNome is
an enabling development, eliminating the requirement for
microgram quantities of RNA per sample to profile the miRNome.
In addition, preamplification makes profiling from other body
fluids that have far less miRNA than serum, such as cerebrospinal
fluid, saliva, and urine, possible without having to process an
excessively large sample volume to attain sufficient RNA.

Principle of the miScript® PCR System for qRT-PCR

Profiling the miRNome of a sample can be accomplished in

not a suitable tool for discovery of new miRNA species.

For miRNA profiling, qRT-PCR remains the preferred method,

While the small size of miRNAs confers some technical
advantages (e.g., miRNAs are less likely than mRNA to be
affected by cross-linking in FFPE samples), their 21–23 bases
leave little room for maneuvering of primer or probe design
to optimize an assay. While several approaches have been
commercially developed, the differences between them are
primarily about flexibility, as a properly designed assay using
any of the currently available systems will have roughly
equivalent sensitivity and selectivity.
The miScript PCR System is the only technology that includes
a truly universal, small-RNA-specific cDNA synthesis reaction.
In this patent-pending technology, miRNA is tailed by E. coli

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poly A polymerase, followed by an anchored, oligo dT primed

miScript Primer Assays are designed with several features that

cDNA synthesis reaction. This ensures that any and all miRNAs

favor robust, large-scale miRNA profiling. First, assays are

are converted into cDNA without bias. Critically, this includes

designed with a very restricted amplicon size and Tm range.

miRNAs that have not yet been characterized, ensuring that

This ensures uniformity of assay performance under a universal

a researcher can always return to an archived cDNA sample

set of PCR conditions and makes melt curve analysis easy to

when new miRNA targets are identified. The cDNA is tagged

interpret. Second, the system is designed to tolerate the 3'

with a unique sequence present in the anchored primer and this

heterogeneity commonly found in miRNAs. Extensive NGS of

serves as a common 3' PCR priming site (Figure 1).

miRNA has shown high levels of polymorphism at the 3' end
of many different miRNAs. This data, available at miRBase
(www.miRBase.org), shows that in many cases, a major fraction

miRNA profiling using the
miScript PCR System

of a specific miRNA in a cell can have several additional or
missing bases on the 3' end, resulting in mismatches to the
canonical sequence (Figure 2). This does not present a problem

RNA sample 1

for the reverse transcription reaction in the miScript PCR System,

RNA sample 2

which will convert any miRNA into cDNA, nor does it generally

1. Convert
miRNA to cDNA

present a problem for miScript Primer Assays, as they are
deliberately designed so that their 3' ends do not extend to the
3' end of the mature miRNA sequence. However, as described,

cDNA sample 1

the alternative technology of miRNA-specific priming found in

cDNA sample 2

some commercially available PCR profiling technologies, would

2. Preamplify cDNA

be unable to prime cDNA synthesis from these variants, resulting
in an underestimation of the true levels of many miRNA species

3. Combine amplified cDNA with
QuantiTect® SYBR® Green PCR Master Mix.
Aliquot mixture across miScript miRNA PCR Array.

in a cell (20).

Preamplification using the miScript PCR System
Approximately 0.5–1 ng total RNA per assay is recommended
for maximum sensitivity in qRT-PCR of miRNA using the miScript

4. Run in
real-time PCR cycler

of an miRNA from approximately 100–200 cells, or far less

1.E-000

Delta Rn

1.E+001

1.E-000

Delta Rn

1.E+001

PCR System. This allows quantification of as few as 10 copies

1.E-001
1.E-002
1.E-003

than one copy per cell (assuming 30 pg total RNA per cell).

1.E-001

This level of sensitivity and dynamic range (approximately 107)

1.E-002

0

4

8

12

16

20 24

28 32

1.E-003

36 40

0

4

8

12

Cycle number

16

20 24

28 32

36 40

Cycle number

is sufficient for most experiments. However, when samples are
exceptionally precious, need to be used for multiple analytes, or
are simply available in very limited amounts as commonly found
with isolated, circulating tumor cells, microdissected samples,

5. Analyze data

or extracellular miRNA in biofluids, a preamplification reaction
can enable experiments that would be otherwise impossible.
1

10-5

10-1

Normal breast

p-Value for fold change

10-6

10-4
10-3
10-2

the 10 µl cDNA synthesis reaction as input. The volume of cDNA

10-3
10-4

synthesis reaction used is critical, as RT components

10-5

10-1
1

Preamplification with the miScript PCR System uses just 1 µl of

10-2

-4

-3

-2

-1

0

1

2

Fold change ratio [log2]

3

4

10-6

10-6

10-5

10-4

10-3

10-2

10-1

1

Breast tumor

Figure 1. miRNA expression profiling from samples containing low RNA amounts.

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Figure 2. Deep sequencing reads for hsa-miR-21-5p at miRBase show variant miRNA ends. These data, available at miRBase (www.miRBase.org), show that a large
fraction of a specific miRNA in a cell can have additional or missing bases at the 3' end, resulting in mismatches to the canonical sequence.

must be carried over to the preamplification reaction. The
3

amount of RNA is less critical, but we typically recommend a
cDNA synthesis reaction containing 10 ng RNA (equivalent to

–1
PreAMP

approximately 300 cells). Each cDNA synthesis reaction can
then be used for 10 preamplification reactions, each with 1 µl
input (equivalent to 1 ng RNA or 30 cells). More RNA may be

–5

used in the cDNA synthesis reaction, but it is not necessary. Less
–9

RNA may also be used, however the sampling variation from

y = 0.7497x + 0.0449
R² = 0.9164

less than 3 cells equivalent of RNA increases the variability of
–13
–13

results for moderately to rarely expressed miRNAs (Figure 3).
Preamplification is a highly optimized, highly multiplexed PCR
containing either 96 or 384 assays. These assay pools
correspond to QIAGEN’s predeveloped 96- and 384-assay
miScript miRNA PCR Arrays. For miRNomes that are larger than
one 384-well plate, such as the human and mouse miRNomes,
two or three 384-plex preamplification reactions must be
performed. After 12 cycles of preamplification, the amplified

–9

–5
–1
No PreAMP

3

Figure 3. Low template cDNA input increases variability of results. Preamplified
and nonpreamplified cDNA from the same preps (equivalent to less than 4 cells)
and cDNA synthesis reactions were used for miRNA profiling. A scatter plot
of ΔΔCT values between normal lung and tumor lung FFPE tissue sections
demonstrates low correlation between nonpreamplified and preamplified samples.
The miRNeasy FFPE kit was used to purify RNA from normal and tumor lung
tissue 5 µm FFPE sections. Reverse transcription was performed using the
miScript II RT Kit with miScript HiSpec Buffer and 100 pg cDNA was used for
preamplification with the miScript PreAMP PCR Kit. A 96-plex miFinder miScript
PreAMP Pathway Primer Mix and Array were used for miRNA profiling.

product is mixed with real-time master mix and used for
miRNA profiling. Targets as rare as 10–20 copies to targets
as abundant as 107 copies are preamplified by 4 orders of
magnitude (Figure 4).
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14

A

50

40
Number of assays

CT advantage

12

10

8

30

20
10

6
0

0

10 20 30 40 50 60 70 80 90
Assay on Human Neurological Development and
Disease Array

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

CT advantage

12
CT advantage

800

600
Number of assays

14

B

10

400

200

8

0

6
0

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

200
400
600
800
1000
Assay on Human miRNome Array

CT advantage

Figure 4. CT advantage after preamplification using 96 and 384 assays. After 12 preamplification cycles, most samples consistently show a CT advantage of between
10 and 12 cycles. These CT differences are highly reproducible. Reverse transcription was performed using the miScript II RT Kit with miScript HiSpec Buffer and a pool
of synthetic miRNAs. cDNA was used for preamplification with the miScript PreAMP PCR Kit.
A 96-plex Human Neurological Development and Disease miScript
PreAMP Pathway Primer Mix and Array or a
384-plex Human miRnome miScript PreAMP Pathway Primer Mix and Array were used for miRNA profiling.

Preservation of miRNA expression profile after
preamplification
For the development of miRNA expression signatures as

greatly facilitates non-biased amplification in a 384-assay

biomarkers using preamplified material, it is important that the

multiplex reaction. Finally, the chemistry of the cDNA synthesis

preamplification reaction is extremely reproducible to preserve

reaction severely restricts any cDNA side reactions, so there is

relative changes in miRNA expression. It is not absolutely

much less background cDNA synthesized and therefore lower

critical that every assay has exactly the same efficiency in

background in the preamplification reaction. The robustness

preamplification, although we make every effort to achieve

of the system is demonstrated in Figure 5, in which the fold-

that, but it is more important that each assay performs the same

difference of expression is compared between 2 samples — one

way on every sample. This is the case for optimized miScript

preamplified and one nonpreamplified sample. It is important

PreAMP Primer Mixes. It is challenging to multiplex such high

to note the values on the axes are not CT or log change values,

numbers of assays; however, several design features make this

they are fold-change values. These data show that the fold

possible. First, since the miScript PCR System uses a universal

changes between these 2 samples are essentially identical,

3' PCR primer, the complexity of the preamplification primer

despite the fact that 1000-fold less starting material was used

pool is reduced by 50%. Second, as mentioned earlier, all the

in the preamplified sample.

amplicons are both the same size and very close in Tm, which
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type and numbers are similar (Figure 6). However, due to the

A
15

variations in fixation and storage, careful normalization is
required. This can be accomplished by normalizing against
invariant miRNA or snoRNA or by normalization against the
mean of expressed miRNA targets.

7
36

3
y = 0.9097x - 0.0832
R2 = 0.9563

-1

28
CT value

Fold change preamplified

11

-5
-5

-1
3
7
11
Fold change nonpreamplified

20

15
FFPE isolation 1
FFPE isolation 2
FFPE isolation 3

12

B
8

4

Fold change preamplified

0
4

10

20 30 40 50 60 70
Assay on Human miFinder Array

80

Figure 6. Adjacent FFPE sections provide consistent expression patterns. cDNA
derived from 3 different FFPE sections from the same sample were used for miRNA
profiling. CT values were highly consistent for all assays tested between the samples.
The miRNeasy FFPE Kit was used to purify RNA from lung tumor FFPE samples.
cDNA was prepared from 125 ng total RNA using the miScript II RT Kit with
miScript HiSpec Buffer. Samples were not preamplified. The Human miFinder
miScript miRNA PCR Array was used for miRNA profiling.

0

-4

y = 0.9531x - 0.0536
R2 = 0.9228

Preamplification strategies for body fluids

-8
-8

-4
0
4
Fold change nonpreamplified

The discovery of reproducible changes in cell-free miRNA levels

8

in the circulation of people with various diseases has sparked

Figure 5. Preamplification preserves expression patterns in FFPE samples using
1000-fold less input cDNA. Preamplified cDNA and nonpreamplified cDNA from
the same prep were used for miRNA profiling. Scatter plots of x-fold expression
change calculations (2-ΔΔCT) between normal and tumor sections demonstrate
high correlation between nonpreamplified and preamplified samples. Normalization
was performed against housekeeping controls.
96-plex miFinder miScript
PreAMP Pathway Primer Mix and Array or
384-plex miScript PreAMP miRNome
Primer Mix and Array were used. The miRNeasy FFPE Kit was used to purify RNA
from normal and tumor lung tissue 5 µm FFPE sections. cDNA was prepared
from 10 ng total RNA using the miScript II RT Kit with miScript HiSpec Buffer
and preamplified using the miScript PreAMP PCR Kit.

great interest in developing miRNA profiles from human body
fluids as biomarkers. Serum and plasma in particular have been
the subject of intensive profiling. Generally, there is sufficient
miRNA in just 20 µl serum or plasma for a sensitive miRNA
profiling experiment by qRT-PCR. If the volume of plasma or
serum is not limited, we recommend using 100–200 µl per
RNA preparation. However, when samples are very valuable
or even more limited, a preamplification reaction can be used

Preamplification strategies for archival,
FFPE tumor samples

to further decrease the amount of serum or plasma required.
For example, following preamplification with the miScript PCR

QIAGEN provides the miRNeasy FFPE Kit for purification of
miRNA from formalin-fixed, paraffin-embedded (FFPE) tissue
samples. After purification with the miRNeasy FFPE Kit, a typical
5 µm section often yields enough RNA for a miRNome profile.

System, a full human miRNome panel can be screened in
triplicate using only ~1 µl serum equivalents. In addition to the
lower sample requirement, preamplification results in a significant
increase in detected miRNAs (Figures 7 and 8).

However, for fine needle biopsies, smaller samples, or valuable

Compared to plasma or serum, whole blood contains large

samples, far less RNA can be used to obtain high-quality miRNA

amounts of miRNA. However, if the sample is severely limiting,

expression data. In our experience, profiling data derived from

for example a 1 µl blood spot, preamplification can be performed

adjacent sections can be extremely similar as long as the cell

in the same way as for serum or plasma with good success.

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CT mean: 3 RN

20

y = 0.9728x + 0.7671
R2 = 0.9757

16
16

A

20
24
28
CT: individual RNA isolation from serum

32

B

21

03
E+

02
E+

1.

Nonpreamplified
Preamplified
2–ΔCT: normal serum

1.

1.E–01
25

01

32

E–

20
24
28
CT: individual RNA isolation from serum

1.

16

29

01

16

33
1.E+00

E+

y = 0.9728x + 0.7671
R2 = 0.9757

1.

20

1.E+01
37

1.

24

1.E+02

00

28

E+

2–ΔCT: colorectal cancer serum

1.E+03

Mean CT

CT mean: 3 RNA isolations from serum

32

33
1.E+00

03
E+

02
E+

01
E+

1.

Nonpreamplified
Preamplified
2–ΔCT: normal serum

1.

1.

21

1.

E–
1.

E+

1.E–01
25

00

29

17
0

10

20 30 40 50 60 70
Assay on Serum Plasma Array

Detectable miRNAs on Serum Plasma Array

B
1.E+01
37

01

Mean CT

A

2–ΔCT: colorectal cancer serum

1.E+03
Figure 7. Reliable miRNome profiling from 1 µl serum. Total RNA was purified from 3 different 5 µl normal serum samples and 3 different 5 µl colorectal cancer serum
samples using the miRNeasy Serum/Plasma Kit. cDNA was then prepared from 0.7 serum equivalents (SE) using the miScript II RT Kit with miScript HiSpec Buffer.
µl
17
cDNA was preamplified using the miScript PreAMP PCR Kit with Serum Plasma 384HC miScript PreAMP Pathway Primer Mix prior to profiling. miRNA profiling was
0
10 20
50 60 70 80
performed with the with the Serum Plasma 384HC miScript miRNA PCR Array. Scatter plots show
high correlation in30 40T values achieved between 3 RNA
mean C
Assay on and colorectal Array
isolations from1.E+02and an individual RNA isolation from serum, and
serum
differences in miRNA expression between normalSerum Plasmacancer samples.

80
70

60

50
40

30

80

Nonpreamplified

Preamplified

Detectable miRNAs on Serum Plasma Array

Figure 8. 100% increase in miRNAs detected from 10-fold less cDNA after preamplification from serum. Total RNA was purified from 5 µl human serum using the miRNeasy
Serum/Plasma Kit. cDNA was then prepared from 0.7 µl serum equivalents (SE) using the miScript II RT Kit with miScript HiSpec Buffer. cDNA (0.7 µl SE) was used
directly for miRNA profiling or one-tenth of the cDNA preparation (0.07 µl SE) was preamplified using the miScript PreAMP PCR Kit with Serum Plasma miScript
80
PreAMP Pathway Primer Mix prior to profiling. miRNA profiling was performed with the with the Serum Plasma miScript miRNA PCR Array. Plots of
mean CT values
achieved and
number of miRNAs detected demonstrate highly superior results from 10 fold less starting cDNA due to preamplification.
70

Some extracellular circulating miRNAs appear to be restricted

Urine is a body fluid that also shows promise for biomarker

60
to exosomes. Exosome enrichment traditionally requires an

discovery, particularly for diseases of the kidney and prostate.

ultracentrifugation step to pellet the exosomes. This pellet can

The amount of miRNA recoverable from 200 µl urine is usually

50
then be processed with the miRNeasy Serum/Plasma Kit. There

not enough for a 96-assay or 384-assay PCR array. Processing

are several alternative methods to enrich for exosomes, but the

a much larger sample would help increase RNA yield, but

reproducibility of these methods is as yet undetermined.

would also cause increased copurification of any inhibitors

Nevertheless, the miRNeasy Micro Kit and miRNeasy Serum/

present in the sample. For analysis of cellular miRNA, cells and

Plasma Kit can be used for RNA isolation after polymer
Nonpreamplified
Preamplified

debris should be pelleted and the pellet should then be used

precipitation, immunocapture, or other methods to enrich or

for purification with the miRNeasy Micro Kit. For analysis of

purify exosomes.

cell-free miRNA from urine, we recommend removal of cells

40

30

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and cell debris by performing a pre-clearing spin or filtration.

Our initial experiments with other body fluids, including

For cell-free miRNA purification, we recommend processing 100–

cerebrospinal fluid, milk, and bronchial lavage suggest that the

200 µl urine using the miRNeasy Serum/Plasma Kit, followed

yield of RNA depends on whether the sample comes from a

by cDNA synthesis using 1.4 µl eluate, and preamplification

healthy or disease sample and on the extent of cellular content

using 1 µl cDNA synthesis reaction. Preamplification enables

in the sample. For exosomal and extracellular RNA, a clarifying

practical and robust miRNA profiling from human, mouse, or

spin is always required to remove cells and cellular debris.

rat urine (Figure 9).

For small amounts of cultured cells, sorted cells, and laser
capture microdissection (LCM) samples from cryosections, as

A

well as various animal and human tissues, we recommend

40

the miRNeasy Micro Kit, which is specifically designed for
purification of total RNA, including miRNA, from small samples.

Raw CT value

35

If after miRNA purification, the RNA content of the eluate is not
known, QIAGEN offers a prespotted miRNA control plate, the

30

miScript miRNA QC PCR Array, as a useful aid to determine
25

whether preamplification is required or how much the

PreAMP
No PreAMP

preamplified sample needs to be diluted. Following the protocol

20

provided with this array, it is straightforward to determine
0

10

20 30 40 50 60 70
Assay on Human miFinder Array

whether there is sufficient miRNA in the sample or whether a

80

preamplification step is warranted (Figure 10). In addition, this
control array can be used to determine whether inhibitors are

B

present in the samples, making it a useful tool for quality control

CT mean (4 replicates)

32

prior to performing a pathway or miRNome experiment.

Normalization control for cell-free miRNA

28

Small, noncoding RNAs, such as snRNAs and snoRNAs, are
frequently used for normalization of miRNA expression data.

24

However, these RNAs are not expressed in serum and plasma
and for this reason alternative methods of normalization are

20

necessary in experiments involving these sample types. We

y = 0.9992x + 0.1024
R2 = 0.9837

recommend spiking a synthetic RNA into the sample prior to
RNA purification. The spiked-in RNA can be later detected and

16
16

20

24
28
CT values (1 replicate)

this data used to normalize for differences in recovery during

32

the purification procedure and differences in amplification

Figure 9. Preamplification enables miRNA profiling from urine. Total RNA was
purified from 200 μl urine using the miRNeasy Serum/Plasma Kit. cDNA was
then prepared from 1.5 μl using the miScript II RT Kit with miScript HiSpec Buffer.
cDNA was either used directly for profiling or preamplified using the miScript
PreAMP PCR Kit with Human miFinder miScript PreAMP Pathway Primer Mix.
Profiling was performed with the Human miFinder miScript miRNA PCR Array.
CT values show that preamplification provides reliable expression data from
miRNAs undetectable in nonpreamplified samples.
A scatter plot shows the
high correlation in mean CT values achieved between 4 RNA isolations from
urine and an individual RNA isolation from urine.

efficiency. QIAGEN provides the miRNeasy Serum/Plasma
Spike-In Control for this purpose. This synthetic RNA is amplified
during the preamplification procedure and an assay to detect
this RNA is provided in the miRNeasy Serum/Plasma Kit and on
the miScript miRNA QC PCR Array.
Following calibration for differential RNA recovery, the global
CT mean of commonly expressed targets (for miRNome and
pathway expression profiling) or the CT mean of invariant
miRNAs (for small panel expression profiling) can be used for
qRT-PCR data normalization (21, 22).

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miScript II RT Kit
(with miScript HiSpec Buffer)

miScript PreAMP
PCR Kit

qPCR and data analysis

Yes
Need
preamplification?

miScript miRNA
QC PCR Array

Optimal
dilution factor?

No

Figure 10. Workflow for samples of unknown RNA amount and quality. Control assays included in the miScript PreAMP PCR Kit and on the miScript miRNA QC PCR
Array can be used to determine the need for preamplification and the optimal dilution factor for preamplified cDNA, and the presence or absence of PCR inhibitors.

Conclusion
miRNA biomarker discovery research presents major challenges

PCR System for miRNA quantification by qRT-PCR. Combined

due to the fact that the very samples that are the most promising

with specialized miRNeasy Kits for miRNA purification, this

are also those that may be in shortest supply and have very

enables complete miRNA biomarker discovery experiments.

low RNA content. At the same time, the discovery process

Preamplification allows researchers to uncover previously inac-

requires screening for large numbers of miRNAs with a wide

cessible miRNA expression data. This will undoubtedly add

range of expression levels in multiple replicates. In a single

to the already extraordinary discoveries identifying how these

step, preamplification can overcome these issues by providing

small molecules contribute to disease and cell biology, and

reliable, nonbiased, highly multiplex amplification of miRNAs in

facilitate the practical application of miRNA expression profiles

a sample. Preamplification has been integrated into the miScript

to diagnostics and drug development.

References
1. ee, R.C., Feinbaum, R.L., and Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
L
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2. Shabalina, S.A. and Koonin, E.V. (2008) Origins and evolution of eukaryotic RNA interference. Trends in Ecology and Evolution 10, 578.
3. Brodersen, P. et al. (2008) Widespread translational inhibition by plant miRNAs and siRNAs. Science 320, 1185.
4. He, L. and Hannon, G.J. (2004) microRNAs: small RNAs with a big role in gene regulation. Nature 5, 522.
5. Lee, Y. et al. (2004) microRNA genes are transcribed by RNA polymerase II. EMBO J. 23, 4051.
6. Chen, K. and Rajewsky, N. (2007) The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 8, 93.
7. Bartel, D.P. (2009) microRNAs: target recognition and regulatory functions. Cell 136, 215.
8. ai, X., Hagedorn, C.H., and Cullen, B.R. (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs.
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9. Zhou, X. et al. (2007) Characterization and identification of microRNA core promoters in four model species. PLoS Comput. Biol. 3, e37.
0. Kim, Y.K. and Kim, V.N. (2007) Processing of intronic microRNAs. EMBO J. 26, 775.
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1. Iorio, M.V. et al. (2005) microRNA gene expression deregulation in human breast cancer. Cancer Res. 65, 7065.
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12. Mitchell, P.S. et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc. Natl. Acad. Sci. USA 105, 10513.
3. Chim, S.S. et al. (2008) Detection and characterization of placental microRNAs in maternal plasma. Clin. Chem. 54, 482.
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Arroyo, J.D. et. al. (2011) Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma, Proc. Natl. Acad. Sci.
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2

Scientific article

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Ordering Information
Product

Contents

Cat. no.

miScript II RT Kit (12)

Reagents for 12 x 20 µl cDNA synthesis reactions

218160

miScript II RT Kit (50)

Reagents for 50 x 20 µl cDNA synthesis reactions

218161

miScript PreAMP PCR Kit (12)

HotStarTaq® DNA Polymerase, buffer, primers, and controls
for 12 preamplification reactions

331451

miScript PreAMP PCR Kit (60)

HotStarTaq DNA Polymerase, buffer, primers, and controls
for 60 preamplification reactions

331452

miScript PreAMP Pathway Primer Mix

60 µl primer mix for preamplification; for use with a
Pathway-Focused miScript miRNA PCR Array

Varies

miScript PreAMP miRNome Primer Mix

60 µl/tube primer mix for preamplification; for use with a
miRNome miScript miRNA PCR Array

Varies

miScript SYBR Green PCR Kit (200)

Reagents for 200 x 50 µl PCRs

218073

miScript SYBR Green PCR Kit (1000)

Reagents for 1000 x 50 µl PCRs

218075

miScript PCR Starter Kit

Reagents for 10 x 20 µl cDNA synthesis reactions and
40 x 50 µl PCRs

218193

miScript Primer Assay (100)

miRNA-specific primer for 100 x 50 µl PCRs

Varies*

Pathway-Focused miScript miRNA PCR Array

Pathway or disease panels of miRNA assays

331221

miRNome miScript miRNA PCR Array

miRNome panels of miRNA assays

331222

Custom miScript miRNA PCR Array

Custom panels of miRNA assays

331231

miRNeasy Micro Kit (50)

Columns, plasticware, and reagents for 50 preps

217084

miRNeasy Serum/Plasma Kit (50)


217184

miRNeasy Serum/Plasma Spike-In Control

10 pmol C. elegans miR-39 miRNA mimic spike-in control
for serum/plasma samples

219610

miRNeasy FFPE Kit (50)


217504

* Visit GeneGlobe to search for and order these products (www.qiagen.com/GeneGlobe).

For up-to-date licensing information and product-specific disclaimers, see the respective QIAGEN kit handbook or user manual.
QIAGEN kit handbooks and user manuals are available at www.qiagen.com or can be requested from QIAGEN Technical Services
or your local distributor.

For more information on QIAGEN’s miRNA portfolio for biomarker discovery, visit
www.qiagen.com/Serum-Plasma.

10

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QIAGEN

Note

Scientific article

www.qiagen.com

11

Trademarks: QIAGEN®, GeneGlobe®, HotStarTaq®, miScript®, QuantiTect® (QIAGEN Group); SYBR® (Molecular Probes, Inc.).
1075462 06/2013

© 2013 QIAGEN, all rights reserved.

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