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AUTOMATED SAMPLE PREPARATION
automation—using a conveyor line, barcode reading,
and whole rooms of machinery to completely automate
workflows. In many cases, the user simply inserts the
sample and, sometime later, gets a result.”
Automated sample
preparation
Devices to prepare cells, nucleic acids, proteins, and other
samples for analysis are becoming increasingly sophisticated, running faster and more accurately than ever before.
In addition, their ease of use is making it possible to quickly
train almost anyone to run automated sample preparation.
By Mike May
A
utomation increases the throughput and consistency of preparing samples for protein analysis,
genetic sequencing, and other methods of data
collection. The key challenges of automating
sample preparation, explains Michael McGinley, core products manager for Phenomenex in Torrence, California, is
“turning vision into reality.” He adds, “It’s all about how to
get a sample from point ‘A’ to point ‘B,’ but that can be a
Herculean task at times.”
Traditionally, most automated sample preparation involves liquid handling, which uses robotics to dispense
and collect specific amounts of liquids to, for example,
add reagents or wash samples. These tasks remain fundamental to automated sample preparation, and such liquidhandling platforms work with various containers ranging
from tubes to multiwell plates, to automatically prepare
samples for various downstream processes, such as liquid
and gas chromatography (LC and GC) and next-generation
sequencing (NGS).
“The challenge for data collection is to prepare samples
in a consistent manner, and automation can be used to
reduce human error,” says Eric Grumbach, a product
manager at Waters Corporation in Milford, Massachusetts.
“The health science marketplace has made the most of
Overall, companies produce tools for automation in two
ways. The sample preparation can either stand alone,
meaning that it is used only to get a sample ready for analysis on another platform; or automated sample preparation
can be integrated with an analytical platform, so that a
sample is loaded, prepared, and analyzed within one device. Choosing an approach really depends on the user’s
requirements and the reason they want to add automation
into their workflow. For instance, Grumbach says, “If you
handle preparation separately then you’re not tying up
test instrumentation while samples are being prepared.”
However, when the preparation and analysis are integrated,
user intervention is essentially eliminated after the samples
and methods have been loaded onto the machine, and that
frees lab members to do other things.
Many labs use a standalone approach with LC or GC to
separate samples into components that can be analyzed
on another platform, such as mass spectrometry (MS). LC,
for example, pushes a sample and a liquid solvent through
an adsorbent-filled column. The components of the sample
move through the column at different rates based on how
they interact with the adsorbent, and that separates them.
In GC, the sample is instead vaporized for separation.
Getting the best results from chromatography starts with
sample preparation. For example, solid phase extraction
(SPE) can be used to increase the concentration of targeted
components before either LC or GC.
McGinley says of Phenomenex, “We live and breathe
chemistries of separation,” and this includes GC, LC, and
SPE. He adds, “We’re good at the chemistries and making
sample preparation devices, but what do we do if the scale
goes from 20 samples a day to 200 or 2,000?” In this case,
the answer is to team up with an expert in liquid handling.
In 2015, Phenomenex and Switzerland-based Tecan
combined their skills to automate SPE. The resulting
platform consists of Phenomenex’s SPE-chemistry products—Phenomenex Strata and Strata-X SPE sorbents—and
Tecan’s Freedom EVO, which provides robotic liquid handling. McGinley says, “This collaboration came out of being
at a scientific conference with people from Tecan and finding a customer who wanted to use their robots and our assays.” This system can run tubes or 96-well plates. McGinley adds, “You can start with a manual process and move to
automation as needed.”
One example of integrating sample analysis and detection involves titration, which measures a solution’s concentration. Medical laboratories, for instance, use titration to
measure chemicals in blood or urine samples. Metrohm
USA in Riverview, Florida, automates this process. By focusing on one key task, Metrohm has made its automated
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Two tactics
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AUTOMATED SAMPLE PREPARATION
for phosphopeptide
titration platforms easier
enrichment for LC/
to use. “This technology
MS applications.
is good for labs with mul“Phosphopeptide
tiple analysts who rotate
enrichment from complex
through,” says Lori Carmixtures is one of the
ey, Metrohm’s titration
most challenging sample
product manager. “You
preparation tasks to
just weigh the sample,
perform reproducibly for
put it on a tray, and press
LC/MS,” Edwards says.
‘start.’” These platforms
“The AssayMAP Fe(III)
can also perform au“Four or five years ago, NGS was incredNTA cartridge addresses
tomated dilution of the
ibly manual, but now it comes with quite
this challenge in a
sample, add a solvent if
simple workflows so that almost anyone
scalable, reproducible,
needed, and remove preand automated manner.”
cise volumes. A range of
can adopt the technology.”
This cartridge can be
scientists beyond those
— Andy Felton
used as part of an LC/MS
in medical laboratories
workflow to discover and
can use these titration
characterize biomarkers
platforms. As an examand biotherapeutics or to analyze the selectivity and
ple, Carey mentions researchers working in environmental
toxicity of candidate drugs.
labs, who also require high-throughput capabilities.
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Prepping proteins
To study specific proteins or peptides, scientists
often label them. The labels can then be used to isolate
specific proteins or peptides for further study. Agilent
Technologies in Santa Clara, California simplifies
protein isolation with its AssayMAP platform. David J.
Edwards, senior director of mass spectrometry marketing
in Agilent’s life sciences and applied markets group,
describes this platform as “a fully automated solution for
high-throughput protein and peptide sample preparation
and purification.”
The AssayMAP Bravo Platform consists of the Agilent
Bravo liquid handler and comes equipped with AssayMAP
microchromatography technology, which features
disposable cartridges that can accommodate a variety
of separation chemistries. These chemistries include
AssayMAP Affinity Purification, which can be used to
attach an antibody to a target protein, for example.
Edwards says, “AssayMAP is especially effective when
used upfront of LC/MS analyses, delivering consistent
samples that allow users working in biopharma and proteomics to achieve superior mass spec results.” The AssayMAP Bravo Platform uses the Bravo AssayMAP liquidhandling head, which contains precision-flow syringes.
“The syringes enable liquid flow to be precisely controlled
to accommodate quantitative protein/peptide binding and
elution in a single pass and deliver reproducible and consistent coefficients of variation,” Edwards says. In addition,
AssayMAP comes with software that includes predefined
workflows, but which can also be customized if the user
wishes. The software eliminates “any need for the user
to learn a scripting/instrument-control programming language,” adds Edwards.
Agilent recently released an immobilized metal affinity
chromatography (IMAC) cartridge for AssayMap that
uses nitrilotriacetic acid (NTA) chelated with Fe(III)
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Preparing DNA
For scientists looking to explore an organism’s genes
or isolate DNA for specific applications such as forensics,
DNA sequencing is key. The high-throughput capabilities
of NGS, however, only provide useful data if the right
library is used. To build a library, scientists use enzymes
to generate random DNA fragments of a specific size
from their sample. Making the library, though, is more
complicated than it sounds.
As Andy Felton, vice president of product management
for Ion Torrent at Thermo Fisher Scientific,
headquartered in Waltham, Massachusetts, explains:
“Library preparation is a set of fairly complex molecular
bioprocesses,” and has traditionally required a lot of
manual work. Consequently, it takes hours—at least two
and up to seven, depending on the specific process being
used. Felton adds, “There’s always room for error with a
manual process.”
Thermo Fisher Scientific adapted its Ion Chef system
to perform library construction. Instead of taking hours
of hands-on time at the bench, Felton says, the Chef can
build a library in just 15 minutes.
“Four or five years ago, NGS was incredibly manual,”
says Felton, “but now it comes with quite simple workflows
so that almost anyone can adopt the technology.” It’s so
easy to use that Felton says he could teach almost anyone
how to set it up in less than an hour.
Besides being easier to use, the Ion Chef boosts the outcome of NGS. “Removing user interaction typically reduces
the error rate and improves the overall repeatability of the
results,” Felton says. That really matters in clinical applications, which need less complex and extremely robust methods. The increasing simplification of NGS is also spreading
the use of this technology, and Felton says it can be used
for “measuring gene expression, target detection, metabolomics, epigenetics, and beyond.” continued>
301
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AUTOMATED SAMPLE PREPARATION
Featured Participants
Agilent Technologies
www.agilent.com
Thermo Fisher Scientific
www.thermofisher.com
Metrohm USA
www.metrohmusa.com
Washington University
School of Medicine
in St. Louis
medicine.wustl.edu
Phenomenex
www.phenomenex.com
QIAGEN
www.qiagen.com
Waters Corporation
www.waters.com
Tecan
www.tecan.com
Identifying nucleic acids in the clinic
The throughput of NGS makes it useful for clinical settings
in which researchers must analyze a large number of samples. By simplifying the sample-preparation steps in NGS, a
wide variety of clinical applications become more practical.
For instance, the growing interest in the health ramifications
of the human microbiome—the microorganisms that live in
and on us—generates the need to isolate and analyze these
microbial samples.
As Markus Sprenger-Haussels—senior director, head of
sample technologies product development for life sciences
at Germany-based QIAGEN—explains, researchers use
nucleic-acid extractions to study the composition of microorganisms in the human gut, for example. Unfortunately,
about 95% of the NGS reads from such a sample are usually of human origin, not microbial. “So we developed a method to selectively isolate microbial DNA,” Sprenger-Haussels
says, “and after using it, 95% of the reads are from microbial DNA, which increases the amount of valuable information per sequencing run almost 20-fold.” This enrichment
method is included in QIAGEN’s QIAamp DNA Microbiome
Kit and the QIAamp FAST DNA Stool Mini Kit, which isolate
microbial DNA for further analysis. Using these kits, “you
can look at the correlation between certain disease states
and the microbial community composition on the skin or in
the colon,” Sprenger-Haussels says.
In addition to NGS, today’s medical experts also use assays based on the polymerase chain reaction (PCR). For
instance, PCR can be used when treating cancer. To track
the impact of a cancer treatment, an oncologist might use
a liquid biopsy to analyze a patient’s blood for signs of
cancer. QIAGEN provides PCR-based tests that can be
used manually or automated with the QIAsymphony sample
preparation system to isolate circulating tumor cells, free
circulating nucleic acids, and exosomes (vesicles released
from cancer cells that can trigger tumor growth). “These
all carry information about a [patient’s] cancer,” SprengerHaussels says, “and the QIAsymphony provides unmatched
sensitivity due to its capacity to process large sample
302
volumes.” With respect to circulating tumor cells, for example, QIAGEN’s AdnaSelect and AdnaDetect technology
finds them 95% of the time if there are only five cancer cells
in 5 milliliters of blood; and it detects them more than 70%
of the time even when there are only two circulating tumor
cells in 5 milliliters of blood.
QIAGEN’s sample-preparation technology for PCRbased assays can also be used for prenatal diagnostics.
“Just draw blood from the mother,” Sprenger-Haussels
says, “and it includes fetal DNA that can be analyzed for
[Down syndrome] or other genetic disorders.” SprengerHaussels adds, “There’s no risk to the fetus, and it
provides much higher accuracy than other noninvasive
tests, like imaging.”
Creating custom systems
Even with the various commercial options available for
automating sample preparation, scientists sometimes need
a custom system. Daniel Ory, professor of medicine, cell biology and physiology at Washington University School of
Medicine in St. Louis, Missouri, and his colleagues create
custom analytical systems for academic and industry scientists. He says, “The projects that we take can vary from a
handful of samples to sample sets of thousands—3,000 to
4,000.” Given that breadth of projects, Ory points out that
each needs a different approach. The level of automation
that Ory applies depends on the project’s size. For instance,
if a clinical project includes 1,000 samples, he might develop a method that uses 96-well plates. “There are lots
of liquid-handling stations that can work with a multiwell
format,” he says. Nonetheless, many of the solutions turn
out semiautomated. Ory says, “If we can get to a point with
minimal manual work, that’s the best, and that’s what we
aim for.”
A lab or company’s decision to automate sample preparation, however, includes an economic component. “Automation could cost hundreds of thousands of dollars,” Grumbach says. “Automation also requires routine maintenance.
Organizations often hire specialists specifically to care for
these automation platforms.” If a process does not include
enough samples to justify that level of spending, it might
make more sense to stick with a manual approach.
Regardless of the sample-preparation approach, Ory
makes a key point: “Your project will only be as good as the
quality of the data that comes out of it.” To get the highestquality data, a scientist must employ the best sample preparation. Moreover, the analytical system must be validated.
As Ory explains: “If you have a sample set of 1,000 from a
clinical study, you would like to know that sample number 1
and sample number 1,000 can be compared.”
As tools for automating sample preparation become easier to set up and use, more scientists can incorporate the
technology in their labs or in the clinic.
Mike May is a publishing consultant for science and technology.
DOI: 10.1126/science.opms.p1600101
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