LIMS SupportS reSearcH & cLInIcaL nGS ServIceS LaB€¦ · LIMS SupportS reSearcH & cLInIcaL nGS ServIceS LaB ... it realized it had outgrown its legacy LIMS ... you needed to have
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GenoLogics LIMS Helps EdgeBio Build Services Business
LIMS SupportS reSearcH & cLInIcaL nGS ServIceS LaB
Page 3 | © 2011 GenoLogics Life Sciences Software, Inc.
» A single point of entry and return for sequencing
requests and results that has also enabled EdgeBio
to be more deliberate and thorough in collecting
necessary data from customers to drive sequencing
and analysis
» Critical out-of-the-box support for standard Illumina
sequencing workflows
» A flexible Rapid Scripting™ Application Programming
Interface (API) that enabled the lab team to quickly
automate routine manual inputs and implement
workflows for the Ion PGM™ Sequencer.
Implementing the GenoLogics LIMS has enabled EdgeBio
to eliminate sources of manual, human error and improve
overall lab efficiency, goals that have supported the
company as it has applied for and successfully attained
CLIA certification.
“CLIA was the next logical step for our business, and
we’re excited about extending NGS services to clinicians
so that they can help patients and gain a better
understanding of genetic disease,” said Johnson. “And
while I think our staff sometimes feels that they could do
things faster if they didn’t have to keep track of data,
doing things manually simply isn’t as accurate,
particularly under CLIA. A LIMS slows you down in a good
way, by making sure you’re doing things right.”
EdgeBio, one of the first purveyors of nucleic acid
purification services, has used a commercial LIMS since
it began offering sequencing services in 2009. At first,
the company thought the bulk of its business would be
Sanger-based sequencing. However, when the company
decided to make a play to become one of the leading
providers of next-generation sequencing (NGS)
services, it realized it had outgrown its legacy LIMS—
particularly given an expanding lab environment that
included three different sequencing platforms and
associated, highly changeable workflows.
“We needed something to solidify project management
and organize sample data and metadata in a way that
would help us work more efficiently and track what we
were doing,” said Justin Johnson, director of
bioinformatics at EdgeBio.
EdgeBio recently replaced its legacy LIMS with the
GenoLogics LIMS. The GenoLogics LIMS offered several
advantages over EdgeBio’s legacy system, including
LIMS SupportS reSe arcH & cLInIcaL nGS ServIceS L aB
GenoLogics LIMS Helps EdgeBio Build Services Business
Page 1 | © 2012 GenoLogics Life Sciences Software, Inc.
“We knew we’d need a LIMS to be successful with CLIA, because
CLIA is all about... being able to reproducibly prove you are doing
what you say you are doing—, and that’s what a LIMS does best.”
Justin Johnson, Director of Bioinformatics, edgeBio
next-Gen Sequencing equipment requires next-Gen LIMSEdgeBio’s pioneering work in the 1990s led to the
development of several innovative sequencing products,
including dye terminator removal products, high-
throughput PCR purification products, sample
preparation systems, bacterial competent cells; and
an array of accessories. The company prides itself on
being the “sequencing purification provider of choice”
and maintains a solid commitment to providing high-
quality results and maintaining consistent
communications with its customers.
For all of EdgeBio’s experience in sequencing, Johnson
is forthright about his organization’s naiveté when it
implemented its first LIMS in 2008. “The thinking at the
time was that if you wanted to run multiple sequencers,
which we did, you needed to have a LIMS,” said Johnson.
“But this type of thinking is usually a sign that you don’t
really understand your fundamental processes, and not
understanding your fundamental processes, in turn,
makes it hard to implement a LIMS, because a
successful implementation is all about knowing what
processes the LIMS needs to support.”
Even as EdgeBio added more sequencers to its fleet,
throughput was still such that lab scientists remained
more comfortable tracking files using file folders or
spreadsheets. “When one run takes two weeks, and six
months of data takes up about 10 rows in a spreadsheet,
a LIMS feels like overkill—our scientists ultimately felt it
was more work to use the LIMS,” Johnson explained.
“The legacy LIMS withered on the vine.”
Sequencing at EdgeBio, however, continued to thrive.
The lab began to scale up its NGS fleet and was up to
seven SOLiDs and two Ion PGM™ Sequencers when it
implemented the GenoLogics LIMS in 2011. “We realized
it was time to get organized,” Johnson explained. “We
could finish a run in a matter of hours with the Ion PGM™,
and when you’re doing 3, 4, 5, or 6 runs a day, it’s a much
bigger burden to keep up with all the data.”
Additionally, EdgeBio was interested in pursuing CLIA
certification. “Having demonstrated our ability to offer
research sequencing services that people would use
and refer others to, the natural progression for our
business was to bring NGS services to the clinic,” said
Johnson. Gearing up for its application required EdgeBio
to take stock of its research processes and workflows.
“We wanted to start acting CLIA before we were CLIA so that
we could adjust processes and understand what we were
doing: What processes are fast, which are slow, how much
slower they are, how many more can we do in a week,” said
Johnson. EdgeBio knew that some organizations
successfully achieve CLIA compliance tracking samples
and processes using spreadsheets or documents. But
its experience with its legacy LIMS demonstrated the
need for something more robust.
Page 2 | © 2011 GenoLogics Life Sciences Software, Inc.
Page 3 | © 2012 GenoLogics Life Sciences Software, Inc.
“We knew we’d need a LIMS to be successful with CLIA,
because CLIA is all about tracking and process
management—being able to reproducibly prove you are
doing what you say you are doing—, and that’s what a
LIMS does best,” said Johnson.
Supporting next-Gen Sequencing WorkflowsEdgeBio opted to replace its legacy LIMS with the
GenoLogics LIMS in order to accommodate a modern
sequencing workflow. EdgeBio now runs a mixed fleet of
nine machines comprising five SOLiD 4s and one SOLiD
5500 from Life Technologies, one Illumina HiSeq 2000,
and two Ion PGM™ Sequencers. Out-of-the-box support
for Illumina workflows and kits enabled EdgeBio to rapidly
get the Illumina instrument up and running. However,
EdgeBio was an early adopter of the Ion PGM™, an
instrument so new that workflows had not yet been
created in the GenoLogics LIMS. The EdgeBio team was
able to build out these workflows by adapting existing
scripts using the GenoLogics LIMS API.
“Interestingly, Ion Torrent Systems has put a lot of thought
into its on-board software and includes a lot of hooks for
LIMS and other third-party systems, which made
integration quite easy,” noted Johnson. “SOLiD had little
or none of that initially, so it’s clearly something machine
vendors are starting to think about.”
The SOLiD 4 workflow was built from the ground up. “We run
more SOLiD sequencers than almost anyone in the country,
so we offer a unique perspective that has helped GenoLogics
evolve the workflow pipeline for these instruments,” said
Johnson. “It was a really collaborative project.”
GenoLogics followed an iterative process that started
with an initial look at EdgeBio’s protocols and cycled
through modifications and consultation before running
configurations in a test environment.
“We used scripts to ensure that the LIMS implementation
mapped to some of their internal processes associated
with labeling samples and also assisted with ensuring the
LIMS interfaced correctly to driver files for the
instrument,” said Paul Jenkins, field implementation
specialist at GenoLogics. “Meanwhile EdgeBio leveraged
EdgeBio now runs a mixed fleet of nine machines comprising five SOLiD 4s and one SOLiD 5500 from Life Technologies, one Illumina HiSeq 2000, and two Ion PGM Sequencers.
Figure 1
“When you’re buying a system like a LIMS, you aren’t just buying software, you’re buying extensibility and the support of a technology partner. We definitely traded a product for a company.”
Justin Johnson, Director of Bioinformatics, edgeBio
their relationship with Life Technologies and used our API
to build out a backend integration to collect information
directly off the instrument into the LIMS. So we each
handled different aspects, but provided mutual support
to ensure a smooth and painless implementation.”
“When you’re buying a system like a LIMS, you aren’t just
buying software, you’re buying extensibility and the
support of a technology partner,” said Johnson. “There
aren’t a lot of technical differences in most LIMS systems
today. But from the sales and technical staff all the way
up in the organization, GenoLogics proved that even
when the product isn’t quite there yet, as was the case
with the Ion PGM integration, the support is in place to
get it where it needs to be. We definitely traded a product
for a company.”
automating to eliminate errorsMotivated by CLIA’s insistence on tracking processes,
EdgeBio was extremely interested in using the LIMS to
automate data entry and streamline key workflow steps.
The LIMS helps by providing three things: A single point
of data entry and results return, reduced data entry by
scientists, and standardized workflows.
Every EdgeBio customer must enter its data through
LabLink, a web portal that connects directly into the
GenoLogics LIMS. The portal ensures that critical
metadata is collected before sequencing even
begins, including data necessary for downstream
Process wizard for the barcode printing process
Figure 2
Page 4 | © 2011 GenoLogics Life Sciences Software, Inc.
analyses. “In the past, we often had to go back to clients
and request certain material for an analysis,” Johnson
explained. “Now, we can to some extent blame the LIMS to
be sure we get everything we need upfront—‘Sorry, but it’s
the LIMS… it won’t let us get started on your samples until
you get us that information.’”
reduced Data entry by Scientists
The GenoLogics LIMS interfaces with EdgeBio’s barcode
system, a capability that has significantly reduced the
need for scientists to key in data manually (see figure 2,
pg 4). “We now have just one point where scientists have
to manually enter sample data—when they get the
physical vials in and load them into the 96-well plates,”
said Johnson. Once samples are labeled, scientists
proceed with follow-on steps by scanning barcoded
plates and following standardized drop-down workflow
options presented by the LIMS. “The integration between
the barcoding system and the LIMS has not only reduced
error, but streamlined downstream procedures.
Standardized naming schemes and other factors
associated with barcoding means we can automate things
that happen to samples post-LIMS.”
Standardized Workflows
The GenoLogics Rapid Scripting™ API has enabled EdgeBio
to develop several key integrations tailored to its specific,
unique workflows. For instance, EdgeBio has a standard set
of genomes to which they align data when runs are complete.
Prior to implementing the GenoLogics LIMS, EdgeBio
scientists would use free text on the Ion PGM to enter
information on the reference genomes and then upload the
FASTA for alignment. Now, information on the reference
genomes is stored in the LIMS, which populates the Ion PGM
Sequencer directly when sequences are ready for alignment
(see figure 3, pg 6). “There’s a drop-down menu of possible
choices that scientists can select before sequencing begins,
which keeps people from getting creative about how they
perform alignment, ” explained Johnson.
Another integration primarily benefits EdgeBio
bioinformaticians. EdgeBio uses a specific cloud
computing platform for some of its post-sequencing
analysis. For analysis to proceed, bioinformaticians
previously had to wait until sequencing was complete,
then copy the data over and upload it to the cloud
computing platform. “The process could take 15 minutes
or more because bioinformaticians often had to dig into
the project management software to get key background
on the project, such as submission details and the name
of the researcher,” said Johnson. The LIMS integration
reduces all of this effort to a single button checked at the
beginning of the project to indicate if the data should be
analyzed on the cloud computing platform. When the box
is checked, the LIMS automatically copies the data and
uploads it to the cloud. Bioinformaticians receive an email
when the cloud platform has performed the analysis.
“We save at least 15 minutes per sample, which doesn’t
sound like a lot until you factor in that there’s probably 200
samples per analysis run,” said Johnson. “That’s quite a bit
of time saved on the backend. Plus, even a manual
procedure that takes 15 minutes ultimately takes more than
Page 5 | © 2012 GenoLogics Life Sciences Software, Inc.
that. There’s the 5-10 minutes someone will need to get
their head out of what they were doing and into the manual
activity, and then another 5-10 minutes to start something
else. That’s measurable time that adds up quickly when it’s
something my scientists are doing over and over again.”
enabling efficiencies and Improving accuracyUltimately, Johnson noted that the benefits of the LIMS
aren’t so much about speed as efficiency and accuracy.
“Our business model requires high-throughput, yes,
because when someone comes to us with work, we need
to be able to do it and do it well,” he said. “The LIMS hasn’t
made much of an impact on the number of samples we
can process. But it has helped ensure that we can process
those samples more efficiently with less labor and time.”
“Prior to implementing the LIMS, we were probably
making 2-3 data entry mistakes a week,” Johnson
continued. These errors did not prevent EdgeBio from
working with the data or delivering quality results to
customers, but they did require time to investigate and
fix. “Now, mistakes are rare. That’s where we’ve seen the
value of the LIMS—it keeps us more accurate.”
Process wizard for creating an Ion PGM run definition
Figure 3
“The LIMS has helped ensure that we can process samples more efficiently with less labor and time.”
Justin Johnson, Director of Bioinformatics, edgeBio
Page 6 | © 2011 GenoLogics Life Sciences Software, Inc.
Implementing a LIMS has also supported EdgeBio’s
efforts to become CLIA certified. While being a CLIA lab
doesn’t require a LIMS, a LIMS makes it easier to
demonstrate CLIA’s documentation and consistency
mandates than documents or spreadsheets. Additionally,
EdgeBio also aspires to be CAP/CLIA accredited, which
requires deeper and more rigorous certification and
digital signatures not just from labs, but from their
supporting instrumentation and software vendors.
“Given the level at which we want to be working, the LIMS
not only lends credibility to our initiative as it’s reviewed
by governing bodies, but also helps in preventing sample
issues and ensuring we are doing what we say we are,”
said Johnson.
For lean organizations like EdgeBio, investing in a LIMS
enables the organization to change workflows and,
inevitably, mindsets. “We have five people feeding our nine
sequencers, and another five bioinformaticians to work
with the data,” said Johnson. “So we wanted a system that
offers balanced value: key functionality out of the box, the
ability to adapt and extend the system over time, and
professional help and support for the long haul.”
“Prior to the LIMS, sample tracking and management was
something our staff would get around to when they had
time,” Johnson concluded. “We’ve definitely changed the
paradigm so that now sample tracking is something that
our scientists and bioinformaticians do as a matter of
course, and when they have time, they do something else.”
“Now, mistakes are rare. That’s where we’ve seen the value of the LIMS—it keeps us more accurate.”
Justin Johnson, Director of Bioinformatics, edgeBio
Page 7 | © 2011 GenoLogics Life Sciences Software, Inc.
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