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

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


“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.



“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.”


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


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


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.”



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.”



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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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