This week, GenoLogics launched Clarity LIMS, a laboratory information management system designed to manage sequencing data in CLIA-regulated environments and research settings.
In addition to providing some of the same functionalities that are available in GenoLogics’ existing LIMS software, such as its backend application programming interfaces and reporting tools, Clarity also includes a newly designed interface and a set of capabilities that enable clinical laboratories to adhere to current regulatory requirements, CEO Michael Ball told BioInform.
Specifically, users can plan experiments as well as track and manage samples as they travel through relevant workflows in the lab, adhere to standard operating procedures, and handle the complexities of next-generation sequencing, GenoLogics said. Users can also gather metrics from lab instruments as well as create and enforce experimental procedures to minimize errors, Ball said.
The launch of Clarity signals a shift in GenoLogics’ business focus, one which the company has hinted at for more than a year.
Historically, the company has peddled its products in research markets only but decided to move into the clinical setting so that it could tap into the nascent market for next generation sequence-based clinical applications and diagnostic tests, Ball told BioInform.
That particular move was precipitated by requests from current research customers who are starting to switch over to clinical applications and need LIMS systems that are not only tailored to the space but are also easy to install, use, and modify as necessary, he said.
“We attacked [those requirements by] simplifying the way that people interact with our software and making the user interface very simple to use and straightforward,” Ball explained. “[We also changed] the paradigms so that … the person in the lab can really understand how to plan out their day, how to make themselves more efficient, [and] get rid of tedious tasks that they might be doing on a regular basis.”
A Friendlier Interface
GenoLogics customers who tested the beta version of Clarity praised the product’s user-friendly interface, which they said improves on the company’s previous LIMS product.
Marc Sultan, head of the NGS unit in the vertebrate genomics arm of the Max Planck Institute for Molecular Genetics, told BioInform that Clarity’s interface is “a big improvement [on] the prior user interface of [the GenoLogics] system,” which his team has used for a year and a half.
“The Clarity LIMS appears intuitive, and will very probably be much easier to be used by our lab technicians,” he said.
“Clearly a lot of thought has been put into making the interface as intuitive and friendly as possible, even for complex processing steps,” Conrad Leonard, bioinformatics engineer at Queensland Center for Medical Genomics, said in a statement.
“It is a real step forward in LIMS experience for the lab user,” he told BioInform this week. “First up, it's a web application and needs nothing more than a browser installed on the user's machine.”
Furthermore, “the interface itself is very attractive and uncluttered by options not required by the typical lab user. Actions are accomplished using intuitive everyday semantics — drag and drop, shift- and control- for multiple select, [and so on.”
Both Max Planck’s Sultan and QCMC’s Leonard noted that they have only tested a limited version of Clarity and as such could not provide in-depth reviews of its functionalities. However, both are optimistic about its usefulness in their labs based on past experiences with GenoLogics' software and plan to upgrade to the new interface.
At Max Planck, Sultan is in charge of a next-generation sequencing pipeline, “where we process tissue, blood and cell samples for RNA-sequencing, whole genome sequencing, exome sequencing, and so on.”
His lab uses GenoLogics for sample and library management and to track all the processes that samples undergo in the lab.
“We have currently 13 funded projects for which samples are being processed here and for various sequencing applications [with] the majority of projects … related to cancer genomics and gene regulation studies,” he explained. “[We needed] a very flexible system [that would] enhance the traceability of each sample tube that is being generated throughout the different processes and to minimize human errors that occur when using spreadsheet-based methods.”
“We didn't have a LIMS for sample management prior to [GenoLogics],” he said. “We [had] an SQL-based database for all the post-sequencing part.”
For his part, QCMC’s Leonard told BioInform that GenoLogics' software replaced “a combination of Google Docs spreadsheets” — which couldn’t handle complex data models and were difficult to access programmatically — and “an in-house application to record lab workflow,” which was challenging to maintain and support long term.
His lab uses it to record workflows in the wet lab including sample reception, quality control processes, library preparation, arrays, and sequencing. The LIMS also automates the transfer of data from instruments to analysis pipelines and records metadata from those pipelines.
QCMC’s Leonard said his team has in place tentative plans to migrate to Clarity as early as the first quarter of 2013.
All Eyes on the Clinic
In a statement, Tristan Orpin, Illumina’s senior vice president and chief commercial officer, described Clarity’s launch as “timely, given the speed at which the sequencing market is moving into the clinical space.”
Orpin is also a member of GenoLogics’ board of directors. He took on that role following an Illumina-led investment round last October, during which GenoLogics raised $8 million (BI 10/21/2011).
“The new GenoLogics software tightly integrates to our sequencing instruments and includes support for all of our standard workflows and kits,” Orpin said in a statement. “We see great growth potential in the clinical market for products like this that ease the transition of NGS into the clinic.”
Clarity supports Illumina’s HiSeq, MiSeq, and Genome Analyzer sequencers; Life Technologies’ Ion Torrent system; Roche’s 454 sequencers; as well as arrays provided by these vendors.
In an email, Marc Laurent, Illumina’s director of genomic services, told BioInform that his firm “values the unique data management capabilities GenoLogics brings to the industry,” especially because its LIMS software “allows labs to move into production more quickly by incorporating de facto standards and best practices for NGS implementations.”
In addition to its financial investment, Illumina also inked a co-selling agreement with the LIMS vendor last year that allowed the sequencing firm to market a version of GenoLogis LIMS that was preconfigured to handle Illumina’s sequence data (BI 2/4/2011).
That version of the software is now part of Clarity’s infrastructure and will be made available to customers directly from GenoLogics and through the existing co-seller agreement with Illumina, GenoLogics said.
One Product; Two Markets
GenoLogics first signaled its intent to move develop software for the clinical space in May 2011 when it released a development roadmap that outlined proposed enhancements to its software — which used to be called Geneus LIMS.
At the time, CEO Ball said that the firm planned to make changes to the newly renamed GenoLogics LIMS — including the addition of CLIA and CAP/ISO capabilities for clinical genomic lab applications — that would make it a "comprehensive information management system for next-generation genomics labs (BI 5/13/2011).”
He reiterated those comments in a conversation with BioInform last October, and noted at the time that the company didn’t plan on launching a separate clinical product. Rather, "we want to provide people the ability to work in a research environment but then allow that product to take them to the clinic without having to make a complete change of software."
GenoLogics believes it has fulfilled that obligation with Clarity because the software can “address both markets equally well,” Ball told BioInform this week.
Furthermore, it “works on the same foundation" and has many of the components of GenoLogics LIMS, he said. That means that “for our current customers there is a path forward [so] it’s not a completely separate product.”
It’s also a notch above “generic” offerings from enterprise LIMS vendors like StarLIMS, Labvantage, and LabWare, which can be used in clinical settings but lack NGS-specific workflows and protocols that are included in the Clarity package, Ball said.
Another advantage is that NGS-associated protocols in Clarity can be changed quickly — in minutes — whereas most enterprise LIMS require months of software reprogramming to update pre-set protocols, he said.
Although GenoLogics will continue to sell GenoLogics LIMS for the “foreseeable future,” its marketing efforts moving forward will center on Clarity, Ball said, adding that the company will work with current customers to determine which of its two products best suit their needs.
“Many organizations have both research and clinical labs, and see great value in having the same LIMS system work across both,” he said. “We will be working with current customers to determine if and when they want to move to Clarity LIMS, as there are some inherent benefits to this solution as we discussed.”
GenoLogics isn’t disclosing Clarity’s pricing details. Ball said that the cost varies based on several factors including the number of people using the system and the sorts of lab instruments that the software will be integrated with.