Illumina Opens BaseSpace Suite as End-to-End Solution for Genetic Testing Labs

By Bio-IT World Staff

April 21, 2016 | Illumina, the world’s leading provider of DNA sequencing instruments, has released a new service that includes a complete collection of cloud-based software tools for interpreting DNA data from its machines. The service, called the BaseSpace Informatics Suite, allows a lab with no genomic computing infrastructure of its own to track genetic tests through the laboratory, find genetic variants in human DNA, interpret the clinical importance of DNA test results, and create reports for physicians to consult when making treatment decisions. Expanded versions of the offering also allow for population-based genomic analyses in a hospital system or clinical trial.

The suite is a new formulation of the BaseSpace environment Illumina launched in 2012, which the company marketed as an “app store” for genomics. This environment, where both Illumina and third-party developers offer tools that can be mixed and matched in data-processing pipelines, will remain intact as the BaseSpace Sequence Hub. After three years providing storage and analysis in BaseSpace as a courtesy to its customers, Illumina settled on a commercial model for the app environment in October, charging users for data storage over one terabyte.

The new Informatics Suite is fully integrated with the Sequence Hub, letting customers pull any BaseSpace app into the basic set of Illumina-developed tools that make up the suite.

“The value proposition of the BaseSpace Suite is that it’s an integrated, end-to-end solution already, so the customer doesn’t have to integrate the analysis part with the interpretation part with the reporting part,” Sanjay Chikarmane, Illumina’s Senior Vice President for Enterprise Informatics, told Bio-IT World earlier this month at the Bio-IT World Conference & Expo in Boston, where his team was exhibiting the new service. The BaseSpace Suite received the People’s Choice Award in the Best of Show competition for new products at the conference.

Most of the individual tools in the BaseSpace Suite, including the read mapping and variant calling algorithms needed to process raw sequencing data, were already available as apps in BaseSpace. However, a major new addition is the BaseSpace Variant Interpreter, which flags genetic variants that have been linked to important medical outcomes—like rare genetic disorders, heightened risk of cancer or other chronic diseases, or atypical drug responses. While the Variant Interpreter cannot provide firm diagnoses or medical advice, it can point physicians to potentially actionable genetic information. The tool also produces reports that can be exported directly to a patient’s electronic medical record (EMR).

“When you get into whole exome or whole genome, you’re literally looking at millions of variants,” says Chikarmane. “So we’re providing the tools to filter these things down to a small number of potentially relevant variants.”

Like many interpretation tools, Variant Interpreter searches for mutations that have been documented in public databases like ClinVar, where diagnostic labs can share their data on variants they believe to be disease-causing. Illumina’s tool, however, also consults two proprietary sources of information. The first is a database that the company acquired in 2013 with NextBio, a software provider whose analysis platforms have formed the basis for many tools in BaseSpace.

The other is Illumina’s own genomic testing lab, Illumina Core Services, which provides sequencing tests in cases including undiagnosed rare disease. “This is in beta right now,” says Chikarmane. “We’re working with about 16 hospitals, including here in the U.S. and in Europe.” But already, he says, Illumina Core Services has provided clinical interpretations of more variants than have been posted to ClinVar. All of these are available to help guide analyses in the BaseSpace Suite.

Consulting the Core Services database does somewhat limit the information Variant Interpreter can offer physicians. Typically, programs like this will provide transparency into how an interpretation was reached, for instance with a link to ClinVar where the evidence linking a variant to a disease may be documented. However, for now Illumina will only provide broad statistical information on variants that were found and analyzed in its Core Services lab.

Clinical Integration

Variant Interpreter also stands out for using phenotypic data on patients—clinical traits like their symptoms and treatment histories—to filter variants of interest. For labs embedded in hospitals, this information can be funneled straight from the EMR to the laboratory information management system, Clarity LIMS, that comes with the BaseSpace Suite. This feature can save physicians from a deluge of genomic data that may be irrelevant to the case in front of them.

The biggest market for the suite is likely to be smaller labs just beginning to use genetic testing. A lab buying its first Illumina sequencer is likely to need a great deal of new compute infrastructure to make use of it; BaseSpace provides that as a unified service. “Our mission is basically to lower the barrier to genomics,” says Chikarmane. “One of the things we’re finding more and more is that, while the cost of sequencing is going down, the cost of processing all the data that comes off the sequencer and doing the interpretation has been stuck in the same place it has been for years.”

However, Illumina is also pitching its unified analysis product to established labs doing genomics on a larger scale. These labs already have their own systems in place to handle their analysis and interpretation, often through a combination of vendor-provided, open source, and custom-built software. But Chikarmane says that the volume of DNA sequencing is starting to outpace many of these legacy systems, and a comprehensive service offering may be attractive even to labs that have traditionally dealt with their bioinformatics in-house. It helps that the pieces in the BaseSpace Suite are exchangeable, just like in the BaseSpace Sequence Hub, so users are not bound to exclusively using Illumina-designed tools. Many of the most popular software kits, like GATK and the Tuxedo Suite, are already present in Illumina’s “app store.”

The BaseSpace Suite also includes two programs geared to the interests of larger labs connected to hospital networks or pharma companies. Cohort Analyzer, previously called NextBio Clinical, connects genomic data with individual patient IDs, to track traits and outcomes across groups of individuals and over time. Correlation Engine, previously NextBio Research, is aimed more at basic research, tapping into the NextBio and Illumina knowledge base for gene pathway analyses and preclinical studies on disease models.

Illumina is not the only sequencing company to move heavily into software in recent years. Thermo Fisher has a similar unified solution in its Torrent Suite and Ion Reporter software, and QIAGEN, which recently released its first sequencer, embedded analysis and interpretation software as a package with the machine.

The BaseSpace model, however, is slightly less of a walled garden, letting users add or swap in third-party tools from the Sequence Hub while keeping their data inside the Illumina cloud. There are currently around 80 apps in BaseSpace, almost half from outside developers, who may make their tools free or charge on a subscription or pay-as-you-go basis. Because Illumina charges for storage and for the BaseSpace Suite as a service, not for the use of its tools, the company’s incentive is to invite as many new programs into the Sequence Hub as possible, even where they overlap with its own products.

“If I look at the whole industry, there’s a lot of do-it-yourself out there, but especially the [customers] that are commercially focused are looking for package solutions,” says Chikarmane. “We want to make sure that between our own applications we are as seamlessly integrated as possible, so they have a certain advantage. But we don’t do anything to prevent them from adopting third party applications.”