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Competition Heats up for Next-Gen Sequencing, Clinical Data Analysis Software in 2011


By Uduak Grace Thomas

As the world bids farewell to another year, observers of the life science informatics sector will remember 2011 for some surprise acquisitions, an influx of newcomers to the next-generation sequence analysis space, and continued efforts to develop new software tools for clinical data analysis and personalized medicine.

In addition, the ongoing economic slump forced some bioinformatics providers to pinch pennies and pare down their activities while others closed up shop permanently.

This year brought increased pressure on pure-play bioinformatics firms from major sequencing instrument manufacturers as well as non-life science companies looking for a slice of the next-gen sequencing analysis market.

For example, Illumina in October launched a free cloud-based analysis environment for its MiSeq personal sequencer system. It said it plans to eventually extend the environment to its high-throughput HiSeq sequencer and other genomic analysis platforms (BI 10/14/2011).

In addition to its own analysis tools, Illumina now also markets a version of GenoLogics' Geneus Laboratory Information Management System (BI 2/4/2011).

In April, Pacific Biosciences launched an open source secondary-analysis suite, dubbed SMRT Analysis, to handle its RS single-molecule real-time sequencing system's long read datasets (BI 4/8/2011). The sequencing instrument vendor later tapped Cycle Computing to provide a cloud-enabled version of the software (BI 9/23/2011).

Pac Bio also distributes software from DNAStar for sequence assembly and analysis (BI 2/4/2011).

Life Technologies this year launched its own sequence-analysis software, named LifeScope Genomic Analysis, for analyzing and managing data from its 5500 Series SOLiD systems, including an online portal that allows researchers to analyze their data in a cloud computing environment (BI 5/27/2011).

Representatives from several bioinformatics software companies who spoke to BioInform said they weren't rattled by these competing offerings, however. They said that while these tools could seduce a fraction of their customers, none constituted a broad threat to their businesses (BI 10/2/2011).

Newcomers to the life science informatics market in 2011 include Samsung SDS, a subsidiary of the Samsung group, which began beta testing its new next-generation sequencing cloud-based data analysis service in September (BI 8/26/2011); and cloud computing firm Appistry, which released a version of its CloudIQ platform that provides a complete data-analysis pipeline for next-generation sequencing data (BI 9/9/2011).

A Tough Economy

The year was not yet two months old when the National Center for Biotechnology Information said it was going to phase out the Sequence Read Archive and other database resources over the next year as a result of reduced federal research dollars (BI 2/18/2011). The institute later reversed the decision somewhat, stating that it had enough funds to maintain the resource in its current form until October this year (BI 6/17/2011). NCBI has not disclosed its plans for the resource beyond this date.

Another resource to fall victim to funding problems this year was the Kyoto Encyclopedia of Genes and Genomics, which switched to a paid subscription model for its FTP site when the Institute for Bioinformatics Research and Development arm of the Japan Science and Technology Agency refused to continue supporting the database (BI 5/27/2011).

Given the current economic climate, evolving markets, and the influx of new players with competing offerings, bioinformatics vendors have had to adapt to stay competitive. Several made significant updates to their existing portfolios while others revised business models to keep current customers loyal and woo new ones.

DNAnexus, for example, extended its NGS analysis platform to include a cloud-based variant analysis workflow to help researchers analyze and manage genomic variation data (BI 2/4/2011). CLC Bio, meantime, opened up its informatics platform to third-party developers to create applications that target more specialized markets (BI 2/11/2011).

Similarly, GenoLogics revealed a series of planned upgrades for its LIMS software in order to increase its adoption in the sequencing market (BI 5/13/2011), while Bangalore, India-based bioinformatics firm Geschickten revised its business model and released several new product lines to increase its customer base and expand its footprint (BI 6/3/2011).

Meanwhile, Accelrys launched the NGS Collection for its Pipeline Pilot platform (BI 2/25/2011), which it is tailoring to work with Oxford Nanopore's upcoming sequencer (BI 3/18/2011 and 5/20/2011); while Golden Helix, which has traditionally focused on software for analyzing genome-wide association studies and copy number variation data, threw its hat into the NGS ring with the launch of a variant analysis tool for its SNP and Variation Suite software (BI 1/28/2011) and (BI 5/20/2011).

Finally, Simulations Plus sold its computer-based communications systems subsidiary so that it could focus on expanding its footprint in pharmaceutical markets (BI 11/18/2011).

On the downside, some vendors lost their fight to keep their heads above water in 2011.

Commercial casualties of the economic downturn include Integrated Genomics, which early in the year sold its intellectual property to IG Assets in an attempt to do away with its debts and pursue new research directions (BI 1/14/2011). Also, bankrupt biosimulations firm Entelos in September sold its assets to secured lender Imperium Master Fund, which placed a credit bid of $1.95 million (BI 9/30/2011).

Cloud Computing

Cloud computing remained a watchword in 2011 with groups in the commercial and open source communities embracing the approach to manage computation needs.

Amazon still holds sway over much of the life science market that adopts cloud technology, although Google, perhaps not so surprisingly, appears to be attempting to tap into the space. In September, DNAnexus announced that Google was one of several investors in a $15 million funding round and that it was working with the company to provide a cloud-based version of NCBI's SRA (BI 10/14/2011).

In addition to cloud offerings from Illumina, Pac Bio, and Life Tech, Complete Genomics also inked a deal with DNAnexus to provide its sequencing services customers with a place to store and visualize their data (BI 3/18/2011).

On the open source front, the Galaxy development team at Pennsylvania State University and Emory University launched a version of the web-based open-source sequence analysis platform that runs on Amazon Web Services and other cloud platforms (BI 11/11/2011).

However, while cloud proponents gained some traction in 2011, activity in the space didn't increase significantly during the year. Widespread adoption still appears to be hung up by concerns about data security and the difficulties associated with moving large quantities of data over current Internet connections.

While the cloud may be the future of bioinformatics, purveyors of earth-bound compute power and storage can still make a living in the life science market place, at least for now.

DataDirect Networks, for instance, netted several customers, including the Wellcome Trust Sanger Institute, which tapped the company's offering for its NGS data storage needs (BI 3/18/2011); and Virginia Tech, which selected the platform to support research efforts at the Virginia Bioinformatics Institute (BI 6/17/2011). Bielefeld University, meantime, bought one of TimeLogic's DeCypher systems to support research aimed at discovering new functions of genes and proteins (BI 9/16/2011).

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SGI also added to its life science customer roster. The University of Minnesota purchased an SGI system for multi-scale modeling, chemical dynamics, bioinformatics, computational biology, and biomedical imaging (BI 4/22/2011); the Technical University of Denmark purchased an SGI Altix supercomputer to support research efforts aimed at producing chemicals in living cells from inexpensive and sustainable raw materials (BI 6/17/2011); and Kyoto University bought a new SGI machine that will support a network of databases and computational services for genomics and related biomedical research as well as computational chemistry research projects (BI 11/4/2011) .

Several hardware vendors also optimized well-known bioinformatics algorithms for their platforms in an attempt to pull new customers in.

In February, DRC Computer announced that its implementation of Smith-Waterman on its massively parallel processor achieved 9.4 trillion cell updates per second and claimed that this was the first implementation of the sequence-alignment algorithm to achieve the mark of several trillion cell updates per second (BI 2/4/2011).

Not to be outdone, Convey Computer claimed its latest software release, GraphConstructor, accelerates de novo genome assembly algorithms up to 8.4-fold on the company's hybrid-core architecture (BI 5/20/2011), and later said that its implementation of the Burrows-Wheeler aligner algorithm increases genome reference mapping rates by a factor of 15 compared to commodity servers (BI 10/14/2011).

Personalized Medicine

In line with efforts to move genomic sequence data into clinical practice, several companies are developing software tools to identify clinically relevant variants in whole-genome sequence data (see related story this issue).

Also on the personalized medicine front, several groups are building infrastructure to extract information from patients' electronic medical records that could be used for select treatments and to stratify patients for clinical trials and other research studies.

In February, Aurora Health Care announced that it was collaborating with Oracle to develop software to select patient samples from its biorepository, which holds patient DNA and is linked to de-identified electronic medical records, for use in clinical trials and biomarker discovery (BI 2/4/2011). That same month, the Coriell Institute for Medical Research and Ohio State University Medical Center embarked on a project aimed at understanding how physicians can use genomic information in EMRs to personalize health care (BI 2/11/2011).

Meanwhile, the Electronic Medical Records and Genomics Network, or eMERGE, project published a study on the feasibility of using EMRs to identify disease phenotypes for use in genome-wide association studies (BI 4/22/2011) as well as the challenges of sharing data culled from multiple systems, among other informatics lessons (BI 2/18/2011).

In September, the Lucille Packard Children's Hospital at Stanford University received a $25 million investment, to be spread over 10 years, from Hewlett-Packard to support the development of bioinformatics tools to analyze clinical data in EMRs (BI 5/13/2011).

Acquisition Activity

Two trends emerged on the merger and acquisition front in 2011: a series of informatics purchases by instrument manufacturer PerkinElmer; and increased acquisition activity among science publishing firms.

Early in the year, PerkinElmer began beefing up its lab informatics portfolio, beginning with its acquisition of Artus Labs and CambridgeSoft in March for a combined purchase price of $220 million (BI 3/25/2011). Then in May, PerkinElmer picked up both NGS software developer Geospiza (BI 5/6/2011) and Ontario-based Labtronics (BI 5/20/2011) for undisclosed sums.

Shortly afterwards, Accelrys, whose software tools compete with some of PerkinElmer's offerings, purchased Contur software for $13.1 million, claiming that the purchase complemented its ELN offering, Symyx Notebook by Accelrys (BI 5/27/2011).

On the publishing side, Elsevier continued a trend begun by Nature's parent company Macmillan publishers and Thomson Reuters in late 2010.

In 2011, Elsevier bought the business assets of Ariadne Genomics (BI 12/9/2011) for an undisclosed amount. That deal followed Elsevier's launch of Genome Viewer, a browser that displays information from GenBank within journal articles (BI 8/5/2011).

Late last year, Thomson Reuters purchased the assets of privately held pathway informatics firm GeneGo (BI 12/3/2010) and began integrating the company's software with its biomarker database this year (BI 5/6/2011). Hot on Thomson Reuters' heels, Macmillan launched Digital Science in late 2010 to provide software tools and services (BI 12/10/2010).

It isn't clear how these offerings will compete with existing software tools in the market as these firms are keeping the details of their plans for the new purchases under wraps.

Other acquisitions for the year include Instem's purchase of Cambridge, UK-based life science data-mining firm BioWisdom in a cash and stock transaction valued up to £1.5 million ($2.4 million) (BI 3/11/2011); Persistent's purchase of Agilent Technologies' software marketing and development business, which provides data acquisition and control software for scientific instruments (BI 6/3/2011); Premier Biosoft's acquisition of privately-held Redasoft, which markets sequence analysis software dubbed Visual Cloning (BI 8/5/2011); and BioData's purchase of competing firm LabLife Software (BI 9/18/2011).

Software's Bright Future

In spite of a tough economy in 2011, it isn't all doom and gloom for software markets, according to analysts at Leerink Swann.

In a recent research note, analysts from the investment bank forecast that the demand for scientific software will rise in 2012, particularly as a result of increased research development spending that has created a "scientific data landscape that is extremely complicated and fragmented" and will require software to "simplify this legacy data infrastructure and integrate dissimilar silos of data."

The report also indicates increased demand from pharma for "new backbone platform technologies" that integrate disparate laboratory information management systems as well as for enterprise electronic laboratory notebooks.

Other areas of growth, according to Leerink Swann, include software for use in academia and tools to address next-generation sequence data bottlenecks.

Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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