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Smith T.M.,Geospiza, Inc.
Advances in Experimental Medicine and Biology | Year: 2010

Next Generation Sequencing technologies are limited by the lack of standard bioinformatics infrastructures that can reduce data storage, increase data processing performance, and integrate diverse information. HDF technologies address these requirements and have a long history of use in data-intensive science communities. They include general data file formats, libraries, and tools for working with the data. Compared to emerging standards, such as the SAM/BAM formats, HDF5-based systems demonstrate significantly better scalability, can support multiple indexes, store multiple data types, and are self-describing. For these reasons, HDF5 and its BioHDF extension are well suited for implementing data models to support the next generation of bioinformatics applications. © 2010 Springer Science+Business Media, LLC.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase II | Award Amount: 1.18M | Year: 2011

DESCRIPTION (provided by applicant): Next generation DNA sequencing (NGS) technologies hold great promise as tools for building a new understanding of health and disease. In the case of understanding cancer, deep sequencing provides more sensitive ways todetect the germline and somatic mutations that cause different types of cancer as well as identify new mutations within small subpopulations of tumor cells that can be prognostic indicators of tumor growth or drug resistance. Completing the transition fromproof of principal applications to practical applications, however, requires that many basic and clinical research groups to be able to effectively utilize NGS. Ongoing technical developments and intense vendor competition amongst NGS platform and serviceproviders are commoditizing data collection costs making systems more assessable. However, the single greatest impediment to the adoption of NGS technology is the lack of systems that create easy access to the immense bioinformatics and IT infrastructuresneeded to work with the data. In the case of variant analysis, such systems will need to process very large datasets, and accurately predict common, rare, and de novo levels of variation. Genetic variation must be presented in an annotation-rich, biological context to determine the clinical utility, frequency, and putative biological impact. Software systems used for this work must integrate data from many samples together with resources ranging from core analysis algorithms to application specific datasets to annotations, all woven into computational systems with interactive user interfaces (UIs). Such end-to-end systems currently do not exist. In this project, Geospiza will create integrated methods for robust detection and rich contextualization of genetic variants. Using variation analysis in cancer genomics as a model system, we will conduct research to improve assay sensitivity by deeply characterizing data from existing and emerging NGS platforms, quality value (QV) recalibration tools, and alignmentalgorithms, to understand the systematic artifacts that create errors in the data. To improve how researchers understand a variant's biological context, function and potential clinical utility, we will develop methods to combine assay results from many samples with de novo NGS datasets for assays like RNA-Seq and existing data such as those in GEO and SRA, and information resources from dbSNP, cancer genome databases, and ENCODE. Finally, we will develop the necessary scalable computing infrastructure and novel UI's needed to organize and process the data and explore and annotate the results. Through this work, and follow on product development, we will produce integrated sensitive assay systems that harness NGS for identifying very low (1:1000) levels of changes between DNA sequences to detect cancerous mutations and emerging drug resistance. Our tools and infrastructure can be later applied in assays designed to follow viral epidemics, and understand autoimmune disorders. PUBLIC HEALTH RELEVANCE: TheSBIR project Software Systems for Detecting Rare Mutations will deliver new software technologies to further advance the applications for deep DNA sequencing in personalized medicine by improving methods for detecting rare mutations that define cancer types and determine how a cancer cell may grow and respond to, or resist, treatment. In addition to improving cancer research and diagnostics, the software developed will have general use for any application where DNA sequencing is used to understand the genetic basis of human health, disease, and response to drug therapies.


News Article | January 25, 2011
Site: www.xconomy.com

Geospiza, the Seattle-based maker of software for analyzing genomic data, said today that PerkinElmer (NYSE: PKI), the Waltham, MA-based life sciences toolmaker, has taken a multi-year license to Geospiza’s technology. Financial terms of the license weren’t disclosed.


News Article | February 9, 2011
Site: www.xconomy.com

Seattle-based Geospiza, the maker of software for biologists, said today that it has been awarded a $1.2 million grant from the Small Business Innovation Research program of the National Institutes of Health, along with collaborators at Weill Cornell Medical College and the Mayo Clinic. The grant will support research to help visualize differences in DNA between normal tissue, and samples from tumors, the company said.


News Article | May 5, 2011
Site: www.xconomy.com

Geospiza has been around the block a time or two in the bioinformatics business, and now after 14 years in the game, it has come to the end of the road. The Seattle-based company, which makes software for scientists who analyze data from genetic experiments, said today it has agreed to be acquired by Waltham, MA-based PerkinElmer (NYSE: PKI), the giant maker of tools for life scientists. PerkinElmer, which said it generated $448 million in first-quarter revenue, didn’t disclose to investors how much it paid to obtain Geospiza. PerkinElmer CEO Rob Friel, however, did say in a conference call with analysts that the acquisition will have “minimal impact” on his company’s near-term finances, but that it represents a strong growth opportunity. “Genomic information is becoming increasingly important in understanding and treating disease. Making sense of the unprecedented volumes of data generated by next generation sequencing and other biological measurements is critical to improve the disease diagnosis process and drug discovery,” said Richard Begley, PerkinElmer’s president of emerging technologies, in a statement. Geospiza, which I profiled about a year ago when it turned profitable, has been one of the small and persistent voices in the market that has insisted that biologists need better software to manage genomic information. The company, founded in 1997, struggled to get traction with this argument in the wake of the Human Genome Project, but was able to weather the storm as competitors fell by the wayside, and the market eventually became more attractive. As DNA sequencing instruments from Illumina (NASDAQ: ILMN) and Life Technologies (NASDAQ: LIFE) have made it possible to sequence an entire human genome for as little as $10,000 and in a few weeks, it has created a tidal wave of DNA data points that more researchers are struggling to visualize and analyze. Geospiza has long been forced to compete with old-school Excel spreadsheets in some cases, and custom-made “home-brew” software programs that individual biology labs make for their own projects. But Geospiza has gradually been chipping away at the market, winning over a series of big-name customers at places like the Institute for Systems Biology and University of Washington, Harvard Medical School, Yale University, Children’s Hospital Boston, and the University of Florida. Geospiza, as of a year ago, had about 20 employees. It certainly looks like this deal has been brewing for a while. PerkinElmer took a multi-year license to Geospiza’s technology back in January.


News Article | May 16, 2011
Site: www.xconomy.com

Waltham, MA-based PerkinElmer (NYSE: PKI), a maker of tools for the life sciences field, announced today that it has bought Ontario, Canada-based Labtronics for an undisclosed sum. Labtronics provides electronic laboratory notebook products enabling laboratory routine analysis. Earlier this month PerkinElmer acquired Geospiza, a Seattle-based maker of software for DNA analysis.


News Article | May 6, 2011
Site: www.geekwire.com

Geospiza, a Seattle maker of gene analysis software, has been acquired by PerkinElmer in a deal of undisclosed size. The company was founded in 1997 and led by Rob Arnold, a former executive at Crossport Systems and ST Labs. PerkinElemer, with annual revenue of $1.7 billion and more than 6,200 employees, said that the acquisition will support its growth in the area of DNA sequencing and analysis services. “Genomic information is becoming increasingly important in understanding and treating disease.  Making sense of the unprecedented volumes of data generated by next generation sequencing and other biological measurements is critical to improve the disease diagnosis process and drug discovery,” said Richard Begley, president of emerging technologies at PerkinElmer. The two companies are not strangers. Earlier this year, they entered into a multi-year license agreement for Geospiza’s GeneSifter Lab Edition and GeneSifter Analysis Edition.


News Article | October 19, 2011
Site: www.xconomy.com

Computing in the Age of the $1,000 Genome: Here’s the Program for Monday’s Conference [Updated: 11:18 am PT] One of the most fastest-moving, highest-impact innovation stories in history is happening in genomics. Lucky for those of us who follow the business on the West Coast, this epic story is playing out right where we live, right now. Everyone in the Valley knows about Moore’s Law, and how computing power and speed doubles every 18 to 24 months, but fewer realize that the rate of progress in whole-genome sequencing is outpacing the rate of progress in the semiconductor business. That’s why I’m psyched to have pulled together many of the leaders in this field for a half-day conference, “Computing in the Age of the $1,000 Genome.” The conference is now less than a week away, on Monday October 24. It will be hosted by the folks at QB3, in Genentech Hall at UCSF’s Mission Bay campus. This event will feature a cast of speakers from Complete Genomics, PacBio, 23andMe, Microsoft, EMC/Isilon, PerkinElmer, Stanford University, Mohr Davidow Ventures, and a handful of hot Silicon Valley genomic computing players like DNAnexus, Ingenuity Systems, and NextBio. We’re putting these speakers together with terrific guest moderators from Fortune, Wired, and leading life sciences companies for a series of interactive chats. There will be no PowerPoints, and plenty of time for networking. Promise. So, here’s how the afternoon will flow: 2:05 pm: Opening keynote chat: How new DNA sequencing technologies are creating computing’s next big challenge. 2:40 pm: The challenges big computing companies are wrestling with in genomics. 3:45 pm: Strategies from the new wave of genomics computing startups. 4:15 pm: How will doctors use all these genomes for personalized medicine? 4:45 pm: Closing keynote chat. The big medical and societal implications of the $1000 genome. As with all Xconomy events, we make special discount tickets available for people in startup companies, and for students (which applies to undergrads, graduate students and postdocs at any of the institutions around the Bay Area like UCSF, Stanford, and UC Berkeley). There is still time to get tickets for this opportunity to learn about the state of the art in genomics, and meet the personalities who are driving progress. I’m looking forward to seeing lots of readers there on Monday, and posing a few questions to these folks myself.


News Article | September 14, 2011
Site: www.xconomy.com

Computing in the Age of the $1,000 Genome. Our Next Big Event in SF Oct. 24 The $1,000 genome is coming fast, whether society is ready for it or not. This field has moved so fast, reasonable people have estimated we will have sequenced millions of genomes within a few years. It’s even conceivable that individuals will get sequenced more than once in a lifetime, to track how their health is progressing. As all this DNA data piles up into the stratosphere (or at least somewhere in the cloud for you computing geeks out there), how in the world will scientists be able to zero in on what’s really important to an individual’s health? These are the kind of questions I’m getting ready to ask at Xconomy’s next big event in San Francisco, titled “Computing in the Age of the $1,000 Genome.” This event will be a half-day forum, from 2 pm to 6:30 pm on October 24. It will be graciously hosted by the folks at QB3, who are in the nerve center of SF biotech, at UCSF’s Mission Bay campus. This event will feature an All-star list of speakers from Complete Genomics, PacBio, Mohr Davidow Ventures, Microsoft, EMC/Isilon, Life Technologies, 23andMe, plus a number of hot computational biology startups. But since this is only our second life sciences event in San Francisco, I figure it’s worth letting folks know how the conversation—and I really mean conversation—will unfold at this event. First off, there will be no PowerPoint presentations (speakers, and attendees, you can exhale now). Instead, I’m planning this to be a series of moderated, interactive chats, in which speakers won’t be allowed to drone on to fill up airtime, and attendees will get plenty of time ask questions. So, here’s how the afternoon will flow: 2:05 pm. Opening keynote chat: How new DNA sequencing technologies are creating computing’s next big challenge. 2:40 pm. The challenges big computing companies are wrestling with in genomics 3:45 pm. Strategies from the new wave of bioinformatics startups: 4:15 pm. How will scientists use all these genomes for personalized medicine? 4:45 pm. Closing keynote chat. The big medical and societal implications of the $1000 genome I’ve personally been covering biotech for 10 years now, and the $1,000 genome strikes me as having the greatest potential for the kind of impact that makes the history books. I think people will look back on this time as an inflection point in healthcare and wellness. Come join this fascinating conversation, and maybe have a beer with, the people who are working to make this happen today.

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