Sequencing Platforms / Comparison of Sequencing Technologies
February 13, 2013
Is it time to switch?
With recent advancements and a radical decline in sequencing costs, the popularity of next generation sequencing (NGS) has skyrocketed. As costs become less prohibitive and methods become simpler and more widespread, researchers are choosing NGS over microarrays for more of their genomic applications.
Click on the link below to read the full article.
November 8, 2012
Ten experts discuss innovations needed to analyze the millions of genomes soon to be sequenced.
With over 50,000 human genomes and exomes resequenced and >600 animal or plant genomes sequenced de novo, generating genome sequence data is becoming increasingly commonplace. The question is whether the tools and infrastructure to analyze these data are keeping up. Nature Biotechnology asked experts in academia and industry to share their thoughts on two of the sequencing field's key computational challenges—assembling genomes and developing pipelines to interpret genomes.
Click on the link below to read the full article (free download).
November 6-10, 2012
The ASHG Annual Meeting is the largest human genetics meeting and exposition in the world. ASHG members and leading scientists from around the world are selected to present their research findings at invited, platform, and poster sessions. Abstracts of work submitted for presentation at the Annual Meeting are published online. ASHG's Annual Meeting also features a trade show floor that offers attendees the opportunity to view state-of-the-art medical and laboratory equipment, products, services, and computer software designed to enhance human genetics research, teaching, and consultation.
CEO Michael Heltzen attended ASHG 2012 Meeting. "It was a great success and it was interesting to listen to presentations by some of world's leading genetics. It was amazing interacting together with passionate people talking about how the research is constantly changing the world," Heltzen said.
CHI chose BlueSEQ to represent next-generation sequencing in a moderated panel discussing the pros and cons of both NGS and digital PCR. BlueSEQ was represented by Shawn Baker, CSO. "BlueSEQ was chosen because of our expertise and our neutral stance on the next-gen sequencing market. It represents a validation of our business model."
September 5, 2012
Is NGS in your future? Get it right the first time with these tips.
Things to think about before you start your next-generation sequencing (NGS) project:
1. Biological question trumps all: Don’t get seduced by the marketing hype surrounding next-generation sequencing. It does offer a plethora of advantages over older technologies like microarrays, but if you’re asking a very simple or specific question, cheaper and easier technologies might be an appropriate substitute.
2. Platform choice: Once you’ve decided that your project does require the power of next-generation sequencing, make sure you pick the right platform. There are a wide range of technologies available, each of which is optimized for different attributes. For example, some may generate the largest total output per run while others are optimized for speed, low error rate or read length. Make your choice based on the needs of your research project. Don’t just use what the local core lab has because it’s ‘convenient’. Instead, consider outsourcing your project to a service provider that has the exact technology you need.
3. Technology combinations: Sometimes no single technology can provide everything you need. For example, some researchers are taking advantage of the long, but error-prone, reads of the Pacific Biosciences RS platform by using it in combination with the shorter, low-error-rate output of Illumina’s HiSeq platform to yield more complete coverage of the genome.
4. Sample variation: Carefully consider where your greatest sources of variation are likely to come from and design the experiment to properly control for them. Remember that the ‘power’ of next-generation sequencing doesn’t magically eliminate biological variation. Therefore, it is prudent to include biological replicates in your experimental design. In contrast, technical replicates are rarely necessary as the platforms have very good reproducibility.
5. Sequencing depth: It’s important to carefully consider how much sequencing coverage or depth you need. Sequencing too much means you’re wasting both money and time, not to mention causing unnecessary data storage complications. If you sequence too little, your analysis will be underpowered and you won’t get a meaningful answer. Here’s where having a solid understanding of what your research project needs and what the platform limitations are will pay off. For example, RNA sequencing projects can range from needing as little as five million reads for a simple sample classification study to 100 million reads or more for a full analysis of the transcriptome.
6. Data analysis: Knowing how you’ll analyze the data before you generate it will help prevent headaches and frustration down the road. Assembling the right tools and expertise ahead of time will help ensure that your experiment was designed properly from the beginning. The alternative might be to start your analysis, only to find that you don’t have the appropriate data to fully answer the research question at hand.
September 1, 2012
Next-Generation Desktop Sequencers
The field of next-generation sequencing (NGS) has experienced explosive growth over the past several years and shows no sign of slowing down in the near future. Dramatically lowered costs have expanded NGS’ reach beyond that of the human genome into nearly every corner of biological research including cancer biology, metagenomics, and plant biology, to name just a few.
In the past 10 years, the cost of sequencing a human genome has dropped precipitously from $100M to under $4K and is anxiously anticipated to dip below the $1K mark in the next year or two. Increasing capabilities, easier-to-use instruments, and plummeting costs are attracting more and more genomics researchers who may have previously lacked funding or technical expertise to adopt NGS strategies.
However, keeping up with the latest advancements and choosing a platform can be a challenge. There are thousands of journal articles citing NGS technologies, with over 3,000 alone for Illumina. For those new to NGS, navigating through the various platform options can be a daunting task.
Maximum Data with Minimum Costs
The research community has obviously benefited from the competitive environment among the NGS vendors as they’ve driven down the cost of sequencing. Fierce competition continues to push the current high-throughput platforms to generate more data for less money.
For example, Illumina’s HiSeq® machine can generate 600 Gb—that’s enough data to sequence six whole human genomes, 60 human exomes, or 200+ RNA samples in a single run.
Lowering the “per Gb cost” while keeping error rates to under 1% are the key metrics that have been driving this industry. The most competitive instruments today have lowered the cost per Gb by becoming massively parallel, with as many as three billion sequences generated concurrently.
Output has also improved by increasing the read lengths of each run. While Sanger sequencing can generate reads of 1 kb or more, the high-throughput instruments of the past started out with reads as short as 25 bases. High-throughput NGS machines have steadily improved over the past few years, with read lengths reaching 150 bases.
While extremely successful, achieving the goals of “more data for less money” has not come without sacrifices. High-throughput sequencing machines are expensive and require long run times. Instruments with the highest output (and the lowest cost per Gb) are priced in the range of $600K to $700K.
While the cost per Gb is quite competitive, the minimum run cost for these machines is still several thousand dollars. And the longer read lengths have come at the expense of substantially longer run times, which now generally range from 6 to 11 days.
For researchers with large projects and big budgets, long runtimes and high minimum run costs aren’t such an issue. They’ve got enough samples to “feed the machine.” Projects with flexible timelines could possibly spare the additional time required to pool samples with other researchers to create a complete run, but researchers with smaller budgets may not have the capital to purchase an instrument of their own.
For those with time-sensitive projects, a quick turnaround is high priority. For example, researchers testing the quality of a library or new preparation methods with multiple iterations need results quickly. Clinicians dealing with patient samples (where sequencing results may be necessary for diagnoses or choosing treatment options) require results even faster.
Desktop NGS Platforms
Major platform companies have recognized the need for faster, maximum throughput sequencing with minimum costs and have responded to these market trends. They are focusing on smaller, less expensive desktop instruments with faster run times and lower run costs.
The first to respond was 454 Life Sciences with its GS Jr™ system in early 2010. With this machine, capital costs are reduced to $125K and the running cost are reduced to $1K. While each run only generates 35 Mb of data (which is just 0.035 Gb compared to the 600 Gb generated by the HiSeq), it does so over a period of just 10 hours.
Life Technologies followed in late 2010 with the launch of its Personal Genome Machine or PGM™, based on the Ion Torrent platform. Depending on the chip format, this $50K machine can generate between 10 Mb and 1 Gb in 2 hours at a cost per run range of $349 to $749.
Illumina followed suit with the introduction of its desktop sequencer, the MiSeq®. With a runtime of up to 27 hours, the $125K MiSeq is not as quick as the PGM, but substantially faster than its own HiSeq high-throughput machine. The MiSeq boasts the greatest output of any of the desktop machines with up to 4 Gb of sequence per run for $750.
The lower, more budget-friendly pricing of these new desktop instruments is introducing next-generation sequencing to a whole new group of researchers. The smaller, less expensive outputs are enabling these researchers to focus on smaller genomes (e.g., bacterial and viral) or on targeted sets of genes (e.g., those implicated in cancer).
While everyone will benefit from the rapid run times, this will undoubtedly be a critical feature as NGS moves into the clinic, where patient samples need to move from DNA to data as quickly as possible.
Looking at the Future of NGS
While high-throughput instruments are still generating the majority of the world’s sequencing output, the new desktop machines are where the market is moving to and where the vendors are placing their bets.
Life Technologies has stated that its primary focus will shift toward the Ion Torrent technology, explicitly at the expense of its SOLiD® platform. Toward that end, the PGM instrument will be joined by the Ion Proton™ later this year. At $149K, it will be more expensive than the PGM, but is projected to start with outputs in the 10 Gb range, growing to 100 Gb by early 2013.
Illumina plans to improve the output of the MiSeq, with read lengths expected to reach the 400 base range. In order to expand the utility of Illumina’s high-throughput HiSeq machine, they are giving it some “MiSeq-like” capabilities via a $50K “fast-mode” upgrade, which will allow it to generate 120 Gb in 27 hours.
Since the MiSeq and the HiSeq share similar chemistries, advances on one platform will likely make their way to the other.
One thing’s for certain, next-generation sequencing isn’t going away anytime soon. As NGS instruments improve, they are becoming the technology of choice for ever more areas of research. And as researchers continue to push them to their limits, vendors will continue to respond by offering instruments and consumables that perform better and faster with pricing competitive enough to fit researchers’ budgets.
The SCALEit accelerator program is an opportunity for startups to rapidly globalize. SCALEit seeks talented entrepreneurs and scalable technologies and business models from Denmark to come and take advantage of the Silicon Valley ecosystem.
Being a part of the SCALEit program has been a great success for BlueSEQ and the use of SCALEit's network and knowledge has made it an inspiring visit.
Building on the success at the X-Gen Congress earlier this year, BlueSEQ was again asked to present at the 'Sequencing 101' short course held prior to the NGx Conference held in Providence, RI this past August. Shawn Baker, BlueSEQ's CSO, presented material covering all major NGS platforms, including how well each performs for the various research applications.
July 1, 2012
BlueSEQ proudly announces that Dr. Shawn Baker, curator of the BlueSEQ Knowledge Bank, has started working full-time as the CSO.
Baker was one of the first employees in Illumina and has watched the company grow from 15 people to over 2200. "Having spent many years both as an R&D scientist and as a product/market manager, I am excited to bring my experience to BlueSEQ," Baker said.
June 19, 2012
While next-generation sequencing has become the technology of choice for genomics research, a number of experts who attended Copenhagenomics, held here last week, say that they still use and will continue to use microarrays in their research.
Copenhagenomics is a nonprofit conference focused explicitly on next-generation sequencing technologies. Talks at the conference ranged from the discussion of FarGen, a project that aims to sequence the entire population of the Faroe Islands, to using next-gen sequencing to uncover the impact of circumcision on the penis microbiome.
But many scientists also presented array-related data and projects, and some researchers who mainly use sequencing said they might use the older technology in the future.
Still 'Cutting Edge'?
Shawn Baker has witnessed the adoption of next-generation sequencing in genomics research. He said he was Illumina's 15th employee, and held a number of positions at the San Diego company, including marketing manager of expression and epigenetics. Now, Baker is chief science officer at BlueSEQ, an Aarhus, Denmark-based "sequencing exchange" that matches researchers' sequencing service needs with labs that have extra capacity on their NGS instruments.
Baker told BioArray News that researchers continue to use arrays for a number of reasons, including ease of use, installed instruments, and legacy data. He also said that the market continues to demand new chips, citing the success of Illumina's recently launched exon arrays, but that firms that sell arrays are investing more in developing other technologies.
"Arrays are still cheaper, for the moment; people are comfortable with them, the analysis has been worked on for a long time, but even on … the cutting edge of things, you are still seeing arrays being adopted," Baker said. "Illumina said they were surprised that their exon arrays took off as well as they did," he noted. "They made that product, weren't sure what it was going to do, and all of a sudden they got caught off guard because so many people wanted it."
Illumina introduced its exome family of arrays last year. CEO Jay Flatley said during the firm's first quarter earnings call in April that since the launch, Illumina has shipped enough arrays to survey 1.3 million samples. Christian Henry, general manager of Illumina's genomic solutions business, said last month that the market's reaction to the new chips exceeded the company's expectations (BAN 5/15/2012).
Still, Baker said that it is "definitely true" that researchers are switching to sequencing. "We are seeing slowly or not so slowly people move away from array platforms to sequencing," he said. "It is possible that that phenomenon will plateau," he added. "It is not that arrays will go away, they will still always be around for a long time."
A real issue for the future of arrays lies in research and development. "Unless something happens on the protein [array] side, it is unlikely that you will see massive innovation on the arrays," said Baker. "It's not even that they are not a good platform, it's just that there is only so much focus to go around and the traditional array companies are not doing that anymore," he said.
"Illumina still makes arrays, but the vast majority of innovation is going on in sequencing," he noted. "Affymetrix still makes arrays, but they are pushing into that lower multiplex area."
Anne-Mette Hein, a senior scientist at Aarhus, Denmark-based CLC Bio, confirmed that most of the bioinformatics software firm's innovation is focused on sequencing data analysis. "We have some array-related tools and I would say that the downstream tools we have available are applicable to both arrays and NGS," Hein told BioArray News.
According to Hein, the company continues to serve clients who use array technology.
"I think a lot of people have [valuable] experience with that technology; they know what to do with that type of data, and for sure they will keep on using microarrays," said Hein. "Also they have valuable data that they have processed on these microarrays and they can't go back and reprocess those all, so there will be at least for a while the need to combine the two technologies."
'An Honest Hope'
During the conference, there were several recurring themes that might have caused array users to experience déjà vu. One was the issue of cross-platform comparisons, which, in the array space, eventually led to the initiation of the US Food and Drug Administration-hosted Microarray Qualty Control consortium and the first two phases of the group's project, both of which were detailed in several publications (BAN 8/3/2010).
The third phase of the project, called Sequencing Quality Control, aims at assessing the technical performance of next-generation sequencing platforms by "generating benchmark datasets with reference samples," and "evaluating advantages and limitations of various bioinformatics strategies in RNA and DNA analyses," according to the project's website.
But BlueSEQ's Baker warned that it would be more difficult to carry out such projects than it has been for similar, array-focused projects.
"Sequencing platforms are changing so much more quickly than the array platforms that it's really difficult to do these kinds of projects," Baker said. "Groups don't move quickly, you are dealing with a bunch of institutions and companies coming together on borrowed time, and instruments last a year to a year and a half before they are replaced by an upgrade or a new technology," he said.
Baker characterized the sequencing market as "extremely competitive" and said that it has "more active players" than the array market did. "I have a list of between 30 and 40 companies that are trying to make the next, next-generation technology," he said, while he noted with arrays there were only a handful of dominant players, namely Affy, Illumina, and Agilent Technologies.
Another factor that may be familiar to array users is the belief that the new technology will answer most scientists' questions.
"There is a lot of NGS hype now, just as there was array hype 10 years ago," said CLC Bio's Hein, adding that there would be hype about whatever technology is popular in five years. "I think scientists are optimists, they tend to believe in what is promised by the new technology," she said. "With sequencing there is an honest hope that this technology will answer our questions."
Hein acknowledged that sequencing data is "more precise" than array data, but said that a host of other issues make data analysis complex. "We thought that counting reads would be easier than counting signals from an array, but there are others statistical issues that arise," she said. "So I think that sequencing does supply more information, but it is not the end, and there are new technologies that could be better, and more promising."
March 20, 2012
"The money will be used to continue developing its products and expand its web service lines," CEO Michael Heltzen explains. "The investment will go toward developing new software features that are expected to be launched in 2013. It will also be used to develop marketing strategies in an effort to attract new business."
The investment round was led by a German investment group and will take BlueSEQ to the next level. "BlueSEQ will be able to develop a professional sequencing exchange and service experience that will live up to the expectations of all its customers," Heltzen said.
February 1, 2012
Readying Sequencing for the Crowd
Under the headline: “Readying Sequencing for the Crowd” the BlueSEQ Exchange concept is described in Nature Methods.
Nature Methods see themselves as: “a forum for the publication of novel methods and significant improvements to tried-and-tested basic research techniques in the life sciences. This monthly publication is aimed at a broad, interdisciplinary audience of academic and industry researchers actively involved in laboratory practice. It provides them with new tools to conduct their research and places a strong emphasis on the immediate practical relevance of the work presented.”
From the BlueSEQ article:
New Technologies for Simpler Paths to Sequencing
Attracted by cheaper run costs and instruments, many small labs and clinics are seeking their first genome sequencing services and high-throughput instruments. Especially for this group, the range of technical approaches and commercial technologies can be overwhelming. A family of more “plug-and-play” services and sample preparation technologies are evolving in response to growing selection pressure from researchers new to sequencing.
Planning the Experiment
“Simply figuring out which approach would be the best—and what the approaches would cost—is a big problem,” explains Michael Heltzen, founder of the web service BlueSEQ. “It takes many hours to call up providers for quotes.” He says that despite providers’ efforts to decipher sequencing freshmen’s needs on the phone, researchers often end up with quotes for projects that are difficult to compare. A long call can sometimes turn out to be a bust: the desired technology isn’t available from that provider.
Heltzen and his team founded BlueSEQ to be the “neutral middle partner” that helps sequencing newbies (and veterans) define their project requirements and efficiently solicit bids from multiple providers. For newbies, BlueSEQ has a knowledge bank for an overview of technologies and a plain-language decision tree that helps de-code actual project requirements. “We chop it down into small questions,” says Heltzen. “We start out by asking questions like: What type of organisme are you sequencing?” BlueSEQ staff screens recommendations for errors before bids are solicited. Only providers with the relevant technology and throughput can see the request and provide bids, often at a discounted rate because BlueSEQ enables them to fill unused instrument capacity. BlueSEQ currently has 40 vetted providers balanced between Europe and North America, and the number is growing fast.
BlueSEQ is glad to announce that Dennis Cassøe has started as the CTO.
Cassøe has over 16 years of work experience as a systems architect and webmaster in tandem with the interaction between technology and business development. Cassøe comes from a CTO position in Denmark's largest webshop, selling white goods. "I am very excited to have Dennis lead the IT development and I look forward to benefit from his competencies in the interaction between the IT development and business development," CEO Michael Heltzen said.
March 5-8, 2012
Present and upcoming sequencing technologies
This will be a guide to today’s NGS platforms and a peek into the future, by Shawn C. Baker, Ph.D., Knowledge Bank Curator and Matthew Nesbitt, MSc, Knowledge Bank Curator.
The field of next-generation sequencing (NGS) has been experiencing explosive growth over the past several years and shows little sign of slowing down. The increasing capabilities and dramatically lowered costs have expanded NGS’s reach beyond that of the human genome into nearly every corner of biological research. An overview of the platforms on the market today, including an assessment of their relative strengths and weaknesses, will be presented. The presentation will conclude with a peek into where the technology is going and what will be available in the future.
The Key to Quality: Sample Preparation
The emergences of next-generation sequencing technologies have revolutionized genomic research. This dramatic increase, however, still involves complicated and labor intensive workflows for upstream sample preparation, library construction, and template amplification. Instructors share their solutions to prepare for sequencing runs (including the specific requirements of sequencing platforms) by addressing customizability, compatibility and cost effectiveness.
See full program
BlueSEQ gets interviewed about our look at the present and future Sequencing market
Michael Heltzen and Shawn Baker were interviewed by the kind program host, Theral Timpson (http://mendelspod.com/about/theral-timpson), in regards to our Sequencing Exchange and the Sequencing Knowledge Bank.
Mendelspod is reporting the last trends within NGS
Mendelspod produces fascinating one-hour shows at least once a week on highly relevant topics to those in life science and clinical research. An hour-long show enables them to go in depth with scientists who are leaders in their field or with CEO’s of the leading companies, to explore trends and the latest technology.
The last 3 interviews prior to BlueSEQ’s:
We are honored to be in a group with these Sequencing world leaders.
Listen to interview
January 24, 2012
Accelerace is a company growth program facilitated by the Danish state that picks young companies with international growth potential to help them achieve their strategy goals.
Out of approx. 200 candidates only 14 were picked and BlueSEQ was one of the cherries.
Read more about the program here: www.accelerace.dk (the page is in Danish).
BlueSEQ is strengthened
BlueSEQ gets a long list of benefits out of becoming an Accelerace company.
Just to mention a few of them:
October 27-28, 2011
BioConference Live is the world’s largest producer of online conferences focused on the life sciences, laboratory animal sciences and the clinical diagnostics community, produced by LabRoots. BioConference Live brings together research scientists, veterinarians, clinicians, medical experts, thought leaders and professionals from around the world exclusively online.
See more at http://www.bioconferencelive.com/about_us.php
BlueSEQ’s Review of the Next-Generation Sequencing Market
BlueSEQ’s BioConference Live Presentation, represented by Peter Jabbour.
Abstract of presentation:
The field of next-generation sequencing (NGS) has been experiencing explosive growth over the past several years and shows little sign of slowing down. The increasing capabilities and dramatically lowered costs have expanded NGS’s reach beyond that of the human genome into nearly every corner of biological research. Keeping up with these advancements, however, can be a challenge. BlueSEQ, having built a platform-agnostic NGS service exchange, is able to offer a neutral and unbiased assessment of the various NGS platforms. An overview of the platforms on the market today, including an assessment of their relative strengths and weaknesses, will be presented. In addition, there will be a summary of the various trends in how NGS is currently being used by researchers. The presentation will conclude with a peek into where the technology is going and what will be available in the future.
Feel free to see our re-recording on YouTube: http://www.youtube.com/watch?v=NpQxMiRk9hE
June 10, 2011
The purpose of Copenhagenomics (CPHx) is to present new areas of research and interesting findings. Also, to share new knowledge and best practices using the latest DNA sequencing technologies for translational research on improving life.
The main focus of the conference is to share knowledge about some of the challenges you encounter when working with genomics and NGS research.
Themes that will be covered are:
The 2012 conference will be held on Thursday the 14th and Friday the 15th of June.
May 5, 2012
Aarhus, Denmark — May 5th, 2011 — Today the Danish startup company BlueSEQ publicly unveiled their global Sequencing Exchange, a service that matches sequencing service providers with researchers and organizations looking for sequencing capacity for their projects.
Since late 2010, BlueSEQ has been developing their global Sequencing Exchange where sequencing capacity can be bought and sold. Key to the exchange was the development of a free Project Design web service, which allows researchers to easily design detailed sequencing projects by answering multiple choice and interdependency questions. After going through the step-by-step guide on BlueSEQ’s Project Design web service and completing a project design, it is easy for researchers to submit their projects to BlueSEQ’s global Sequencing Exchange, allowing sequencing service providers worldwide to bid on the project.
CEO of BlueSEQ, Michael Heltzen, states, “There are a lot of sequencing service providers with excess sequencing capacity, but they often lack the sales capacity to reach new customers. Also, there’s a huge increase in the number of researchers wanting to utilize next generation sequencing, but who have no sequencing instruments of their own. Our Sequencing Exchange will facilitate an outlet for the sequencing service providers to easily sell their extra capacity, and at the same time our Project Design tool will always ensure uniform and error-free project designs, easy communication, as well as optimal and fair sequencing agreements between the involved parties.“
“Our Project Design software ensures a standardized and ideal way to design a sequencing project, taking everything into consideration, from the type of biological sample to be sequenced, which sequencing platform’s application is ideal, including suggesting the best protocol – all the way down to recommending downstream bioinformatics if needed“, continues Service and Support Manager at BlueSEQ, Peter Jabbour. He adds, “In our Sequencing Knowledge Bank industry experts accumulate cutting-edge knowledge within sequencing to provide a detailed technology overview. This enables inexperienced users to make an informed decision about which sequencing approach is most optimal to achieve relevant results – critical knowledge that someone new to next generation sequencing would have quite a hard time obtaining otherwise. For the more experienced users in this field, it is possible to get direct access to the BlueSEQ Sequencing Exchange so decisions about outsourcing any sequencing need becomes easy.”
The BlueSEQ Exchange has officially launched today at www.blueseq.com where researchers can try the Project Design web service and Sequencing Exchange. BlueSEQ’s Project Design web service, Sequencing Knowledge Bank, and Sequencing Exchange are all free to use for researchers and organizations. The sequencing service providers pay an exchange fee when they finalize project agreements via the exchange, but can sign up at no cost.
April 29, 2011
Danish startup BlueSeq is preparing to launch an online business that matches academic and commercial sequencing-service providers with researchers looking to outsource their sequencing needs.
The company recently completed beta testing the platform and plans to officially launch it on May 5.
The web-based platform offers a project-design tool that asks a series of questions to help users plan and design their sequencing projects, and then matches them to sequencing providers based on the specific needs of each individual project.
The software-as-a-service platform is based on a series of proprietary algorithms, decision trees, and interdependency models, which the Aarhus-based firm built from the ground up, CEO Michael Heltzen told BioInform.
Clients request sequencing services by responding to a set of questions — what kind of organism they are working on, what sort of sequencing is required, the size of the organism’s genome, and so on.
Based on a user’s answers, the system selects relevant follow-up questions whose answers help it select what sequencing technology and protocols are optimal for each project or, in some cases, offers users a choice of technologies.
With this approach, “even though a [client can’t] say exactly what they need … [their] answers will give us precise knowledge about how a project can fulfill their needs,” Heltzen said.
Once a project is created, it is moved to the system’s “exchange module,” where it is matched to providers based on the parameters selected during the design phase.
Sequencing providers are only required to provide details about the instruments they have and when their platforms are available for use. When a project is entered into the system, BlueSeq e-mails the providers on behalf of the users. Providers can then make bids, which are sent back to the project designers who can either make a selection or continue to “fish” for the best deal.
The first version of its system is “relatively simple,” Heltzen said, though BlueSeq plans to make changes to it based on feedback it receives from customers.
In fact, based on feedback from its beta run, the company has already decided to implement additional parameters in the project-design side of the platform for future iterations of the tool.
For instance, with the current version, users needing their projects finished within a month will be able to select sequencing providers based only on the restricted time frame or prices listed by the providers.
In the future, clients will also be able to select services based on more specialized parameters, such as providers that are experienced in, say, ChIP-seq protocols, and can include these parameters in their requests.
Though bioinformatics analysis isn’t part of the current package, “it is something we will look into” depending on customer demand for future versions of the platform, Heltzen said.
Project design is free for users, while sequencing providers pay a fee for successful bids. Prices start at 10 percent of the bid for smaller projects and fall to five percent on larger ones.
Heltzen explained that the smaller projects are charged a higher percentage “due to the relatively more time and service use on them.”
The fee is used “to keep the portal neutral in regards to collecting and updating NGS knowledge overviews for both buyers and sellers of NGS service[s], developing more online tools, and upgrading the exchange as we go,” he said.
BlueSeq also provides information on current sequencing technologies via a knowledgebank, and keeps customers up to date on the capabilities of each resource as they change.
The company will market the platform to customers who don’t have in-house machines and to genome centers that may own sequencers but need additional capacity.
On the provider side, Heltzen said BlueSeq has caught the eye of core facilities with intermittent excess capacity and groups with underused sequencers.
Although he could not give the names of specific groups, Heltzen said that 10 sequencing providers have already signed on with the company, and more than 20 others are in the process of signing up.
While BlueSeq is one of the pioneers of this kind of service, it does not appear to be the only one. BioInform’s sister publication In Sequence reported this week that Findini, a German online service operated by Berlin-based Moosbaum, offers similar services.
According to the firm’s website, researchers submit descriptions for microarray or next-generation sequencing projects and receive quotes from participating service providers.
April 27, 2011
A Danish startup is setting out to match researchers who require next-gen sequencing services with providers who have spare sequencing capacity.
In early May, BlueSeq, based in Aarhus, plans to launch an online exchange to link next-gen sequencing customers with providers. The company also offers online project-design tools as well as information about next-gen sequencing platforms and applications. Services are offered at no cost to users, while providers pay a fee for successful bids.
Michael Heltzen, BlueSeq’s CEO, said he first thought of the idea for the company about two and a half years ago while working for bioinformatics software provider CLC Bio. At the time, he came across many owners of next-gen sequencing machines who did not use them to full capacity, as well as researchers interested in the technology but lacking access and detailed knowledge about its capabilities.
“It was difficult for me as an entrepreneur to see how there was a lot of capacity wasted around the world, when at the same time, there were a lot of people who had a big need for the same capacity,” he said. “That was a driving factor of why we started BlueSeq.”
“It was clear that the most optimal way both for providers and users of sequencing services would be an exchange, if we could find a way to decode the next-generation sequencing needs of people and a good way to communicate them,” Heltzen said.
About six months ago, he and a group of programmers and sequencing experts started to build a project-design software tool based on a decision tree that outlines the different ways a next-gen sequencer can be used, including all types of projects, applications, and protocols. The software, which guides users through a series of questions about their projects, helps them not only to describe their studies precisely and uniformly, but also to come up with the best sequencing approaches. Depending on the particular study, it could suggest one platform and protocol or provide several alternatives.
Heltzen is quick to point out that BluSeq has no preference for one technology over another. “We are a neutral player in this game,” he said. “All our decisions will be fact-based and we are not under the influence of any specific company.”
After a user submits a project, BlueSeq’s team — currently a staff of 10 — looks at the information to make sure it is clear and optimized.
Sequencing providers then receive information about those projects that fit their criteria, for example their sequencing platforms and the applications they run, and the capacity they currently have available. “Providers are as much hunting as the project owners are in some cases,” Heltzen said, and “they can pick the projects around the world that fit their free capacity.”
Based on the bids they receive from providers, users can then decide who to go with. Their decision might not necessarily be based on cost alone but also on wait time, or the experience a provider has with a certain protocol. In a future version of the exchange that is already under development, users will be able to specify additional parameters, such as low price, bioinformatics services, or phone-based customer service.
So far, BlueSeq has signed up 10 sequencing providers, about half of them commercial and half academic, which have several types of sequencing systems among them. Any provider worldwide with any platform is welcome to join, Heltzen said.
St. Louis-based Cofactor Genomics is one of the providers, but BlueSeq is not disclosing the others at this time. Another 20 providers are in the process of signing up, according to Heltzen.
In addition to the project-design tool and project exchange, BlueSeq also provides an online “knowledge bank” with basic information about sequencing platforms, applications, accessory tools, and relevant conferences.
BlueSeq’s services are free for users, or “project owners.” Sequencing service providers pay an exchange fee each time they make a successful bid, ranging from 5 to 10 percent of the total project fee. The company is betting that the fee will be worth it for service shops, “especially for providers selling capacity that they would otherwise throw in the bin because they would just run the machines at half capacity,” Heltzen said.
BlueSeq “provides an opportunity for us to work with clients that may not be aware of our expertise,” said Jon Armstrong, chief operating officer of Cofactor Genomics. The service “has the potential for reaching clients that our normal marketing channels may not cover.”
Cofactor, which operates Illumina, SOLiD, and 454 sequencing systems, currently runs at 75 percent to 80 percent capacity and might add additional capacity if BlueSeq succeeds in bringing in more customers, Armstrong said.
In the future, BlueSeq, which is currently funded with private equity from founders and investors, might add new software tools and services — for example, quoting tools that would help providers calculate their internal costs as well as suggest a possible sales price. “That is a big problem for a lot of providers right now, that they actually have a hard time understanding their own cost structures,” according to Heltzen. Those additional services might require the firm to raise more funding, he added.
BlueSeq is not the only firm seeking to match customers and providers of sequencing services, though. Findini, a German online service operated by Berlin-based Moosbaum, offers similar services. According to the firm’s website, researchers can submit descriptions for microarray as well as next-generation sequencing projects and will receive quotes from participating service providers.
Heltzen said that BlueSeq will be different because of its project design software and because its staff helps find the best matches on the provider side.
German sequencing service provider GATC Biotech said that it has used Findini before and that its experience with the service has been “very positive so far” because “all inquiries we received were real and serious ones,” according to a company spokesperson. “We feel that it is an additional and quite interesting lead channel. Obviously, it seems to be an interesting business model, too, and now we have to wait and see which platform will succeed in the long run.”