[Editor's note: We asked a group of Xconomists to answer the following question: "If you could patent one thing, what would it be?"]

A DNA sequencing technology that results in full genome scans in less than 24 hours. This would enable real-time profiling of cancer patients, which would be of tremendous value in determining the best treatment approach for an individual patient as well as, their likely response to certain therapies.

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NABsys, a Providence, MA-based gene-sequencing startup, announced today it has closed a $10 million Series C investment led by return investor Stata Venture Partners, the Needham, MA-based firm founded by Analog Devices (NASDAQ: ADI) co-founder and chairman Ray Stata (a member of the NABsys board of directors).

The new money, which brings NABsys’ total financing since inception to $21 million, will go to development and commercialization of the company’s solid-state electronic systems for single-molecule DNA sequencing and analysis. The technology uses silicon chips to detect the DNA sequences. Semiconductor pioneer Stata’s firm also led the $7 million Series B round in NABsys in February 2010.

There’s been a bit of buzz lately surrounding gene-sequencing technology developers. Ion Torrent, a new unit of Carlsbad, CA-based Life Technologies (NASDAQ: LIFE) is also developing a gene-sequencing machine that relies on semi-conductor technology. And earlier this year, UK-based Oxford Nanopore raised $41 million from investors including San Diego-based gene-sequencing giant Illumina (NASDAQ: ILMN).

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Some interesting funding news in the biotech world today. Lexington, MA-based T2 Biosystems, a diagnostics technology firm, says it has closed a $23 million Series D financing round led by new investor Aisling Capital. The round also included previous investors Flagship Ventures, Polaris Venture Partners, Flybridge Capital Partners, Physic Ventures, Partners Healthcare, Arcus Ventures, RA Capital, Camros Capital, and WS Investments.

The company says the new money will be used to support ongoing development and clinical trials for its diagnostic technology—a benchtop machine that T2 says can identify biological substances such as proteins, small molecules, viruses, and DNA much more quickly and cheaply than traditional optical-based machines (which require purification of samples). It works by using miniaturized magnetic resonance detection in combination with magnetic nanoparticle probes.

T2 Biosystems was founded in 2006 by an all-star cast of researchers and business people, including luminaries from MIT (Tyler Jacks, Bob Langer, Michael Cima) and Mass General Hospital (Ralph Weissleder, Lee Josephson). The company is led by CEO John McDonough.

The field of molecular diagnostics is progressing rapidly, as this recent interview with Stéphane Bancel of BG Medicine and Knome points out.

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Metamark Genetics has graduated from stealth mode. Now the Cambridge, MA-based startup, founded by top scientists at Harvard University and elsewhere, has hired a diagnostics industry veteran as its chief executive, and set a public goal for releasing a product that could change the way physicians decide how to treat prostate cancer in its early stages.

Mark Straley, the company’s chief executive, says he joined the company in November 2010 after serving as president of the healthcare giant Johnson & Johnson’s (NYSE:JNJ) global diagnostics group. He joined other heavy hitters at the startup such as Kenneth Weg, the company’s co-founder and chairman, who was previously the chairman of the cancer drug maker Millennium Pharmaceuticals (sold to Takeda Pharmaceuticals for $8.8 billion in 2008). Also, Lynda Chin, a scientific founder from Dana-Farber Cancer Institute in Boston, was part of the founding team at Aveo Pharmaceuticals (NASDAQ:AVEO), another Cambridge cancer drug developer that’s been on a roll of late.

Now Straley, who says he previously had about 1,500 people working under him at J&J, is wearing multiple hats as chief of a 20-person startup that hasn’t yet made a big name for itself in the diagnostics world. The company, founded in 2007, has raised about $30 million from undisclosed investors. But, according to the big plans the CEO laid out to me, the company’s star might rise pretty quickly over the next couple of years.

Metamark aims to release a molecular test to provide prognostic information that will help physicians make better treatment decisions. This test is scheduled to be available in the second quarter of 2012, Straley says. The firm raised its profile in the scientific community this month when some of its academic founders published their findings, in the prestigious academic journal Nature, about four gene markers that help predict whether a man’s prostate cancer is programmed to spread to other organs or is relatively harmless. This could give doctors more data with which to decide whether to take aggressive actions against the tumors (such as surgical removal and chemotherapy) or to basically just monitor the disease.

The startup is using those findings—based on the work of its co-founder Ron DePinho (another Aveo founder), the director of Dana-Farber Cancer Institute’s Belfer Institute of Applied Cancer Science, and others—to develop a panel of gene markers for its prostate cancer test, Straley says. Today, doctors can take tissue samples from the prostate and inspect the cells under a microscope, which can give them clues about whether the tumor could become lethal or remain relatively docile. Yet Metamark’s test in development might be able to expose the true nature of the cancer at the molecular level.

“We have to do a better job of … Next Page »

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Lexington, MA-based RainDance Technologies, a maker of genomic research tools, said today it has closed a $37.5 million Series D financing round co-led by new investor Quaker BioVentures and existing investor Mohr Davidow Ventures. Previous investors Alloy Ventures and Acadia Woods also participated in the round. RainDance, founded in 2004, has developed a system that can conduct thousands of DNA experiments per second, contained in ultra-tiny fluid droplets. The company is led by CEO Roopom Banerjee, who came on in early 2010.

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Pleasanton, CA-based QuantaLife, which has developed a “digital PCR” method to quantify small amounts of DNA for gene expression analysis and other applications, said that it has collected $17.2 million in Series B financing. The round was led by Series A investor Paladin Capital Group and was joined by new investors Merieux Developpement and Vital Financial. The startup said it would use the funds to “accelerate application development” and bring its technology to market in 2011.

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Compendia Bioscience has evolved significantly since it spun out of the University of Michigan with its cancer genomics research software four years ago. Instead of just selling software and moving on to the next customer, Compendia co-founder and CEO, Daniel Rhodes, says that his firm has prospered by forming close ties to pharmaceutical companies that rely on the firm’s expertise and technology.

“We’re transforming from a software company only to really a collaboration partner with pharma, where we are licensing them access to our technology but also providing expertise and services,” Rhodes says. “So it’s a really exciting time for our company right now.”

Ann Arbor, MI-based Compendia is capitalizing on large pharmaceutical companies’ greater reliance on external firms like itself for developing new products, as their own internal research pipelines have run dry. As its name suggests, Compendia has built a compendium of cancer genetic data from published journal articles, academic and government databases, and about the molecular profiles of about 43,021 actual cancer patients’ tumors.

The firm’s software includes advanced analytics and search capabilities that enable scientists to mine its database and conduct analyses for their cancer research. For example, the firm’s Web-based software aims to give drug researchers insights into the biology, regulation, pathways, and patient populations to aid in the development of new therapies to combat tumors.

A major source of demand for Compendia’s software comes from life sciences firms that want to find out which genes are found in patients that are likely to benefit from a certain drug. The firm formed an alliance last year with MDS Pharma Services, in which the companies would use both Compendia’s cancer genomics software and MDS’s cancer cell screening services to help drug companies predict which patients would be likely to respond to their new cancer therapies. Separating the winners from the losers early on is a big deal in an industry where only one out of every 10 drugs that enters clinical trials ever becomes an FDA approved product.

Besides helping its pharma customers boost the odds of success, Compendia has also made some discoveries of its own. For instance, Rhodes and his team used the firm’s software to discover a gene called SPINK1 that is over-expressed in a subset of men with … Next Page »

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A quiet competitor in the gene-silencing game has surfaced with good news. Kalamazoo, MI-based ProNAi Therapeutics says that it’s started to treat cancer patients with its first experimental DNA interference drug, which is essentially made to specifically silence disease at the fundamental level of DNA. And the firm is relying on molecules from Bothell, WA-based Marina Biotech (NASDAQ:MRNA) to deliver the treatment where it needs to go inside cells.

ProNAi‘s drugs are at a much earlier stage in development compared with other gene-silencing methods such as antisense and RNA interference. This is an important trial for ProNAi, as it seeks to gather the first evidence that its drugs work in humans. Now, the firm is testing its lead experimental drug, PNT2258, in patients with tumors for which there are no effective treatments, according to the company. The primary goals of the trial are to show the safety and tolerable dosages of the drug, but it’s also going to give the firm its first glimpse at the effects of its treatment in patients.

The company, which has raised $17 million from investors, has taken a long road get to this point. Founded in 2004, the startup’s novel approach to silencing disease genes has been under development for about as long as RNA interference but has lacked the huge investments and notoriety enjoyed by the latter technology, said Mina Sooch, a managing partner at Apjohn Ventures and an director at ProNAi. The company got the green light from the FDA to start this trial back in March 2008, but has only recently begun enrolling patients because the firm didn’t have enough money until recently.

On the other hand, Cambridge, MA-based Alnylam Pharmaceuticals (NASDAQ:ALNY), a leading developer of RNA-interference drugs, has raised hundreds of millions of dollars and has taken at least three gene-silencing treatments into clinical trials since its founding in 2002. Of course, Craig Mello of the University of Massachusetts and Andrew Fire won a Nobel Prize in 2006 for their discovery of RNA interference, raising the profile of the gene-silencing technology to new heights. (Conversely, ProNAi’s technology was first conceived at Wayne State University by a less well-known scientist named Reza Sheiknejad, who has since moved to Iran, according to Robert Forgey, the firm’s chief operating officer.)

“We’ve spoken to all the big players in this field, and they … Next Page »

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This week saw a long-awaited FDA approval for a Boston-area drug maker, speculation about a possible buyout of a local biotech giant, and some in-depth profiles on other key life sciences players.

—Hospital software maker Picis, of Wakefield, MA, said it is being acquired by Ingenix, an Eden Prairie, MN-based healthcare intelligence and analytics firm. The companies didn’t disclose financials details of the transaction, but Ingenix said it will maintain Picis’ locations in Wakefield and throughout the U.S. and Europe.

—Cambridge, MA-based Momenta Pharmaceuticals nabbed a long-sought FDA approval for a generic version of the anti-clotting drug it developed with Novartis unit Sandoz. The regulatory approval proves that Momenta (NASDAQ: MNTA) can make equivalents of more complex drug mixtures, which pose a greater challenge for would-be generics makers than do more conventional small-molecule pills, Luke wrote.

—Ryan took a look at RainDance Technologies, a Lexington, MA-based company developing next-generation genomic analysis technology. The startup’s first commercial product is a system that conducts thousands of DNA experiments simultaneously, which has caught the eye of research houses and pharma companies.

—Cambridge-based BioScale has flown relatively under the radar while developing a method of measuring biological samples using sound wave technology, Ryan wrote. But the company has caught the eye of another Cambridge biotech player: Millennium, The Takeda Oncology Company, which is using BioScale’s technology to measure cancer-related proteins for its drug research. The access comes as part of BioScale’s beta release of its technology.

—Following last week’s talk of a potential acquisition of Genzyme by drug giant Sanofi-Aventis, Ryan asked readers to weigh in on how much they thought Cambridge-based Genzyme’s stock would be worth in a buyout. Their answers averaged out to $76.29 per share, for a total value of about $20.4 billion. That’s well above the $70 per share that the Sanofi (NYSE: SNY) board authorized the company to offer for Genzyme (NASDAQ: GENZ).

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Until recently, BioScale had operated out of the public eye for some eight years as it engineered a new way of measuring biological samples with sound wave technology. Now the Cambridge, MA-based startup has garnered some validation for its acoustic technology from a very visible player in biotech—Millennium, The Takeda Oncology Company.

Cambridge-based Millennium has used BioScale’s technology to measure cancer-related proteins for its drug research. While the results of the research have not been published, Millennium revealed in two posters at a recent science meeting that BioScale’s analyzers bested in a few ways the traditional Western blot method and Waltham, MA-based PerkinElmer’s (NYSE:PKI) AlphaScreen system in detecting specific proteins in tumor samples from cell cultures and mice. Millennium is the first group outside of BioScale to report such findings, says Mark Lundstrom, founder and chief executive of the startup.

The firm’s analyzers are designed to detect proteins in multiple types of samples, including blood, urine, and tissue, among others. In pharmaceutical research, measuring the presence of proteins in a sample can show whether a drug is hitting its molecular target. In diagnostics, the technology can be applied to tell whether a person has a virus or other molecular indicators of disease in their system.

The startup—which made its first public announcement last month about the closing of a $25 million Series C funding round—has made its technology available to Millennium and other top corporate and academic research groups as part of a beta release, Lundstrom says. The CEO says expects more studies involving the firm’s technology to be revealed in the coming months, though he wouldn’t say yet who else is using the technology.

At Millennium, researchers found that BioScale’s “Vibe” analyzers required fewer steps than a protein-measuring technique known as Western blot. Also, the acoustic analyzers provided measurements from complex tumor samples, which can often skew results when measured with optical systems. Millennium, which is a subsidiary of Japanese drug giant Takeda Pharmaceutical, tested the BioScale analyzers to measure two specific molecules: a DNA damage protein and a protein that helps tumors grow. In the DNA damage protein tests, Millennium found that BioScale’s results were devoid of the chemical and optical interferences it found in PerkinElmer’s optical system.

“When you look at the data that Millennium has put out, it basically concludes that … Next Page »

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Roopom Banerjee, the chief executive of genomic research tool maker RainDance Technologies, is aware of the criticisms facing genomics. “There’s been a lot of talk recently about how productive has the Human Genome Project really been in terms of delivering on the promise of personalized medicine,” he says.

RainDance is helping scientists conquer part of this major challenge and question in disease research: Now that we’re able to map our DNA quickly and cheaply, how do we use these vast stockpiles of genomic data to actually improve our health? The company bridges part of this gap by giving researchers the tools to rapidly perform experiments of specific genes, helping them figure out how those genes affect a variety of diseases. This could expedite the development of treatments and diagnostics personalized to individuals’ specific genetic makeup.

The Lexington, MA-based company launched its first commercial product—a system that can conduct thousands of DNA experiments every second, contained in ultra-tiny fluid droplets—in April 2009. And it’s already found an audience for the system, called the “RDT 1000,” at major research hubs such as Memorial Sloan-Kettering Cancer Center and The Rockefeller University as well as at big drug companies like Paris-based Sanofi-Aventis.

RainDance’s micro-droplet technology is helping researchers at these institutions do what is known as targeted genetic sequencing, which involves studying specific genes within the vast genome to better understand specific illnesses such as cancer, rare diseases, autoimmune disorders, and other ailments. It’s also making these studies—which amplify specified genes using a tried and true technology known as polymerase chain reaction, or PCR—faster and cheaper than previous processes by orders of magnitude.

“In the space that a customer would traditionally do one or 96 samples of PCR, we do … Next Page »

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Cambridge, MA-based Stromedix is behind schedule on developing drugs that could stymie a cellular process that causes peoples’ bodies to transplanted kidneys to fail. Yet schedule delays are common in the unpredictable biotech business, and we’re only hearing about this one because of the candid nature of its co-founder and CEO, Michael Gilman.

When Stromedix closed its $25 million Series B funding round in April 2008, Gilman told Xconomy he wanted to be well into a mid-stage clinical trial of the firm’s lead drug for interstitial fibrosis in kidney transplant recipients by this point in 2010. However, the FDA has concerns about the safety of how the drug works in those patients, and Gilman and his startup now find themselves more than a year behind in their development plan.

The company’s drug, STX-100, is a therapeutic antibody licensed from the Weston, MA-based biotech giant Biogen Idec (NASDAQ: BIIB), where Gilman used to be a research executive. The antibody targets molecules linked to a cellular process called fibrosis, which causes organs to form scar tissues and ultimately fail. While fibrosis is common among all organ failures, Stromedix initially targeted kidney transplant patients because they are easily identified compared with other victims of fibrosis, and there’s a great need for ways to help them keep their new kidneys functioning for as long as possible.

Fibrosis is also a leading cause of peoples’ heart tissues to fail, something that hit close to home for Gilman last year. The 55-year-old CEO got an aortic valve replacement in November 2009 that sidelined him for six or seven weeks, he says. “I feel … Next Page »

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Franco Cerrina, a Boston University engineering professor, was found dead in a lab at BU’s Photonics Center on Monday morning, the university reported yesterday. He was 62. Colin Riley, a BU spokesman, said in an e-mail this morning that the cause of death is not yet known. Police are not treating Cerrina’s death as a criminal matter, according to BU. Cerrina joined the faculty of BU in 2008 after spending 24 years on the faculty at the University of Wisconsin-Madison. He co-founded five companies, including NimbleGen Systems, Genetic Assemblies (merged with Codon Devices in 2006), Codon Devices, Biolitho, and Gen9, according to Nanowerk News. NimbleGen, a Madison, WI-based provider of DNA microarray technology, was sold to Basel, Switzerland-based Roche in 2007 for $272.5 million.

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Tumors are kicking our butt in the war on cancer. What’s more, big drugmakers are cutting their budgets at the expense of some cancer treatments under development. But now there’s Tesaro, a drug development outfit that formed this spring to buy some of those promising therapies for cancer in the early stages of development and then work to bring them to the market.

Waltham, MA-based Tesaro jumped onto the cancer drug scene in late May, when it revealed that had raised $20 million in a Series A round of funding from the company’s founders and the venture firm New Enterprise Associates (NEA). The company’s big-named backer is NEA general partner David Mott, the former chief executive of Gaithersburg, MD-based MedImmune, which he sold to the drug giant AstraZeneca in 2007 for a $15.6 billion.

Tesaro doesn’t have technology of its own, like many biotech startups in Boston that are hatched in the labs of renowned research institutions here. Rather, Tesaro plans to acquire drugs for cancer patients from other companies and spend its time and money to do the necessary clinical trials to prove they are safe and effective. So Tesaro won’t have to invest big bucks on the earliest steps of drug discovery. The drugs it does acquire are expected to be ready to test in early- or mid-stage clinical trials, giving the firm a shot at having a marketable product before a typical biotech startup that begins from with raw science.

Tesaro expects to have its pick of plenty of cancer drug inventories because of several trends in its industry, company officials say. For instance, there’s been a string of mega mergers in recent years—including the Pfizer/Wyeth, Merck/Schering-Plough, and Roche/Genentech combos. As these giants combine, they are expected to cut costs and shed drugs from their development pipelines. Also, even small biotechs are expected to have molecules on the block because financial constraints are forcing them to focus their resources on fewer drugs, leaving others without resources to develop.

Mott, who built MedImmune into one of the largest biotechs in the world, says that the current … Next Page »

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Women lose a valuable weapon against their breast tumors when the potency of hormone therapy fades. But what if there was a way to “reprogram” breast tumor cells to be receptive to hormone therapy? Waltham, MA-based Syndax Pharmaceuticals might have such a way.

Syndax has shown in a 26-patient clinical trial that its drug, entinostat, could improve the ability of hormone therapies to kill breast cancer. The biotech startup—which was co-founded by scientists from the Salk Institute for Biological Studies in La Jolla, CA in 2005—has embarked on a new human study that will give it a clearer picture than previous studies provided of how well its drug improves breast cancer treatment. Its research has been displayed in recent days at the American Society of Clinical Oncology (ASCO) annual meeting in Chicago.

The company’s new Phase II clinical trial for entinostat for breast cancer patients is a big test of the firm’s technology. The firm has raised $49 million from venture capital firms such as the San Diego venture firms Domain Associates, Avalon Ventures, and Forward Ventures as well as MPM Capital, of Boston and South San Francisco, and Pappas Ventures in Durham, NC. (Eckard Weber, a well-known partner at Domain in San Diego, co-founded and served as an early CEO of Syndax.) Joanna Horobin, the firm’s CEO, said that the startup raised its latest $9 million in venture financing this year to complete its new mid-stage clinical trial, which she hopes will yield evidence of its lead drug’s utility by early next year.

For several years Syndax has been one of the biotechs to watch in the hot field of epigentics, which involves the study chemical changes in cells that impact how genes are expressed or suppressed without changing the underlying DNA code. Epigenetics grabbed the cover of Time magazine in January. For instance, breast tumor cells can undergo epigenetic changes that make them immune to hormone therapies, which are intended to stymie the production of estrogen needed to sustain tumor survival. Syndax’s drug aims to reprogram breast tumor cells in which those detrimental epigenetic switches occur.

“The idea is that you turn off the … Next Page »

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T2 Biosystems has been quiet for a while, but it’s making some noise today. The Cambridge, MA-based developer of a portable diagnostic machine has raised $15 million to carry on its quest for a diagnostic tool that that can beat workhorse laboratory machines on versatility, speed, and price.

Physic Ventures led the round, which included new investors Arcus Ventures, RA Capital, Camros Capital, WS Investments. The round also included T2′s existing backers, Flagship Ventures, Polaris Venture Partners, Flybridge Capital Partners, and Partners Healthcare. The company has now raised about $31 million total since it was founded in 2006. As we’ve pointed out before, there is plenty of intellectual capital lined up behind T2. The company’s advisors include Tyler Jacks, the director of MIT’s Center for Cancer Research; Ralph Weissleder, head of Mass General Hospital’s Center for Molecular Imaging Research; and MIT’s indefatigable bioengineering professor, Robert Langer.

T2 is what Harvard Business School professor Clay Christensen would call a “disruptive” technology, not the kind of more incremental, sustaining kind of innovations that big companies often pursue. This startup is attempting to commercialize technology will identify a huge range of biological substances—proteins, small molecules, viruses, DNA—in a handheld instrument. It aims to do all of this in a machine that costs less than $50,000, a tool that eliminates time-consuming and sometimes costly sample preparation steps, and that can give an answer in the lab, or the back of an ambulance or a jeep, in less than an hour. This technology, if proven in further trials, seeks to be better, faster, and cheaper than the classic optical-based diagnostic machines sold by giants like Becton Dickinson and Abbott Laboratories.

“No one else can do DNA and protein in a single instrument, and no one can get results faster than us,” says T2 Biosystems CEO John McDonough.

The difference with this mini-lab tool is so big, McDonough says, that it can change the way scientists, first-responders, and physicians find out exactly what they are dealing with. “The user can now see the problem and act on it. If you have to send in a sample to a central lab and it takes three days to get a test back, a lot of times you won’t even go through with the test.”

What T2 is up against is an existing paradigm of optical detection machines that are big, powerful, and cost about $250,000, McDonough says. They typically require … Next Page »

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Buying that personal genetic test kit from the drug store is going to take longer than expected. Walgreen says it has postponed its planned sale of kits from San Diego-based Pathway Genomics, after the FDA told company its test needed regulatory approval before it could be sold in stores. Amid a proliferation of companies planning to sell similar genetic tests and services, the FDA is now considering the legality of selling such tests directly to consumers, according to The San Diego Union-Tribune. Pathway had planned to sell a $20 kit through retailers, enabling consumers to send a sample of spit in for tests that range from $79 to $249.

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Dyax (NASDAQ:DYAX), a Cambridge, MA-based biotech company, reports today that it has sold its rights to royalties and fees from sales of a hemophilia treatment it discovered to Paul Capital Healthcare for up to $12 million. The deal includes a $10 million upfront payment and up to $2 million in milestone payments tied to  sales of the hemophilia treatment in 2010 and 2011. Drug giant Pfizer (NYSE:PFE) is commercializing the product, a recombinant Factor VIII therapy, which Dyax discovered with its patented phage display technology.

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The trick to beating cancer could be a single test that shows all known genetic traits in each person’s tumor, and that also matches those results to the best treatments. Boston-based Foundation Medicine reports today that it has raised the first part of a planned $25 million round of Series A venture funding to make comprehensive genomic analyses of tumors a standard tool in the fight against cancer.

A crack team of cancer, genetics, and industry veterans from the Boston area has assembled around the startup. Boston-based Third Rock Ventures, founded by former executives of the cancer drugmaker Millennium Pharmaceuticals, has incubated the company and led the first-round financing. Alexis Borisy, an entrepreneur-in-residence at Third Rock and the former CEO of Cambridge-based CombinatoRx (NASDAQ:CRXX), is the startup’s founding chief executive (something we were the first to report back in February). And Eric Lander, a pioneer of genomics research and an advisor to President Barack Obama on science and technology policy, is headlining the group of scientists and physicians who are advising the startup.

Foundation Medicine, which was formed in 2009, has come into being as high-speed DNA sequencing and a slew of academic studies help to uncover new genetic mutations that, say, protect tumors from certain therapies, or help cancer cells grow out of control. Drug companies are developing cancer drugs for patients who have specific genes that make them likely to respond well to the treatments, building on Roche-Genentech’s success in marketing the breast cancer drug trastuzumab (Herceptin) for women with the HER2 gene. Also, a growing number of startups are focusing on providing new genetic tests that help guide physicians in treating cancer patients.

Foundation Medicine is taking its own approach to personalizing cancer treatments. While many previous firms have focused on developing tests to detect specific genes linked to likely outcomes of cancer treatments, Foundation Medicine is planning to use high-throughput DNA sequencing technologies to expose the plethora of genes and genetic variants in cancer genomes, according to Borisy. Borisy and Third Rock are betting that the future of cancer treatment will involve a single analysis of cancer DNA in guiding treatments, rather than multiple tests that screen for individual genes or groups of genes.

Today DNA sequencing is done primarily in research settings, with extremely limited clinical use. Borisy, however, says that it’s time to put this technology to work for people with cancer. “If many patients would benefit from this deep understanding, then there needs to be a way to take this from being a research tool to something that would be useful and meaningful and work in the routine practice of clinical oncology,” he says. “That has been the driving motivation and inspiration behind Foundation, and it’s quite clear that this is the way the world is going.”

The company’s exact strategy is evolving, according to Borisy, yet some details are clear. The firm plans to set up a central lab in the … Next Page »

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The founders of Boston-based Ginkgo BioWorks think that assembling synthetic biological systems shouldn’t just be for experienced researchers. So they put together a kit that consists of the “scissors and glue for putting together pieces of DNA,” says co-founder Reshma Shetty.

Unlike the electronics industry, which sets standards to ensure compatibility and interoperability, the methods for putting together pieces of DNA are typically much more fragmented and ad hoc. Biologists build biological systems and organisms for functions such as producing everything from fuel to drugs to consumer products. The Ginkgo kit builds on a publicly available standard for connecting pieces of DNA, developed in 2003 by another Ginkgo co-founder, MIT senior research scientist Tom Knight. Called the BioBrick standard, it facilitates the assembly of multi-gene systems, and allows parts to be more easily shared within the synthetic biology community.

Ginkgo’s BioBrick Assembly Kit includes the reagents for constructing BioBrick parts, which are nucleic acid sequences that encode a specific biological function and adhere to the BioBrick assembly standard. The kit, which includes the instructions for putting those parts together, sells for $235 through the New England BioLabs, an Ipswich, MA-based supplier of reagents for the life sciences industry.

Shetty didn’t release any specific sales figures for the kit, but said its users include students, researchers, and industrial companies. The kit was also intended to be used in the International Genetically Engineered Machine competition (iGEM), in Cambridge, MA. The undergraduate contest, co-launched by Knight, challenges students teams to use the biological parts to build systems and operate them in living cells.

The assembly kit is the first product from Ginkgo, which was started in 2008 by Shetty, Knight, and three other MIT PhDs, but the company is also working on rolling out a consulting-style service for more elaborate DNA construction. They plan to work with companies on determining how they can design biological systems to fit their business functions, modeling what that system would look like, and testing it. “We’re focused on the tools and services for engineering biological systems,” says Shetty. “We think of ourselves as a biological design firm.”

Ginkgo (named after the tree) isn’t pursuing any venture capital funding, because it hasn’t needed it, Shetty says. In September 2009, the company received a $150,000 loan from LifeTech Boston, a city initiative aimed to grow the life sciences industry. Ginkgo was also selected that month to be part of an initiative in Scotland to improve synthetic DNA assembly. ITI Life Sciences, a unit formed by the Scottish government to strengthen the life sciences industry in the country, dedicated $4.1 million to the project.

While many established life sciences companies have in-house personnel dedicated to constructing biological systems, many other industries—from cosmetics to cleantech—can benefit from simple tools for the construction of synthetic DNA, Shetty says. A makeup manufacturer who uses a plant compound in its products could use the kit for constructing bacteria or yeast to create a synthetic form of that compound, for example. That way the company wouldn’t be affected by price increases from a bad crop of the plant. “It’s cheaper and more reliable manufacturing,” Shetty says.

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