New England’s life sciences firms reported a lot of encouraging clinical-trials news this week.

—A cholesterol-lowering drug developed by Cambridge, MA-based Genzyme (NASDAQ: GENZ) and Carlsbad, CA-based Isis Pharmaceuticals (NASDAQ: ISIS) reached its goals in a pivotal clinical trial. Genzyme intends to apply for approval of the drug, called mipomersen, first in a small population of patients with a rare genetic anomaly that causes high cholesterol, and later in much larger groups of patients that might turn the product into a blockbuster.

—Cambridge, MA-based startup E8 Pharmaceuticals, along with MIT, filed a lawsuit against Navigenics, a Foster City, CA-based genetic testing company. The suit alleges that Navigenics is infringing on a patent on genotyping technology developed by MIT’s David Housman, one of the founders of E8, by using microarrays manufactured by Santa Clara, CA-based Affymetrix; E8 and MIT filed suit against Affymetrix itself last year.

—Ryan caught up with one of the organizers of Dartmouth College’s first-ever Dartmouth Entrepreneurial Network (DEN) Business Plan Competition. Taking the $50,000 first prize was Hanover, NH-based Novoculi, which is out to develop a non-invasive device for blood-glucose testing that works by projecting light into a diabetic patient’s eye and measuring the rate at which pigments in the retina are regenerated after the retina is “bleached” by the light.

—Luke profiled Vancouver, BC-based Tekmira (TSX: TKM), whose drug-delivery technology is incorporated in Cambridge, MA-based Alnylam’s RNAi-based treatment for liver cancer. Alnylam (NASDAQ: ALNY) launched a trial of the treatment last month in 55 patients, the first significant clinical trial of an RNAi drug designed to circulate throughout the body, rather than being injected locally.

—RiskMetrics Group, an influential proxy advisor, endorsed two of the four people nominated by billionaire investor Carl Icahn to the board of Cambridge, MA-based Biogen Idec (NASDAQ: BIIB). Votes will be tallied on June 3 at Biogen’s annual shareholders meeting.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: VRTX) launched a pivotal clinical trial program for VX-770, its drug candidate for cystic fibrosis. The three planned trials will include 240 patients at 110 clinical trial sites in North America, Europe, and Australia.

—Cancer drug developer Agios Pharmaceuticals of Cambridge, MA, named Genentech veteran David Schenkein as its first permanent CEO. Schenkein, who was the senior vice president in charge of cancer drug development at Genentech, will replace Third Rock Ventures partner Kevin Starr, who has been serving as Agios’ interim CEO.

—A diabetes treatment under development by CombinatoRx (NASDAQ:CRXX), also of Cambridge, MA, helped reduce blood sugar levels and provided other benefits in a mid-stage clinical trial. The treatment is a combination of bezafibrate and diflunisal.

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The stellar plaintiffs in a patent lawsuit over genotyping technology developed at MIT are raising the stakes by dragging a second California company into the dispute.

In 2008, MIT and E8 Pharmaceuticals, a Cambridge, MA-based startup created by MIT biologist David Housman and Harvard biologist Richard Mulligan, sued Santa Clara, CA-based Affymetrix for allegedly including technology in its GeneChip microarray products that infringes on an MIT DNA-screening technology exclusively licensed to E8. That suit has been dragging on for the last 10 months, but now MIT and E8 are going after an Affymetrix partner, a Foster City, CA-based genetic testing company called Navigenics.

In a lawsuit filed Tuesday in the District Court of Massachusetts, the two plaintiffs say Navigenics is infringing on the same MIT patent by using Affymetrix-manufactured microarrays as part of its genetic testing services.

Mass High Tech broke the story on Wednesday. The MHT story pegged the demand for damages at $75 million. But court documents examined by Xconomy don’t specify an exact damage amount, and say only that the amount of the damages requested is greater than $75,000.

It’s the latest development in a fractious story. As Bob explained in an extensive article last July, Housman is one of the named inventors on an MIT-owned U.S. patent, No. 6,703,228, which covers methods for high-throughput genotyping using single-nucleotide polymorphisms (SNPs). The patent was filed in 1999 and granted in March 2004, but Affymetrix claimed in September 2004 that it had actually filed a patent application on substantially the same invention in 1994. In 2007, the U.S. Patent and Trademark office eventually ruled that priority belonged to the MIT group. In its suit last year, E8 and MIT claimed that by continuing to sell its GeneChip equipment, which allegedly uses the same SNP genotyping technology, Affymetrix was infringing on the MIT patent.

Now, in the complaint filed this week, MIT and E8 say that Navigenics is also infringing the patent “by providing, selling and offering to sell, on a nationwide basis, genetic counseling services that use certain GeneChip products manufactured by Affymetrix.” The nub of the MIT-E8 complaint appears to be the fact that in February, Navigenics purchased an Affymetrix facility in West Sacramento, CA, where Affymetrix formerly performed microarray-based clinical testing services. “As part of its purchase of the CLIA facility, Navigenics has taken over infringing activities that were previously performed by Affymetrix and has continued to provide, sell and offer to sell services that directly infringe the ‘228 patent,” the complaint says.

The complaint asks the Massachusetts court to force Navigenics to pay damages and legal fees to MIT and E8. If Navigenics doesn’t ultimately take a license to the MIT patent, the plaintiffs say the court should either force Navigenics to pay royalties, or issue an injunction to keep the company from using the Affymetrix technology.

The legal team representing MIT and E8 includes Wiley Rein—the Washington, DC-based firm that helped NTP Win a $612 million settlement with Blackberry maker RIM in 2006—and Duane Morris of Boston. Navigenics has until June 8 to respond to the complaint; no hearings or other deadlines have been scheduled in the case. Representatives of E8 and Navigenics were not immediately available to comment on the suit.

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It’s an impressive and even intimidating group. Two world-renowned professors, one from MIT, the other from Harvard Medical School; MIT itself; and the lawyers who won a $612 million settlement from Research in Motion, the Blackberry folks. They’ve joined forces in a patent lawsuit, filed without fanfare last week in federal court, against one of biotech’s pioneers: Santa Clara, CA-based Affymetrix. No dollar amount was named in the suit. But analysts and the plaintiffs, who are seeking treble damages, say the technology in question is vital to much of Affymetrix’s business—an indication that many millions of dollars are at stake.

What may also be at stake is a long-standing relationship that MIT has with Affymetrix (NASDAQ: AFFX)—a maker of microarrays and associated tools for analyzing genes—through the Broad Institute, a Cambridge, MA-based biomedical research institute jointly run by MIT and Harvard. The collaboration, focused in part on the very technology at the core of the patent suit, could put MIT in a bind—or at least create the appearance of a conflict—as the case progresses.

The named plaintiffs in the lawsuit, filed on July 1 in U.S. District Court in Massachusetts, are MIT and a newly formed company called E8 Pharmaceuticals. The firm is the brainchild of MIT biologist David Housman, a pioneer in forensic DNA analysis whose co-invention is at the nub of the litigation, and Richard Mulligan, a MacArthur Prize-winning biologist formerly at MIT and now at Harvard Medical School. (Mulligan, an Xconomist, serves on ImClone’s board and was nominated, but not elected, to Biogen Idec’s board as part of billionaire investor Carl Icahn’s attempted takeover of the company.) The plaintiffs’ lawyers are from Wiley Rein, the Washington, DC-based law firm that represented patent-holding company NTP in its infringement suit against RIM; that suit ended with in the BlackBerry firm settling in 2006 for $612 million.

At issue in the suit against Affymetrix is U.S. patent No. 6,703,228. In their complaint, E8 and MIT hail the technology covered by the patent as a pioneering discovery in genotyping and DNA analysis that “enables users to perform accurate, reproducible and cost-effective genetic analysis, using minute amounts of sample DNA and a small number of reactants to generate results that were previously impossible, even in specialized high throughput centers using many thousands of different reactants.” The patent was awarded to MIT in March 2004, with Housman and his group named as the inventors.

The lawsuit alleges that some of Affymetrix’s GeneChip (the firm’s trade name for microarray) products infringe the ‘228 patent, and that by selling these products Affymetrix is causing its customers to also infringe the patent. Neither Mulligan nor Housman would discuss the suit in detail, but they did explain to me that the products at issue are those designed for analyzing a certain type of genetic analysis, called SNP (pronounced “snip”) genotyping. “The issued patent, which is public record, describes the Affy SNP chip genotyping methodology,” says Housman. “It is what it is. Anyone who wants to compare the Affy SNP chip manual to the issued patent is welcome to do so. They are one and the same thing.”

There’s a history here. According to the complaint, in September of 2004, some six months after Housman’s patent was issued, Affymetrix filed its own U.S. patent application claiming the priority date of an earlier 1994 application. Then, in March 2005, Affymetrix added new claims that in effect “asserted the patentability of and ownership of the methods claimed in what is now the ‘228 patent.” An interference was initiated in April 2006 as the U.S. Patent and Trademark Office tried to sort out which group was first to develop the methods at issue, and on May 2, 2007—again according to the complaint–the PTO ruled “that the Housman group at M.I.T. was the first to invent the claimed methods and was therefore entitled to the patent.”

E8 and MIT allege that Affymetrix nevertheless kept on using the methods—and directed its customers to use them—in direct infringement of MIT’s patent. E8, meanwhile, now holds an exclusive license to the patent.

Housman and Mulligan are former MIT colleagues and longtime friends. Mulligan was not …Next Page »

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Personal insights. Conversation starters. Gossip. Whatever the excuse, it’s high time for the second installment in Xconomy’s Who Knew? series, our wildly popular roundup of little-known, offbeat facts about the New England innovation community (and a few outside innovators with ties to the local scene).

In this installment, you’ll learn who runs his own indoor waterfall, who’s hit 40 straight Red Sox home openers, and who has a day named after him in the state of Kentucky. Then, of course, there’s the skinny on what family ties—real or not—to the Car Talk guys can get you. Obama’s Republican fundraiser? Yep, we’ve got that, too. Not to mention who can cough up Broadway tickets and seats at movie premiers.

The tip lines have been open—but we actually had to work harder to uncover these gems than we would have liked. We’d prefer much easier pickings next time, so please send us all the juicy details at editors@xconomy.com.

Meanwhile, here’s the second round:

MIT biologist David Housman tools around in a hard-to-come-by 2006 Volvo C70 convertible. How did he get the ride? Turns out that Josie and Annie, the aunts of Car Talk hosts Tom and Ray Magliozzi, ran kitchen support for the MIT Biology Department. In a ceremony whose details cannot be revealed here, gene hunter Housman was “officially” identified as Ray’s long lost half-brother. The Click and Clack family ties enabled the Prof to jump the queue for his wheels.

Rich Levandov of Avalon Ventures still (apparently) has not gotten his Tacoda tattoo. The body work was originally slated for last fall. Afraid of needles, Rich?

By the way, Levandov’s partner in Avalon’s San Diego home office, Kevin Kinsella, is a producer of the musical Jersey Boys, winner of four 2006 Tony awards (including Best Musical) and a Grammy for Best Show Album.

We bring this up because producing isn’t just a West Coast thing, baby. Todd Dagres, founder of Spark Capital, co-produced the 2008 train thriller Transsiberian, starring Woody Harrelson, Emily Mortimer, and Sir Ben Kingsley. The film, which will hit theaters in August, premiered at Sundance in January. Dagres also produced the 2005 teen comedy-drama Pretty Persuasion.

Speaking of moviedom, Colin Angle, co-founder and CEO of iRobot, had a speaking part as a Professor Hanes in 21, the movie about the MIT blackjack team. Xconomy had the scoop here.

Mark Levin, co-founder of Millennium Pharmaceuticals and Boston’s Third Rock Ventures, bought the most expensive house in Massachusetts in 2007, according to the Boston Globe and the Gloucester Daily Times. Last August, Levin and his wife, Becky, shelled out $11 million for Seahome, a 12,000-square-foot Manchester-by-the-Sea mansion that comes with its own deep-water dock, two kitchens, and an indoor waterfall. The property had been listed at $17.75 million.

Mark Fredrickson, vice president of Marketing Strategy & Communications for EMC, attended his 40th consecutive Boston Red Sox home opener in April. His mother started the tradition in 1969, when Frederickson was in the fifth grade. “My best Opening Day had to be 2005, when the championship banner was hoisted and rings were handed out at long last,” Fredrickson reports.

January 7 is Phillip A. Sharp Day in the state of Kentucky, and there is a Phillip Sharp Middle School, in Pendleton County, KY, where the MIT Nobel Laureate grew up.

Apple co-founder Steve Wozniak, aka Woz, keeps a spare Segway human transporter at the Brookline condo …Next Page »

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