Helicos Biosciences, the Cambridge, MA-based maker of genetic analysis tools, said today in a regulatory filing it is cutting 30 percent of its workforce, about 30 jobs, to conserve cash. The cuts will come between now and the end of the year, and cause the company to take a $450,000 charge for termination benefits. Earlier in the week, Helicos named Ronald Lowy its new CEO, replacing Steve Lombardi, who was demoted to president. Back in July, Lombardi said the company had about 100 employees, and that it planned to grow in Massachusetts because Gov. Deval Patrick’s life sciences initiative included support for workforce training.

We’ve updated the Boston layoff tracker with this news, so if you want to see the full list, click here.

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Helicos Biosciences (NASDAQ: HLCS), the maker of tools for genetic researchers, said today it has promoted Steve Lombardi to CEO. Lombardi, 53, joined the company in October 2007 as president and chief operating officer. He takes over for Stan Lapidus, 59, who will remain chairman of the company’s board. We profiled Lombardi, a veteran of Applied Biosystems and Affymetrix, last month, when he said he was thinking about expanding the company’s manufacturing base in Massachusetts because of Gov. Deval Patrick’s 10-year, $1 bilion life sciences initiative.

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In the future, your doctor might map your whole genome as a routine diagnostic test. Helicos BioSciences, a five-year-old biotech company in Cambridge, MA, has set out to make that happen in the not-too-distant future—by developing an extremely powerful gene-sequencing technology.

The instrument is the size of a refrigerator. A 3,000-pound refrigerator, built on a steel and granite frame, filled with precision mechanic and optics and advanced electronics, with a list price of $1.35 million. Stan Lapidus, the companhy’s founder and CEO, points to different parts of the machinery—the optical system with its solid-state laser, the plastic tubing that handles the chemicals used in the analysis, the glass flow cell for the samples. With these innards, he says, Helicos’ brand-new DNA sequencing machine is capable of doing what used to take months in just a few days or even hours, and at a fraction of the cost. And all it needs to do the analysis is one single molecule of DNA.

“We hope that this instrument will change the paradigm in life science measurement, which has always been based on measuring many molecules,” says Lapidus. That’s a bold statement, coming from a company that only shipped its first commercial instrument to a customer in March. In a press release about that milestone, Helicos also said that it was a significant step toward the “$1000 genome,” that is, the ability to map one person’s total DNA for a just a thousand bucks. (Spurring the development of such sequencing abilities is also is the aim of the $10 million Archon X Prize for Genomics, which is led by Xconomist Marc Hodosh.) Compare that to the billions of dollars spent when the publicly funded Human Genome Project raced against Craig Venter’s Celera to be first in mapping just one human genome.

At that time, in the late nineties, both teams mainly relied on a technology called Sanger sequencing after its inventor, two-time Nobel laureate Fredrick Sanger. Even today the Sanger method is regarded as the “gold standard” in DNA mapping, against which every other technology is matched. It also shares one attribute with gold—it’s expensive. Sanger sequencing takes a lot of sample preparation involving with methods like molecular cloning and polymerase chain reaction, PCR, and the throughput is relatively slow. So, if you are in a hurry, you will need to spend a lot on instrumentation, chemistry, and people. (In its efforts to beat the Human Genome Project, Celera had 300 automatic gene sequencers and a staff of 500 at its center in Rockville, MD, working for about one year to read three billion letters of genetic code as a first draft of the human genome.)

In contrast, one single Helicos instrument reads 25 to 90 million letters per hour by first chopping up the DNA molecule in very small pieces, and then sequencing many millions of the pieces simultaneously—skipping the DNA-copying steps that earlier techniques required. Afterwards, the information is pieced together by a massive amount of computing.

To demonstrate that its technology really works, Helicos has sequenced the whole genome of a virus from a single DNA molecule. The results were published in Science a couple of weeks ago. But the big expected market is not mapping the genomes of virus, bacteria, plants, or animals. It is in mapping your DNA and mine. Whole genome sequencing might become a major diagnostic method, used to pinpoint significant risks for a number of diseases.

“We now know that many diseases are caused mainly by changes in genetics. Diabetes, stroke, cancer are all diseases of the DNA,” says Lapidus. “It might be that you sequence the whole genome of a person just once and then just look at changes in certain regions. Or maybe you will do the whole genome several times in a person life, we will see.”

Lapidus has a background in diagnosis. He is the founder of two very successful bioscience companies, Cytyc and Exact Sciences. The former was sold to Hologic of Bedford, MA, for more than $6 billion.

Helicos is not alone in trying to develop radically faster and less expensive sequencing methods. The phrase “next generation sequencing” has been coined to describe a number of methods that all, Helicos’s included, use a massively parallel approach. Three competitors, Roche, Illumina, and Applied Biosystems have already sold next-generation sequencing instruments.

Roche got its technology in early 2007, when it bought 454 Systems, which in turn had licensed major parts of its technology from Swedish Biotage. Just a few months earlier, Illumina had acquired Solexa and its technology. Applied Biosystems, ABI, is the market leader when it comes to the classic Sanger sequencing method, but has also developed a next-generation sequencing technology of its own called Solid. At the moment it is unclear if one of these companies will dominate the market or if their technologies will coexist in different niches.

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The Personal Genome Project, led by Harvard Medical School professor George Church, got a boost from Google late last year, according to a report today from Bloomberg.

One of several academic and commercial efforts that Church, an Xconomist, is leading to develop tools and practices for sequencing and interpreting individual people’s DNA, the PGP is a nonprofit project aiming to sequence the genomes of 100,000 people. (Church and several other prominent members of the local innovation community will be among the first 10 volunteers.) Church also helms the Personal Genome X-Team (PGx), which is competing for the $10 million Archon X Prize for Genomics, and is the co-founder of Cambridge, MA-based startup Knome, which offers individual genome sequencing and analysis for $350,000 a pop.

According to the Bloomberg story, Church expects that sequencing the 100,000 genomes for the Personal Genome Project and linking the sequence data with individuals’ health information in a massive database will cost $1 billion. And an unspecified chunk of that is now coming from Google, which has recently also thrown its weight behind the California-based personal sequencing startup 23andme, among other health-related efforts. A Google spokesperson told Bloomberg that the Internet giant made a donation to the PGP late last year. On its website, the project lists Google alongside of healthcare investment firm Orbimed and the nonprofit COUQ Foundation as supporting the project with unrestricted gifts; Cambridge, MA’s Helicos and Applied Biosystems, a Foster City, CA-based business group of Norwalk, CT’s Applera, are among a handful of firms that have made unrestricted royalty donations to the PGP.

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It passed the House by a vote of 420 to 3, President Bush is for it, and it has fervent supporters on both sides of the political aisle—but even that didn’t save the Genetic Information Non-Discrimination Act (GINA or S. 358) from unexpectedly stalling in the Senate last spring.

Now, to try and get it moving again, one of the bill’s key supporters, the Washington, DC-based Genetic Alliance has launched a campaign to “turn up the heat” and let lawmakers know “this is a critical issue,” according to Alliance president and CEO Sharon Terry. Anxious to see the bill pass, a large contingent of Boston-area genomics firms is supporting the Genetic Alliance move.

GINA aims to protect people from losing their health insurance or jobs based on genetic test information. Supporters include many biomedical companies, who say the bill is vital to keeping the genomics revolution rolling.

One of the most anticipated fruits of that revolution is personalized medicine—in which drug treatment is tailored to an individual’s biology. Determining that biology can involve genetic tests. “If you want to enroll human subjects in genetic studies, ideally such information can become part of their medical record,” says Raju Kucherlapati, scientific director of Boston-based Harvard-Partners Center for Genetics and Genomics. “People will be reluctant to enroll if they think the information night be used to discriminate against them.”

Many people fear that if information about predisposition to a serious disease goes into their official medical record, insurers or employers will drop them to avoid possibly having to pay for expensive treatments down the road—which is why many women currently getting tested for genes linked to breast cancer already pay for the tests themselves.

GINA’s supporters have been pushing for this legislation for 12 years. “We finally felt certain it was going to pass,” says Patrice Milos, vice president and chief scientific officer at Cambridge-based Helicos, which supports the bill. But then, exploiting an arcane Senate rule, Senator Tom Coburn (R-Oklahoma) placed a hold on the bill, preventing a vote.

The delay has been a serious disappointment to those who, like Kucherlapati, feel “GINA is essential for personalized medicine.” Milos concurs. “As a company that sits at the cutting edge of the science to look at individual sequence data, we think this is critical.”

Kendall Square is one of the birthplaces of genomics. “This is a hotbed of both technologies used to explore the human genome and companies exploiting it for new therapeutics and diagnostics,” says Keith Batchelder, of the consulting firm Genomic Healthcare Strategies, another supporter of the bill. “You’ve got Harvard, Broad, and MIT that have all been at the center of it.”

Surveys suggest fear of discrimination from insurers or employers is one of the major reasons people avoid genetic testing, even when it is advisable because of family history. GINA supporters say this fear seriously impedes research and impacts personal health: People skip screenings that could help them. Some states have passed genetic anti-discrimination laws, but GINA would apply across the entire country.

What’s most frustrating to supporters is that Coburn’s move appears almost whimsical. This is merely one of approximately 90 bills the notorious ‘Dr. No,’ as he has become known, has single-handedly blocked. Others include a gun control bill that even the NRA backed, a bill to prevent suicide among veterans, and one aimed at naming a post office for Rachel Carson. Even Coburn’s fellow Republicans have been miffed by how often he is the lone outlier on a particular bill. (Coburn’s office has not responded to our request for comments.)

The list of GINA supporters is impressive. Organizations such as the Biotechnology Industry Organization (BIO) and the Personalized Medicine Coalition (PMC) have expressed strong support for the bill. (Helicos, BG Medicine, Aureon Laboratories, HistoRx, and numerous other New England-based groups are members of the PMC.) Last week Elizabeth Nabel said that passing GINA would be “the most important step to enable personalized medicine.” Nabel is Director of the National Heart Lung and Blood Institute, and she was speaking at a personalized medicine conference at George Washington University Hospital in D.C. Francis Collins has been a longtime supporter, and he testified to lawmakers about the bill’s importance last spring. Collins, who led the U.S. government team in the race to sequence the human genome, heads the National Institutes of Health’s genomic research program.

The President is also on board. In a 2001 radio address, President Bush said discrimination based on genetic test results “violates our country’s belief in equal treatment and individual merit.” Since GINA has been in process, he has reaffirmed his support.

According to surveys, most Americans are also in favor of outlawing genetic discrimination. “One of the great things about this bill is that it has bilateral support,” says Batchelder. “People are united around this issue.”

Well, not quite everyone is for it. And in this case, one person could be enough to derail it.

A hold is hard to get around. That’s especially true now with the war in Iraq taking up so much discussion time. The bill’s main sponsor, Representative Louise Slaughter (D-New York), has set up a petition to get Coburn to drop his hold, a move the Genetic Alliance is actively supporting in its new campaign. But if he doesn’t back down, the only way around him is to guarantee a huge block of discussion time for the bill—a process called cloture—or to tag it onto something already in process. Terry says she now expects the latter will happen, and that requires keeping the bill on lawmakers’ radar screens.

While they are weary from the long struggle, supporters say they remain determined. “Until we pass this legislation, we are not getting our return on the genome,” Terry says.

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A little over a week ago, legendary venture capitalist Esther Dyson explained her reasons for being one of the first 10 people to have their genomes sequenced—and made publicly available—for Harvard Medical School professor George Church’s Personal Genome Project. Yesterday, Church revealed all but one of the rest of the folks on that list. (One volunteer evidently wished to remain anonymous.)

Blaine Bettinger at The Genetic Genealogist has nice bios of all the named volunteers. Not surprisingly, several members of the local innovation community are included:

—Keith Batchelder, founder and CEO of Genomic Healthcare Strategies, a personalized-medicine consulting firm in Charlestown

—John D. Halamka, whose many appointments include CIO at Harvard Medical School, Beth Israel Deaconess Medical Center, and Harvard Clinical Research Institute

—Stanley N. Lapidus, president and CEO of gene-sequencing-technology firm Helicos in Kendall Square

—James L. Sherley, the controversial ex-MIT stem-cell scientist

—and, of course, Church himself.

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Following on the heels of last month’s disappointing IPO, Helicos BioSciences is making a new addition to its executive suite: Pfizer veteran Patrice Milos. Milos, most recently the executive director of Pfizer Global Research and Development, will serve as Helicos’s VP and CSO.

Alan Louie, research director at Health Industry Insights, says the hire is a good one for Helicos. Louie says that Milos’s contacts and her experience in directing Pfizer’s molecular-profiling efforts position her to help Helicos find the best applications for its technology, which aims to increase the speed and accuracy of DNA and RNA analysis by directly sequencing individual molecules. Even with its stellar scientific pedigree (founders include Steve Quake and Eric Lander), the company will need to find its focus to succeed in a space where there are a number of competing technologies and companies and, Louie says, “a lot of ways to get the same answer.”

Helicos could use the help. It initially planned to offer shares at $13 to 15 apiece but cut the price twice; the stock debuted at $9 and closed its first day at $8.47.

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