Intel and the Oregon Health & Science University are teaming up on a supercomputing project to speed up analysis of human genetic profiles, which could help with personalized treatment for cancer.

The goal for the multiyear partnership is to make genetic analysis a routine part of patient care.

“We are generating an enormous amount of data, which has historically been unmanageable,” said Joe Gray, a research director at OHSU’s Knight Cancer Institute, in an interview.

Gray envisions that the project will involve a “lot of back and forth” between geneticists, engineers, and biomedical scientists before they can map the human genome to identify the mutations that lead to cancer.

Such a map would provide a better understanding of an individual’s genetic makeup, so biomedical engineers can cancer treatment that kills only the mutating cells, not the healthy ones.

It sounds simple, but Gray’s project is grappling with delivering the right kind of computer power for a project of this scale. “We are talking about a terabyte of data per patient that describes the molecular architecture of a disease,” he explained. If this is extended to millions of patients a year, it’s an awful lot of data.

Researchers will use Intel’s Xeon E5 HPC CPU, which offers Intel Trusted Execution Technology (TXT) and Intel Node Manager Server power-management technology.

Aside from the technology, which is steadily evolving to manage this volume of data, the other challenge is an ethical one.

“Privacy is a clear issue, and the data needs to be handled confidentially,” said Gray. When asked about whether the data will be stripped of any personally identifiable information, Gray admits to another “gray area.” Our DNA is like a molecular blueprint — theoretically, it is possible to match and reestablish a patient’s identity without having a direct link.

But the partnership with Intel is designed to explore the architectures best suited to deal with this data, and tackle ethical issues at a later date. The more immediate goal is to identify a number of challenging biomedical projects, and to experiment with hundreds of hardware and software packages.

An example of a project is tracking a typical cancer tumor through its thousands of genomic changes. “Some of them are important in the way that the disease responds to therapy,” said Gray. The team intends to build computer algorithms to predict how best to manage the disease as it progresses.

This isn’t the only partnership between a technology company and medical institution; Illumina and Life Technologies Corp recently announced rival Boston-based clinical genomics initiatives.

“Our joint team plans to do research not only into the mutations but also the ‘circuitry’ that enables malignant cells to spread,” Intel’s general manager for health care Eric Dishman, noted in a blog post. “The ultimate hope here is to learn how, for a specific individual, this circuitry can be “turned off” to stop the spread of cancer cells.”

Dishman, recently had his genome sequenced when recovering from a kidney transplant.

“It, too, took weeks of computing and then months upon months of analysis to make sense of my own unique case,” he concluded. “Today, these tools are too slow, too expensive and too rare—I want to make sure everyone has access to the kind of customized care that I lucked into.”

Curious to learn more? We’ll be inviting world leading geneticists to delve into the tricky, ethical issues at HealthBeat, our health care conference on May 20 & 21 in San Francisco. 

Scientific researcher image via Shutterstock

Digital health incubator Rock Health released data today that shows an increase in funding for med-tech startups in the first quarter of 2013.

Thirty-seven health deals were valued at a total of $365 million, which is 35 percent higher than the first quarter of 2012, “suggesting that 2013 will be another record year for the digital health industry,” the blog post reads.

Rock Health cofounder Halle Tecco said the uptick in venture investment was matched by several acquisitions, including UnitedHealth Group’s buy-up of Humedica (a deal that was reportedly valued in the hundreds of millions). “The players seem to be especially heating up their M&A engines,” she said.

According to Rock Health, the largest and most notable deals of the quarter include:

• Healthcare data warehousing provider HealthCatalyst raised $41 million from Kaiser Permanente Ventures, Norwest Venture Partners, and Sequoia Capital
• Audax Health, led by a 23-year-old college dropout, raised $21 million from former Apple CEO John Sculley
• Kareo raised a $20.5 million sixth round to build out its medical office software
• Mobile health company PatientSafe Solutions raised a $20 million third round from Merck Global Health Innovation

What’s coming up in 2013? Tecco predicts a booming demand for wearable devices from companies like Jawbone, Misfit Wearables, MC10, and Basis. She said Fitbit has been shopping for a $30 million round, which was leaked to the press, but to her knowledge, the deal has not yet closed.

Remote patient monitoring is another rapidly-growing digital health market, which increased to $10.6 billion last year, according to a report by Kalorama Information. Rock Health points to a handful of startups that received funding this quarter, including Bam Labs, a sleep monitoring device placed under a mattress to detect movement and heart rate, and Independa, an independent living solution for the elderly.

Other areas to watch include personalized health and cloud-based electronic health records. On the other hand, bio-tech and medical device entrepreneurs are struggling to gain investment due to complex regulatory issues. Read more on Rock Health’s research here.

Asadi is the founder and CEO of Bina, a healthcare startup working to make ‘personalized medicine’ a reality. Bina applies big data analytics to genomics, making it possible to sequence the human genome in a matter of hours rather than days or weeks.

Today, Bina launched its commercial product. The platform provides physicians, clinicians, and researchers with a detailed picture of a patient’s health. From there, they can make data-driven diagnoses and prescribe individualized courses of treatment.

“Medicine today is very experimental,” said founder and CEO Narges Bani Asadi in an interview with VentureBeat. “Before, there was a bottle neck to crunch the massive amount of genomic data. At Bina, we have created the fastest, most highly accurate, cost-efficient processing solution available in the market today. The next step is to incorporate this genomic data into medical use. Data-driven, information-based medicine is much more targeted. Personalizing therapies for different diseases means a longer and healthier quality of life for all humans.”

There are thousands of genetic disorders. In 2013, over 580,000 Americans are expected to die of cancer. One in 20 babies born in the U.S. is admitted into the neonatal intensive care unit, and 20 percent of infant deaths result from congenital or chromosomal defects. Technology can be used to curb these terrifying trends. Bina’s role is to bridge the gap between DNA sequencing technology and the diagnosticians and clinicians who can apply it to their practice.

“The study of genomics has largely been a research activity done in medical schools and universities,” said Mark Sutherland, Bina’s senior vice president of business development. “They could only look at a few samples at a time because it was too expensive or complicated to do it at scale. There is a tidal wave of data that has not been manageable or in a format physicians can understand. Now we are seeing an inflection point. Sequencing is a powerful way of looking across a broad spectrum to provide insight into the cause of certain diseases and conduct risk assessments, early detection, or predict the possibility of recurrence. It can also be used to find applicable therapies and customize treatments.”

Asadi said her team had to achieve innovations in every step of genetic processing in order to create a scaleable, marketable, effective solution. Bina’s platform includes a hardware box to collect DNA, advanced software to process the data, and applications to turn the data into actionable form. Whereas before a full genetic analysis took weeks or months and could cost thousands of dollars, Bina turns it around within hours for around $200 a sample.

The technology emerged out of Asadi’s PhD work at Stanford. She collaborated with professors from around the world to apply high performance computing and computer architecture to gain a new understanding of human health and disease. Bina was founded in 2011 by three professors from the University of California at Berkeley and Stanford. It is backed by venture funding, and pilot customers include the Stanford Genetics Department and Palo Alto Veteran Affairs Hospital.

Startups don’t often set out to cure cancer or prevent infant mortality. However, as technology continues to evolve and along with it, the healthcare industry, a medical system where diagnoses and treatments are based on hard data, where each and every individual is treated  as such, could be on the horizon.

Read a VentureBeat guest post by Dr. Asadi: The personalized medicine revolution is almost here.

[To learn more about the most transformative IT trends hitting health care, including big data, consider coming to HealthBeat, our event for health care executives and decision-makers, on May 20-21 in San Francisco.]

Photo credit: Shutterstock

Narges Bani Asadi is a founder and CEO of Bina Technologies. 

We are at the dawn of a new age of personalized medicine.

Just as Moore’s law transformed computing – and, as a result, all aspects of our professional and personal lives — so, too, will the interpretation of the human genome transform medicine. We are moving from the inefficient and experimental medicine of today towards the data-driven medicine of tomorrow. Soon, diagnosis, prognosis, treatment, and most importantly, prevention will be tailored to individuals’ genetic and phenotypic information.

As we enter the second decade of the 21st century, investments in molecular biology, bioinformatics, disease management and the unraveling of the human genome are all finally bearing fruit. Personalized medicine promises to revolutionize the practice of medicine, transform the global healthcare industry, and ultimately lead to longer and healthier lives.

The urgent need for personalized medicine

The need for personalized therapies abound, as a recent WSJ article emphasizes. Right now, two of the immediate applications for personalized medicine are cancer diagnostics and newborn screening.

This year, over 580,000 Americans – 1,600 people per day – are expected to die of cancer. Similarly grim numbers can be found with newborn medical care: One in 20 babies born in the U.S. are admitted to the neonatal intensive care unit (NICU), and 20 percent of infant deaths are a result of congenital or chromosomal defects.

Both of these trends can be fixed with the rise of personalized medicine, which is a classic technology-based transformation. The digital information age was made possible by fundamental advances in semiconductor technology, which in turn drove down computing costs. Processing speeds have continually doubled every two years and applications have long since exploded, making the trend ubiquitous.

With DNA sequencing, technology advances are happening even more rapidly. Processing power is doubling every six months, and decreasing costs and increasing speeds have made it far easier to discover links between DNA sequence variations and human disease.

Several key things need to happen in order for us to make major headway, however.  The collection, processing, and storing of molecular information will become a new and significant driver of demand for information technology. While publicity helps spur investment and capture the public imagination, the underlying science behind personalized medicine is what will ultimately allow us to make good a long-held promise.

This TIME magazine cover from a few weeks ago articulates the enthusiasm with which we have taken up the mantle of genome-driven therapy — but it’s nothing new.

Supporters have been talking about the promise of DNA for a long time. Check out this TIME cover from 1971, or this one from 2003. Cost and complexity have been the biggest bottlenecks in the process so far, but we are closer now than we have ever been to harnessing the power of DNA-based therapies.

Here are the key technological and medical advances that we believe need to happen if the vision of personalized medicine is to hold true.

Ultrafast, accurate and low-cost DNA sequencing

Ever since the $3 billion, 13-year Human Genome Project jump-started a new industry in 1990, we have seen a revolution in DNA sequencing throughput and cost. Moore’s law is nowhere on display as clearly as it is in the sequencing market.

Recent innovations in sequencing technologies have dramatically cut the time it takes to work through an entire genome to less than twenty-four hours. Today’s sequencing instruments not only perform the chemistry of sequencing, but they also perform the initial conversion to raw sequenced data, a process commonly known as primary analysis.

Additionally, today’s sequencing instruments dramatically lowered the cost of sequencing to within $5,000 per genome.  In fact the cost of sequencing is no longer prohibitive and many U.S. citizens have said they would be willing to pay out-of-pocket for whole-genome sequencing (WGS).  The key breakthrough here is being able to have entire genomes sequenced in under a few hours and at affordable rates.

But the minimum threshold is practically here: We’re very close to sequencing an entire human genome forty times over in less than a day, with an error rate of less than one in a million in the raw reads. This is why people are excited about personalized medicine. We’re at an inflection point.

Estimated arrival date: Immediately
Companies to watch: Illumina, Life Technologies, PacBio, Oxford Nanopore, Complete Genomics

Rapid, low-cost, and accurate secondary analysis

Elaine Mardis, Director of the Genome Institute at Washington University once mused that while the cost of genome sequencing has plummeted, the cost of the subsequent data analysis has not kept pace. The challenge is threefold: Analysis needs to be fast, cheap, and most importantly, accurate.

Once a genome is sequenced, it must be assembled into a complete genome. This assembly, commonly known as secondary analysis, is typically done using supercomputers and takes several days to complete. During secondary analysis, raw reads are assembled to form a complete genome, allowing scientists to from a complete picture of an individual’s genetic variations.

Imagine putting together a jigsaw puzzle that has a billion pieces. That’s exactly what secondary analysis does.

Because this step requires a supercomputer, infrastructure, and trained bioinformaticians, the costs for secondary analysis are significant. When you factor in the cost of the supercomputers, the supporting physical infrastructure, the system administrators and the bioinformaticians, secondary analysis can reach into the $10,000’s per genome analyzed.

Fortunately there are emerging disruptive technologies that are able to take raw reads off sequencing machines and assemble finished genomes more quickly and at scale.  The key breakthrough here is being able to assemble a complete genome in under a few hours, with high accuracy, and at low cost. 

And then there’s the data question. While sequencing a single genome creates terabytes of raw data, data from assembled genome that has gone through secondary analysis cuts that data a thousandfold to merely gigabytes.

As a result, secondary analysis is also the area in which big data, high-performance computing, and genomics really start to overlap. Recent innovations in the former two categories are what make secondary analysis possible in four hours or less.

Estimated arrival date: 3-6 months
Companies to watch: Bina Technologies, DNAnexus, RealTime Genomics, Broad Institute, Academic Institutions

Connecting the dots between genetic mutations and disease

Completed genomes and their identified genotype then need to be interpreted for biological relevance. This step is commonly called tertiary analysis. This is where a certain mutation (or set of mutations) is matched with a certain disease or physical trait (phenotype).

In a genome of a billion bases, it is estimated that each one of us has roughly 10 million  single nucleotide variants (SNVs). Each SNV alone or in combination can have negligible to extraordinary effects on our normal biological function. The challenge is to find those SNV’s that have an impact on biological function and then prescribe a treatment strategy.  It’s like looking for a needle in a haystack.

This is a big data problem. To make matters worse, there are no standard processes for how this analysis needs to happen. Establishing a standard process and putting some real horsepower behind it will make it possible to perform effective, timely tertiary analysis.

Essentially, we have to create software tools  to enable scientists and clinicians to extract maximum biological meaning from complex genomic data (think: Palantir for genomics). The key breakthrough here is the ability to identify specific disease phenotypes that are linked to specific genotypes — connecting specific mutations to specific markers — in a repeatable way.

Up until now the majority of genomics variations have remained uninterpreted and the so-called look-up table that links our genetic variations to actionable information has been very sparse.

This is a chicken and egg problem. We need to sequence more genomes and put them in the context of disease population studies to learn more. The good news is the unveiling of several very large scale genomics projects — including the Million Veteran Program and the UK’s 100K Genome Project – provide massive new datasets for discovering and building ever-growing knowledge of genome interpretation.

Whoever puts the power of tertiary analysis into the hands of those who need it most will be in a very strategic position to capitalize on the multi-billion dollar opportunity that personalized medicine ultimately represents. This is about creating an industry standard.

The payoff? These toolsets can be used to support clinical trials and develop comprehensive genetic test panels, which in turn make medical interpretation possible.

Estimated arrival date: 6-18 months
Companies to watch: Bina Technologies, NextBio, Ingenuity, Knome, Station X

Injecting genetic information into medical care

Now that you have theoretically sequenced the patient’s genome, and identified the list of candidate mutations, the next step is to combine this knowledge with other medical factors — the patient’s history, environment, family background, microbiome, diet, etc. Improving patient care and developing personalized therapies depends on intelligently leveraging complex molecular and clinical data from a variety of internal, external, and public sources. The key innovation at this juncture is mainly cultural.

Genomic data needs to be integrated with patient health records so that it can be interpreted by trained physicians who can put genomic insights in wider context. The goal is nothing less than redefining disease at the molecular level and integrating this data with patient histories.

The end result? Clinical researchers can translate novel biomarkers and drug responses into improved treatments, which in turn can be tailored to each patient’s genome.

The challenges here are several. Again, there are no standard protocols for pulling this information together in a common environment. Today, too many databases exist in isolation and are not cross-mineable. Even basic availability is an issue, not to mention structure, formatting, and method of data delivery. There will need to be a lot of integration before we’re able to put all of the information at a researcher’s fingertips simultaneously.

More importantly, today’s physicians are not yet widely trained to interpret genomic information. Fortunately, this is a problem that can be solved with education and profitability.

Roughly 100 years ago, a new disruptive technology brought about a new discipline of medicine: radiology.  As radiology matured, the x-ray film became a standard, as did its underlying formats. Before long, radiology data had become part of the patient record and medical schools started introducing radiology as part of their physician training program.

The same must happen with genomics data, which must be standardized before it is effectively utilized. The practice of medicine must likewise introduce new training methods to prepare the next generation of doctors to leverage genomics.

As such, we quickly move from investigating the genome and researching disease  to actually developing diagnostics and insights into therapies.

Accordingly, regulatory approval will be necessary for any such resulting therapy — a further but ultimately surmountable hurdle.

Estimated arrival date: 12-36 months
Companies to watch: 23andMe, InVitae, Personalis

Getting the big guys to pay for it

The final step in making personalized medicine a reality is implementation. The practice of healthcare should change dramatically as new therapies and approaches redefine the roles of hospitals and physicians.

The hurdle here is one of creating favorable economics, which can cement whole genome sequencing (WGS) as a standard of care. Payors and medical insurers have to include WGS as part of their reimbursement program.

We’re already beginning to see the benefits of genome sequencing in public health. The widely publicized account of Nic Volker’s recovery in 2011 captured the public’s imagination in a way that genomics had  never done before.

Numerous scholarly articles are trickling in, touting the benefits of WGS and how it can cut healthcare costs and improve outcomes. As these cases become the norm rather than the exception, insurance companies will inevitably be forced to pick up the tab.

Recently Wellpoint, one of the nation’s largest payors, has hinted that it will approve reimbursements for Sequenom’s MaterniT21 Plus fetal genetic screening tests. Anthem Blue Cross has agreed to reimburse AlloMap’s genetic testing in Stable Heart Transplant Patients  — a big step. Even lab testing giants LabCorp and Quest Diagnostics have been openly bullish on the genomics revolution and have signed numerous partnership agreements with innovative genomics companies.

Payors and providers will likely rely on molecular information to manage scarce healthcare resources. The second major impact will arise from incorporating molecular information into drug discovery and development.

The blockbuster drug model will be redefined. Disparate disorders could actually be caused by similar molecular mutations, so drugs that have a common molecular target but appear to treat seemingly disparate diseases will emerge. Perhaps the most significant impact will come from the rise of synthetic biology, the process of directly manipulating, engineering, and manufacturing cells. Synthetic biology will redefine how researchers study disease and test drugs during preclinical development.

Big payors and pharma companies will be properly motivated by both new profits and major cost savings. It is reasonable to expect that personalized medicine will be a dominant conversation on a national stage, as outcomes dramatically  improve and personalized medicine becomes the locus of medical innovation for a decade or more.

Estimated arrival date: 24-48 months
Companies to watch: Kaiser, VA Hospital, Merck, GSK, Genomic Health, Genentech, Lab Corp, Quest Diagnostics, Roche

The revolution is coming

Here’s a simple chart spelling out the phases of escalation as the genomics landscape matures and draws closer  to realizing our long-held vision of personalized medicine.

It should be pointed out that sequencing — the term most familiar to an everyday consumer — is no longer the locus of innovation. That’s a good thing.

That sequencing has evolved to the point it is at today is nothing less than extraordinary. Sequencing is suddenly cheap, and fast. As a result, sequencing will soon be a commodity however, and the amount of genomic data on our hand is about to multiply by an order of magnitude.

Talent and investment dollars have already started to flow downstream in an effort to address the challenges that cheap and fast sequencing has itself created — namely, taking piles upon piles of data and deriving insights from that pipeline raw material .

There’s a huge opportunity right now, again, at the intersection of high-performance computing, big data, and genomics. I am eager to see these worlds continue to collide, and at increasing speed and frequency. Personalized medicine is closer than you think, but only as a multidisciplinary approach takes hold.

Narges Bani Asadi is a founder and CEO of Bina Technologies. Bina is working to commercialize years of multidisciplinary research at the intersection of systems biology, big data, high performance computing, and genomics. Narges holds a Masters and a Ph.D in Electrical Engineering from Stanford University.

The cost of sequencing the human genome has plummeted. But how will this benefit doctors and patients?

Biomedical researchers hope to harness data about the human gene pool to usher a new era of “personalized medicine,” which could lead to a highly targeted treatment of disease.

Syapse is a Palo Alto, Calif.-based startup that claims to be one of the largest repositories of human molecular profiles. It has raised $3 million today.

The startup is on a mission to bring human genetic data out of the lab, and into the hands of doctors. ”Health care traditionally has been a field of observational science,” said CEO Glenn Winokur in an interview. “With the advent of being able to measure more complex components of the human body through sequencing, we are able to have more precise diagnosis and treatment.

“Many feel this [personalized or precision medicine] is the future of health care,” he continued, but revealed that the problem is “very challenging” as the data is “new, voluminous, and complex.”

The Social+Capital Partnership led the first round of funding. It’s a venture fund launched by a former vice president at Facebook, Chamath Palihapitiya, who will join Syapse’s board.

Syapse is one of a growing number of Silicon Valley startups that seek to remove some of the guesswork out of medicine.

Randy Scott, a cofounder and CEO of InVitae, said he is working with Syapse on a shared goal of “bringing genomics into everyday clinical practice to truly enable personalized medicine.” Syapse provides the software infrastructure to “connect genomic and clinical information across millions of individuals,” he said in a statement.

Scott is the former CEO of Genomic Health and is an important figure in the genomics sector. He has poured his personal resources into the creation of a dream diagnostic test to help geneticists look broadly for rare, inherited genetic disorders.

Related: Read about the efforts of genome entrepreneurs to sequence the DNA of millions of people, and learn more about the human gene pool.

Syapse is currently sequencing 3,000 patient genomes per quarter. It is working with laboratories and clinics using the latest sequencing technologies to diagnose and treat patients. Customers include Foundation Medicine and Genapsys.

Its flagship cloud-based technology, launched last summer, finds use from labs and companies as a way to deliver diagnostic reports. It generates a full report for physicians, which Syapse electronically delivers.

Winokur said by email that the funding will help expand the team, primarily in the hiring software developers. He also hinted at an additional product, which will be geared at delivering “genomics based solutions” to select hospitals, meaning that patients will someday receive drug therapies based on their individual molecular blueprint.

The company was founded in 2008 at Stanford University by a team of entrepreneurs and software engineers. It an undisclosed angel round, it received $1.6 million. Social+Capital’s limited partners include billionaire philanthropist and entrepreneur Eli Broad, and the Mayo Clinic, among others.

Today, scientists made a major step in cancer research; they identified the underlying genetic cause behind a rare form of carcinoma cancer, chordoma.

This discovery puts the emerging field of genomics on the map, may speed up the drug approval process, and reduces the risks associated with groundbreaking research for venture-funded biotech companies. For genetics researchers, it adds credence to the theory that studying rare cancers may reveal more fundamental aspects of cancer biology that are relevant across all types.

“There is a school of thought that rare cancers tend to be more genetically similar and easier puzzles to solve than more common cancers,” said Josh Sommer, executive director of the Chordoma Foundation.

The Chordoma Foundation, a Durham, North California-based nonprofit, identified a specific genetic risk factor that increases the chances that an individual will develop chordoma. Researchers at University College London, Royal National Orthopedic Hospital, and the Sanger Institute, found that over 95 percent of Caucasian chordoma patients have a variation in the DNA sequence at a site on the T gene.

“Our finding that this variation is associated with a five-fold increase in the risk of developing chordoma is remarkable in cancer genetics,” said Dr. Adrienne Flanagan of UCL, who led the study. “It is a major step forward in our understanding of how chordoma develops and can open the door to the development of an effective, targeted treatment.”

This discovery has only been made possible by recent technological developments in Silicon Valley. As we reported, the cost of sequencing the human genome continues to fall, in part due to a microchip and machine designed by genetics company Life Technologies Corp.

“It’s a repeatable and scaleable model that can rapidly push forward early-stage cancer research for pennies on the dollar,” said Greg Piesco-Putnam, cofounder of Aktana, an analytics technology used by large pharmaceutical companies.

“25 percent of everyone who dies from cancer dies from a rare form of it. Traditionally, these forms of cancer have not been economically feasible to find treatments for. This is a huge step forward in that battle,” Piesco-Putnam explained.

Already, the foundation that uncovered the genetic risk factor has partnered with 23andme. With a spit sample, they provide you with a genetic profile and can determine your risk for developing a common genetic disease. 23andme will provide 50 free kits to chordoma patients as part of an ongoing research study into rare cancers.

Read more about the discovery here.

[Top image credit:  Sofiaworld/Shutterstock]

• Trius Therapeutics raises $30M for new antibiotics (release)
• Genomas gets $1.2M grant for genomic side-effect tests (release)
• Provasculon receives $500K, enters Biogen Idec incubator (VentureWire)
• Animal diagnostics firm Quadraspec aims for $5M round (VentureWire)
• MPM Capital names two executive partners (release)
  

Trius Therapeutics raises $30M for new antibiotics – Trius Therapeutics, a San Diego startup developing new treatments for antibiotic-resistant infections, raised $30 million in a second funding round. Investors included Kleiner, Perkins, Caufield & Byers, FinTech Global Capital, Sofinnova Ventures, Versant Ventures, Interwest Partners and Prism VentureWorks.

Trius said the funding will allow it to push its new treatment, an oxazolidinone antibiotic it calls TR-701, into late-stage human tests. The drug, which is intended for drug-resistant staphylococcus and similar infections, is currently in early-stage, phase I trials. Unlike many other new antibiotics, which must usually be taken intravenously, the Trius drug can be taken as a pill.

Genomas gets $1.2M grant for genomic side-effect tests – Genomas, a Hartford, Conn., personalized-medicine startup, received a $1.2 million small business-innovation grant from the NIH. The grant will fund genetic work aimed at identifying people who are most likely to suffer painful side effects from cholesterol-lowering statin drugs.

Statins — particularly Pfizer’s Lipitor, the best-selling drug on the market today — have built up a formidable reputation based on studies that showed they could prevent fatal heart attacks. More recently, however, critics of the drugs have pointed out that stopping one heart attack requires close to 100 people to take the drugs regularly, putting new attention on statin side effects, which can range from painful muscle aches and weakness to memory loss. The Genomas test is intended to reveal whether an individual patient is likely to experience those nerve and muscle effects, known technically as statin-induced neuromyopathy.

• Adnavance pulls in C$3.7M for molecular diagnostics, names new CEO (release)
• “Personalized medicine” co. Proprius sells to Cypress Bio for up to $75M (release)
• Vaccinex raises $25M in wake of GSK deal for antibody drugs (VentureWire)
• Cianna Medical receives $9M for breast-cancer radiation treatment (release)
• Electron-microscope image provider NanoImaging takes in $1.5M (release)
• CrystalGenomics, ProQuest Investments create JV co. Palkion (release)
• Portico Systems, software maker for insurance plans, raises $7.7M (release)
• Stealthy biotech Affomic takes in $7M (peHUB)

Adnavance pulls in C$3.7M for molecular diagnostics, names new CEO – This item is now a standalone post here.

“Personalized medicine” co. Proprius sells to Cypress Bio for up to $75M – Proprius Pharmaceuticals, a San Diego diagnostics maker, sold itself to publicly traded Cypress Bioscience for up to $75 million in cash. The company’s release is here.

Cypress will pay $37.5 million up front, and another $37.5 million to Proprius shareholders as milestone payments. Proprius licenses and develops drugs and diagnostics for various forms or arthritis. Its most immediate product candidates include tests that aim to predict whether certain individuals will develop rheumatoid arthritis and that monitor patients’ response to methotrexate, a common treatment for RA.

Vaccinex raises $25M in wake of GSK deal for antibody drugs – Rochester, N.Y.-based Vaccinex, a developer of antibody drugs, raised $25 million in an add-on to its second funding round, VentureWire reports. Investors included Teva Pharmaceutical Industries, Pan Atlantic Bank and Trust and individual investors.

Earlier this month, Vaccinex and its partner EUSA Pharma licensed a Vaccinex antibody to GlaxoSmithKline for up to $44 million plus royalties. Vaccinex and EUSA will split any profits from GSK’s potential sales of the drug.

Cianna Medical receives $9M for breast-cancer radiation treatment – Cianna Medical, an Alisa Viejo, Calif., developer of devices for delivering local radiation in breast cancer, raised $9 million in a first funding round. Fog City Fund, Windamere Venture Partners and several private individuals provided the cash.

Cianna, which was spun out of BioLucent when it was acquired by Hologic last year, is working on new devices for brachytherapy, the general term for temporarily implanting radioactive material at the site of a tumor in order to provide localized radiation treatment. The Cianna device is designed to improve upon existing brachytherapy techniques in breast cancer.

Electron-microscope image provider NanoImaging takes in $1.5M – San Diego’s NanoImaging Services, a provider of imaging services involving transmission electron microscopy, raised $1.5 million in a funding round. Merck Capital Ventures led the round. The company specializes in the characterization of large biological molecules such as proteins, which are used in a variety of products such as vaccines and drugs.

CrystalGenomics, ProQuest Investments create new JV, Palkion – Today’s award for most baffling announcement comes courtesy of CrystalGenomics, an Emeryville, Calif.-based U.S. unit of the Korean drug-discovery company CG Pharmaceuticals, and ProQuest Investments, a New Jersey VC firm, who together have formed a joint venture they’re calling Palkion. Their release is here.

What is Palkion going to do? Beats me. Here’s what the release says:

Under this agreement, CrystalGenomics will receive up to $6 million in upfront and initial research funding from Palkion, in addition to development and sales milestone payments of potentially more than $200 million. CrystalGenomics will also initially own 50% of Palkion, Inc. ProQuest will capitalize Palkion with a Series A investment and also provide the management personnel for Palkion. CG will use its unique structure-based drug design capabilities to identify drug candidates while Palkion will oversee the clinical development of novel drug candidates.

So, let’s get this straight. CrystalGenomics and ProQuest form Palkion, in which they’ll hold equal stakes despite the fact that ProQuest seems to be putting all the capital and personnel into the venture. Palkion will then start handing the money to CrystalGenomics, which will continue trying to discover drugs while Palkion “oversees” the process of testing those drugs in people. All clear?

The best I can figure is that this is a roundabout way of putting a more “American” face on a basically Korean startup that — to judge from its Web site and, in fact, this press release — seems to have a certain amount of difficulty communicating clearly with a U.S. audience. That could certainly be a problem if its drugs make it into clinical trials, given how dialogue with the FDA becomes rather crucial at that stage. But that’s just my guess at this point.

Stealthy biotech Affomic takes in $7M – Affomic, a New Haven, Conn., biotech startup so stealthy that it can announce a funding without giving anyone a clue as to what it’s doing, raised $7 million in a first financing round, peHUB reports. Investors included Connecticut Innovations, Elm Street Ventures, and Four Seasons Ventures. It goes without saying that Affomic doesn’t have a Web site — in fact, the startup doesn’t even exist so far as Google is concerned.

As I discussed a few weeks ago with respect to deCODEme — a “personal genomics” service hurriedly launched last November by Iceland’s deCODE Genetics in an apparent attempt to beat 23andMe to market (it succeeded by a day or so) — these sorts of services can awfully dense and difficult to navigate. The deCODEme service appears to be particularly bad in that respect, both in terms of its design and even the underlying science used to justify the genetic information displayed in a demonstration user account.

So it’s a pleasant surprise to report that 23andMe, which over the weekend began allowing people to set up demonstration accounts itself, appears to have made the process of understanding your genetic inheritance about as simple and intuitive as it can probably get. The demo accounts don’t display your own genetic information, of course — instead, they show a profile for the fictional Greg and Lilly Mendel and their immediate relatives. (The family name is inspired by Gregor Mendel, a nineteenth-century monk known as the “father of genetics” for his studies on the inheritance of pea plants; the profile uses actual data from an anonymous European family.)

These sorts of demo accounts are particularly useful given that 23andMe and its competitors are charging customers roughly $1,000 for a genetic analysis, which is a lot to shell out when you don’t have any real idea what you’re getting for your money. To sign up for a 23andMe demo account, click here.

Like all these services — of which there are currently at least four, counting the new DNATraits project launched recently by Family Tree DNA — 23andMe takes a genetic sample (here from having users spit repeatedly into a tube) and checks 600,000 or so individual DNA “letters,” or bases, known to vary between people. After analyzing those letters, the company posts your genetic information on a Web site where you can see what your particular genetic pattern says about inherited traits such as your susceptibility to cancer or heart disease, longevity and even eye and hair color. Not only can you spin through the data in as much or as little detail as you like, you can share it with relatives or friends and search for others with similar traits.

One of the first things a new visitor will see is the clean and uncluttered look of 23andMe’s “gene journal,” which lets you scroll through various genetic traits and then dive in to see how you — well, your Mendel stand-in — fare compared to the population at large. (See a screenshot of Greg Mendel’s gene journal using the thumbnail above and to the left.)

More after the jump:

The contrast with deCODEme couldn’t be more striking. Where the Icelandic service offers minimal data and requires lots of clicking just to see how your genes stack up against those of the general population, 23andMe puts almost all that information out front. Each condition is rated according to the reliability of the data that links particular genetic variations (technically known as “single nucleotide polymorphisms,” or SNPs) — I’ve blown up the ratings in the graphic to the left; click for a larger version — which itself is a big step, since deCODEme appears to limit what it shows customers to the most conservative data available. Yes, it’s always possible that people will misinterpret their disease risk based on sketchy data, but here such mistakes are particularly difficult to make, given that the site deploys simple icons and contant boxed reminders whenever gene-disease links are considered preliminary as opposed to established.

You can also sort disease conditions by the affected region of the body — a feature that actually works here, as opposed to a similar feature at deCODEme when I last beamed in.

The individual disease-information pages open with some general information about the condition, but quickly get to the good stuff (here, I’ve chosen heart attack; click the thumbnail at left for a larger image). The site quickly presents you with your general risk versus that of a comparable population — in this example, European males aged 45-54, although you can adjust those settings via drop-down menus — then outlines the extent to which genes, as opposed to environment, are thought to contribute to the danger of heart attack.

Next — and this struck me as particularly cool — you get a graph of the individual SNPs 23andMe is using to make its calculations, which shows the positive and negative effects of each. Clicking on any particular SNP loads a panel immediately below that describes what’s known about it and lists citations from the scientific literature for more background. I could have sworn that the individual SNPs were also linked to a 23andMe database, allowing you to browse more deeply if you care to, but at the moment, if the disease pages permit that, I can’t find it again. You can click on a “technical report” link to the left in order to see the actual SNPs on which 23andMe bases its finding, but those aren’t linked either.

Fortnately, unlike deCODEme, the 23andMe demo accounts are fully functional. The site’s GenomeExplorer lets you browse through your raw data, either in a graphical format displayed by chromosome or by searching on particular genes or SNPs. The output of such searches doesn’t strike me as terribly useful in its current incarnation, but that will presumably improve as time goes by. Instead, though, you can download “your” genetic data for use in other programs designed to read that format (such as this one). Don’t count on reading it directly without special help, though; I now have a 14MB file of “Greg Mendel’s” data sitting on my hard drive that’s simply too large to open with any common text-editing program.

You can also compare your genetics with others who share their information, although from my perspective, this feature is somewhat disappointing. Comparing Greg Mendel to his daughter, for instance, tells me only that they’re 84.15 percent similar across their entire genomes (at least that portion measured by 23andMe), or that across genes related to a limited number of characteristics — muscle endurance and circadian rhythm, for instance — they’re between 85 percent and 89 percent similar. This is probably more fun if you’re comparing yourself to your friends, assuming you’re open to that sort of thing, but I’m still at a loss as to exactly how this sort of stuff can prove useful.

I’ve sidestepped the entire ancestry section for now, although I’ll try to check back later if I have more time to look at it.

The 23andMe service isn’t without flaws, obviously. In many conditions, it also seems to limit the number of SNPs it reports on, much the same as I found at deCODEme. Heart attack is a prime example, since 23andMe omits the very same SNP strongly correlated with coronary-artery disease — rs1333049 — that I criticized deCODEme for skipping. And as noted above, some of the genetic exploration and comparison tools could probably use work. Overall, though, the service as displayed here is a pretty impressive effort.

But don’t take my word for it: Feel free to check out the 23andMe demo account yourself.

UPDATE: Review completed and rewritten throughout.

UPDATE REDUX: For the technically inclined, physician-turned-DNA enthusiast Ann Turner offers a comparative review of 23andMe and deCODEme over at Eye on DNA. (For what it’s worth, Turner also commented on my earlier deCODEme coverage here.)

Separately, 23andMe product manager Brian Naughton wrote to clarify that while 23andMe doesn’t use the rs1333049 SNP, it does use another SNP in the same chromosomal region that correlates highly (80 to 90 percent in Europeans) with rs1333049.

FURTHER UPDATE: deCODEme replies in comments. I’ll let their missive stand for itself, so take a look and see what you think.

• Compact ultrasound maker Zonare Medical raises $30M (VentureWire)
• TherOx raises $30M for hypersaturated-oxygen devices (peHUB)
• Accumetrics, antiplatelet-drug diagnostic maker, raises $29M (release)
• Population Genetics takes in £3.8M for massively parallel genome studies (GenomeWeb)
• “Brain fitness” trainer Dakim raises $11M (release)
• BioIQ, home-diagnostics maker, takes in $2.5M (release)
• Hospital med-tracker Sabal Medical raises funds (release)
• Seattle’s PharmaIN gets $400K NIH grant for nanoparticle staph drug (PDF release)
• SensiGen, molecular-diagnostics developer, receives Michigan state loan (release)
• Arcus Ventures aims for $50M fund, targets cancer (VentureWire)

Compact ultrasound maker Zonare Medical raises $30M – Zonare Medical Systems, a Mountain View, Calif., maker of ultrasound-imaging systems, raised $30 million in a recent seventh funding round, VentureWire reports. Existing investors provided the funding, a group that includes Frazier Healthcare Ventures, 3i Group, Mosaix Ventures, CB Health Ventures, Draper Fisher Jurvestson, Ascension Health Ventures, Kaiser Permanente Ventures, Earlybird, Saints Capital, Merrill Lynch Venture Capital and Texas Instruments.

The company said the funding should set it on the road to profitability and eventually to a hope-for IPO. Zonare makes compact ultrasound systems that can be used in sonography and for a variety of other medical diagnostic purposes.

TherOx raises $30M for hypersaturated-oxygen devices – TherOx, an Irvine, Calif., maker of oxygenation devices for treating heart attacks, raised $30 million in a tenth funding round, peHUB reports. Investors included Kleiner Perkins, Integral Capital Partners and New Science Ventures.

The startup makes devices that supersaturate blood with oxygen, then infuse that blood into areas of the heart at risk of damage from oxygen starvation due to a heart attack. TherOx has now raised over $120 million in venture funding.

Accumetrics, antiplatelet-drug diagnostic maker, raises $29M – San Diego’s Accumetrics, a maker of diagnostics that measure patient response to anti-platelet drugs, raised $28.8 million in a fourth round of funding. Investors included Arnerich Massena & Associates, BBT Fund, Essex Woodland Health Ventures, RiverVest, PTV Sciences, KB Partners and Kaiser Permanente Ventures.

The startup makes a system that measures how well individuals are reacting to treatment with anti-platelet drugs, which are used to prevent or help dislodge major blood clots. Since patient response can vary widely, often as a result of genetic factors (see our coverage of this sort of “personalized medicine” here), such monitoring can help doctors avoid dangerous overdoses or to switch unresponsive patients to higher doses or different drugs as necessary.

Population Genetics Technologies takes in £3.8M for massively parallel genome studies – Population Genetics Technologies, a U.K. startup devoted to technologies for studying thousands of genomes at once, raised £3.8 million ($5.9 million) in a first funding round, GenomeWeb reported. Investors included Auriga Partners, Noble Fund Managers, and Compass Genetics Investors.

The company raised £1.1 million in seed funding from the Wellcome Trust back in 2005 to aid in the development of the technology. PGT is working on a technique devised by Nobel laureate Sydney Brenner that purports to analyze genetic variation in DNA samples from thousands of individuals at once.

In this 2005 release, PGT co-founder Sam Eletr described the method as “will allow the mixing of thousands of samples in one test tube and the simultaneous interrogation [analysis] of all of them in one experiment, instead of in as many experiments as there are genomes in a population…. We expect our technology to allow handling much larger numbers of genomes than pooling does and to have the further advantage of protecting the identities of individuals involved in any population study by allocating them a code that may be kept confidential. We expect it also be applicable to any collection of DNA molecules and genomes, whether from plants, animals, micro-organisms or humans.”

PGT also named Mel Kronick, a former R&D manager at both Agilent Technologies and Applied Biosystems, as CEO.

For instance, can personal genomics really make money for a startup like 23andMe? (To recap briefly for those joining the show already in progress, the company will scan your genome from a tube of spit you send in, and then post the results on a personal Web page for you to browse for information on your ancestry and disease risks.) The official answer is that no one knows, in part because the field is still remarkably young — just three days old, actually — and partly because 23andMe founders Linda Avey and Anne Wojcicki decline to outline their thinking in much detail. For instance, when I spoke to the co-founders earlier today, Wojcicki insisted that “it’s really too early to specify how we might monetize and derive value from the information we’re aggregating. We’ve thought about a lot of different ways to monetize it, but we’re not ready to talk about them.”

Since virtually no one sinks $8.9 million (what 23andMe raised in its first round) into a startup that lacks even an inkling of a business plan, however, it seems safe to say that the company is simply being circumspect. Here’s my best shot at connecting the dots.

To put it bluntly, the real money is likely to lie in selling corporations — specifically, drug companies — access to the aggregate genetic information 23andMe amasses from its customers. During a Webcast this morning, and again in our interview, Avey and Wojcicki emphasized 23andMe’s plans to conduct large-scale genetic-association studies using the genetic-data database their customers will essentially create. (Talk about your ultimate user-generated content.)

Both 23andMe founders, of course, stress that the company won’t disclose personal information, but that’s not really the point. If the company succeeds in attracting the hundreds of thousands of customers Avey and Wojcicki talk about drawing, it will be sitting on one of the largest genetic databases on Earth. And there’s no opting out of any research studies 23andMe wants to conduct at that point, either, since the consent forms to which customers must agree specifically commit their genome-scan results to future research. From that form:

23andMe Sponsored Research: We may analyze your genetic and other voluntarily contributed personal information as part of our scientific research with the purpose of advancing the field of genetics; your account information will never be associated with this research. We may also analyze your genetic and other contributed personal information for the purpose of reviewing and improving our services and creating new features and services. We may ask you questions and you may choose to give us information about yourself through surveys or other features on our website. Contributed personal information might include age, sex, geographic ancestry and diseases or conditions you have, or have experienced. It is entirely within your discretion to provide information or answer survey questions.

Collaborative Research: 23andMe may enter into partnerships with other organizations—non-profit and/or commercial—that conduct scientific research. Prior to embarking on any such projects, 23andMe will establish a research advisory committee to guide such collaborations. 23andMe may grant researchers associated with partner organizations access to our database of genetic and other contributed personal information after such organizations agree to maintain confidentiality consistent with our privacy policy. External researchers will have access to your genetic and other contributed personal information but they will not have access to your account information (e.g. contact and payment information).

In the Webcast and in our interview, Avey and Wojcicki tended to stress the prospect of academic studies over commercial research. For instance, 23andMe is in discussions with foundations that support work on Parkinson’s disease and autism, in hopes of first attracting large numbers of patients to the service, and then using their data to pin down how genetic differences play a role in each disease.

Still, neither academics nor disease-focused foundations are likely to provide the level of funding that could turn a company like 23andMe from an intriguing curiosity into a commercial powerhouse. Who does have that kind of moolah? Big Pharma and Big Biotech, of course. Recall, for instance, that 23andMe is backed not only by Google, but also by Genentech.

What’s more, pharma/biotechs stand to gain tremendous “value” from studies that help pinpoint which patients are most likely to respond to a particular drug, and which ones are likeliest to suffer serious side effects. (For instance, consider the Big Pharma personalized-medicine coalition we wrote about here, and think how much easier its job would be if it could tap a gene database like the one 23andMe envisions building.) It’s almost as if 23andMe and the drug industry were made for one another — as, perhaps, they were. (Wojcicki is a former biotech investor for a San Francisco hedge fund.)

This, of course, helps explain why Avey and Wojcicki are cagey about their business plans, because people might be a little reluctant to sign up for a service that’s effectively going to turn over their genomes to help Big Pharma make more money. I’m not saying they’d be correct about that — this sort of database could conceivable yield some major health benefits in the form of better-targeted drugs — just that public perceptions of the drug industry are bad enough that dwelling on such partnerships could put a damper on 23andMe’s plans.

This sort of strategy still isn’t a slam dunk, of course. With two other personal-genomics services in business or near to it (Navigenics and DeCode Genetics’ DecodeMe), competition for pharma deals could be fierce. What’s more, the genetic databases alone aren’t much good for these sorts of association studies, as researchers will also need to know more about individuals’ “environmental” circumstances — which include anything from their age and lifestyle habits to their medical and family history. If no one answers the surveys intended to elicit this information, the studies, and the dollars behind them, will dry up in a hurry.

A few other items that emerged from today’s discussions:

• 23andMe’s basic $999 fee covers use of its genome-analysis tools indefinitely — the company doesn’t plan to hit customers up for an annual subscription fee, unlike rival Navigenics. (Except that 23andMe may eventually launch some sort of advanced service that requires a subscription fee.)
• Avey and Wojcicki argue that charging $999 for their service alone would make 23andMe a going concern. At the same time, though, 23andMe is offering “friends and family” a discount of just 15 percent to get a genome scanned “at cost,” which suggests that the gross margin on that service is really not that great.
• Regarding the medical utility of the 23andMe scan, Avey says the company urges anyone concerned by a disease-related finding should re-confirm it with a standard genetic test.
• Apparently 23andMe customers will also have access to a range of additional information that’s not available on the company’s public site. Pointers to genetic counseling will be located there.
• The company is looking into launching some form of genome-related social networking in the future.

So what to make of yesterday’s news that seven major drugmakers are joining academic researchers to study genetic variations that might make patients more susceptible to side effects? At first glance, some of the coverage suggests that the industry is rethinking its passive-aggressive opposition to personalized medicine, thanks in part to a bit of a nudge from the FDA. Take, for instance, this AP story:

Dubbed the International Severe Adverse Events Consortium, the project will use genetic data to try to design safer drugs and to identify patients at risk of dangerous side effects because of a variation in their genetic makeup.

“This is what personalized medicine is really about, finding out for the individual, not just the general population … what their risks are,” said Dr. Janet Woodcock, deputy commissioner for operations at the Food and Drug Administration, which is under growing pressure to ensure drugs are safe. “Up until now we’ve been kind of helpless” in dealing with adverse effects, she said.

Reports of such events are on the rise, jumping 150 percent from 1998 to 2005, a recent study found.

Or this, from the NYT story linked above:

Seven of the largest pharmaceutical companies have formed a group to develop genetic tests to determine which patients would be at risk from dangerous drug side effects.

The new group, the International Serious Adverse Events Consortium, is one of a wave of cooperative research efforts sweeping the drug industry, as companies come under pressure to cut costs and increase their success rates in developing medications. The Food and Drug Administration has encouraged the formation of such groups.

First, this is clearly a worthy effort, no matter how late to the party it might seem. Whatever your feelings about the drug industry, anything that might spare patients from severe drug side effects represents a step forward — not just for those who can avoid dangerous health complications, but also for the people who might be put at risk when a drug that could help them is withdrawn for safety problems that are unlikely to affect them.

Second, though, it’s telling to me that one of the first major industry-wide personalized medicine efforts should focus specifically on rare side effects, since it is exactly these sorts of safety problems that pose the biggest threat to the blockbuster-drug model in the first place, as discussed here. (Put briefly, a blockbuster drug by definition is taken by large numbers of people, for long periods of time, or both, which inevitably increases the chance that safety problems will emerge.) Anything that reduces drug toxicities — specifically serious problems such as heart attacks, stroke or nasty immune reactions — also improves the odds that blockbuster products can stay on the market.

In other words, while it’s great to see the industry tackling its safety problems head-on, this consortium isn’t exactly evidence that Big Pharma (or its Big Biotech counterpart) is any more willing to adopt personalized medicine in a comprehensive way. Sure, maybe we’ll see future consortia start to address the questions of why so many drugs still only seem to work for a fraction of the patients who take them — a step that would, if successful, necessarily result in the narrowing of markets for many of these drugs, even though it would also boost public confidence in drug efficacy. Will biotech/pharma embrace that logic? I’m not holding my breath.

Pharmalot and the WSJ health blog have more.

Spinal-implant maker LDR raises $25M — Austin, Texas-based LDR, a maker of spinal implants, raised $25 million in a third funding round. Investors included Telegraph Hill Partners, Austin Ventures, Rothschild Private Equity and PTV Sciences.

LDR sells spinal-fusion devices, artificial disks and other spine-related devices in more than 30 countries, and plans to use the funds for further expansion.

Aldagen adds $9M for adult stem-cell work — Aldagen, a Durham, N.C., biotech developing regenerative therapies with “adult” stem cells, raised an additional $9 million (PDF link), bringing its third funding round to a total of $23 million. Investors in the additional financing include Tullis-Dickerson, CNF Investments, Harbert Venture Partners and Intersouth Partners.

The company’s most advanced experimental treatment uses stem cells derived from umbilical-cord blood to somehow improve the speed and effectiveness of cord-blood transplants in children, although the company doesn’t explain how. Nor has it revealed the results of an early-stage human test. Other treatments now entering clinical trials use stem or related progenitor cells isolated from a patient’s own bone marrow to treat heart failure or clot-related oxygen deprivation in the limbs.

The Triangle Business Journal has more.

ThromboVision raises $4M for personalized-medicine diagnostics — The Houston, Texas, biotech ThromboVision said it raised $4 million in a first funding round. Investors included the private-equity firm National Healthcare Services and private investors.

ThromboVision is developing new tests of platelet activity that may help doctors determine which patients are most likely to respond to low doses of blood thinners such as aspirin or Plavix, which are used to prevent clots that can cause heart attacks or strokes. This is similar — in concept, at least — to the FDA’s recent push to require the use of genomic tests to determine the proper dosing of warfarin, another blood thinner. (See our coverage here.)

MachLabs launches two device companies — MachLabs, a Redwood City, Calif., investor partnership founded by entrepreneurs Michael Laufer and John Lonergan, recently launched two medical-device startups, VentureWire reports (subscription required). Lyten is developing a minimally invasive treatment for obesity, while Permatox hopes to introduce a non-invasive alternative to Botox.

TeleMedicine Clinic receives €7M for radiology services — Barcelona-based TeleMedicine Clinic, a center for the outsourced analysis of medical images such as X-rays and MRIs, raised €7 million ($9.7 million), VentureWire reports. Investors included Kennet Partners, Active Capital Partners and an undisclosed European seed investor.

Featured companies: Clinical Data, Epidauros Biotechnologie, Precision Therapeutics, UMD, Zars Pharma

UMD to close $8M for menstrual pain and osteoporosis — Cincinnati’s UMD, a developer of vaginal drug-delivery technologies, expects to close up to $8 million in a fifth funding round, VentureWire reports (subscription required). The company has backing from an undisclosed new investor, and expects former investors Charter Life Sciences and Asset Management to join the round.

UMD is developing a new version of an off-patent anti-inflammatory drug called ketorolac that can be administered on the end of a tampon for menstrual pain, and hopes to begin mid-stage human tests this year. It plans a similar delivery formulation for the active ingredient in Merck’s osteoporosis drug Fosamax, which loses patent protection this year. The company doesn’t have a Web site.

Precision Therapeutics aims to raise $81M in IPO for personalized cancer tests — Pittsburgh’s Precision Therapeutics, a developer of diagnostic tests that aim to predict patient response to chemotherapy, filed to raise $80.5 million in an initial offering. The company’s tests use biopsied tumor cells to assess the likelihood that a given drug or drug combination will be effective.

This is a fairly low-tech sort of diagnostic — as its filing makes clear, Precision basically just removes tumor cells and then starts hitting them with various drugs in the laboratory to see whether they live or die. The company has only been marketing its current test, which it calls ChemoFx, for the last year or so; although it has had ChemoFx on the market since 1997, it ceased sales activity in 2003 and didn’t resume it until last year. Revenues have been predictably anemic, as until recently Precision didn’t have an active sales force, and last year the company managed the feat of posting a gross loss, in which its cost of sales in terms of lab expenses exceeded incoming revenue.

There’s other bad news, too. Precision notes that two respected organizations — the technology-evaluation center of the Blue Cross and Blue Shield Association and a working group of the American Society of Clinical Oncology — concluded in 2004 that “chemosensitivity/chemoresistance assays” such as ChemoFx lacked supporting data that would justify their routine use.

The company also parses several complex reimbursement decisions in a fairly convincing illustration of the risk that relatively few insurers may actually want to pay for its test. It further notes that clinical data supporting use of its test is “limited,” and although it cites the results of three studies carried out between 2002 and 2006, none of them look particularly convincing. In one of the few bright spots in its filing, Precision says it is currently conducting five additional studies, some of which appear to be fairly rigorous “prospective” studies of the diagnostic.

Zars Pharma sets IPO price target — Zars Pharma, a Salt Lake City specialty pharmaceutical company that reformulates pain drugs for delivery via skin patches, set a price range for its IPO and now seeks to raise as much as $92 million in the offering. (See our previous coverage here; the company has apparently changed its name to “Zars Pharma” from “Zars.”) The company plans to offer up to 5.75 million shares at a price of $14 to $16 apiece.

Clinical Data acquires Epidauros Biotechnologie for $11.8M — Clinical Data, a publicly traded diagnostics and personalized-medicine company in Newton, Mass., agreed to pay $11.84 million (€8.75 million) to acquire Epidauros Biotechnologie of Germany. Founded in 1997, Epidauros studies genetic factors that may determine how individuals respond to drugs.

UPDATE (11am PT on Sunday, 8/26/07): Added Clinical Data/Epidauros item.

Personalized medicine — the idea that doctors will one day tailor your medical care based on your genetic profile — has been a long time coming, as I’ve previously written. As it turns out, that’s no fault of the Food and Drug Administration, which has emerged as one of the biggest fans of the concept. Yet the FDA is now pushing ahead with efforts to pair drugs with genetic tests in a way that has alarmed critics, who claim the agency is forging well ahead of the medical evidence, as the WSJ’s Anna Wilde Mathews reports today.

The current controversy involves warfarin, a one-time rat poison now commonly used as an anticoagulant designed to prevent dangerous blood clots from forming. The generic drug was prescribed more than 30 million times last year, but because it can sometimes cause patients to bleed excessively, it also frequently sends people to the emergency room — 43,000 times a year, by one estimate, making warfarin the second-most dangerous drug after insulin.

Roughly a decade ago, evidence began to emerge that genetic differences between patients might explain why some people were more likely to experience bleeding on the drug. In particular, researchers identified two genes that seemed to play a major role in modulating warfarin’s effects. Some variants of the gene CYP2C9, for instance, appeared responsible for breaking down the drug more slowly, meaning that it tended to linger in the blood, effectively mimicking the effects of a higher dose. Variations in another gene, VKORC1, affect how the body processes vitamin K — a crucial finding because warfarin’s activity depends in part on its ability to interfere with vitamin K.

The FDA concluded that patients with some of these genetic variations should probably receive lower initial doses of warfarin — which is exactly the sort of thing personalized medicine is supposed to do. Today, the WSJ reports, the FDA is scheduled to announce changes to the warfarin label that urges lower doses for patients based on their genetics, albeit with a variety of caveats.

Many doctors, however, think the FDA has moved too fast. The genetic tests, which cost between $300 and $500, are covered by Medicare but not many private insurers, and doctors fear that patients who don’t get them and end up with bleeding problems may sue. It also takes time to get results from genetic testing, meaning that doctors aren’t necessarily any better informed when starting patients on warfarin, often following a heart attack, a stroke, or another blood-clot-related problem.

Adding fuel to the fire is the fact that the link between the genetic variations and better patient outcomes hasn’t been fully established by the field’s gold standard of evidence, a prospective randomized, controlled clinical trial. So one of the fascinating aspects of this story is that it pits two of medicine’s emerging trends — personalized medicine and evidence-based medicine (see our coverage here) — directly against each other.

Has the FDA acted precipitously, or is it pushing forward where other parts of the medical establishment fear to tread? Feel free to give us your take in comments.

UPDATE: The FDA statement is now available here (hat tip: Pharmalot).

For at least a decade, biotech futurists have been predicting that the genomics revolution will lead to medical treatments tailored to the genetic quirks of individuals. And for at least as long, we’ve all been waiting for evidence that this “personalized medicine” revolution is coming to pass.

On Monday, the field took a baby step forward when the FDA approved Selzentry, a new AIDS drug from Pfizer. Selzentry is unique in a number of ways — for instance, it’s the first drug that tries to “lock down” T-cells to prevent HIV (that’s the culprit, above and to the left) from entering and infecting them. Fuzeon, a less-than-successful drug from Roche and Trimeris, does something similar, although it works to gum up HIV’s “landing gear,” not the T-cell’s docking port.

But the particularly interesting thing about Selzentry is that it only works against a particular sub-strain of HIV — those that dock to a T-cell surface protein called CCR5 in order to invade. (Most HIV strains use another protein called CXCR4 or a combination of the two.) That means would-be Selzentry users first have to be tested to ensure that their HIV strain will respond to the drug. And that, in turn, makes Selzentry one of the first drugs to be paired with a diagnostic test that limits the number of people who can try it, but which also greatly enhances the odds that it will work in those who do.

That test, offered by Monogram Biosciences, requires “amplifying” the HIV genome in the lab, producing scads of genetically identical viruses that are used to infect cultures of T-cells that lack either CCR5 or CXCR4. When infection occurs, a transplanted gene in the cell cultures begins to produce fluorescent proteins, making it easy to tell whether the viral strain is CCR5-specific. (There’s more info in this Monogram press release.)

Of course, Selzentry — generically known as maraviroc — most likely wouldn’t appear to work at all if tested in a general population, which helps explain why Pfizer was willing to pair it with a diagnostic. Genentech’s breast-cancer drug Herceptin — long the sole poster-child for the nascent field of personalized medicine — likely would have gone the same way had researchers not realized that it appeared to work particularly well in an identifiable subset of tumors.

So far, however, there aren’t too many other similar personalized treatments out there, or even in development. One exception is the beta blocker bucindolol being developed by Arca Discovery, which aims to test the drug in patients who have specific genetic variants; I wrote about them here.

Why aren’t there more? The simplest explanation is that most drug developers, whether pharma companies or biotechs, don’t want to risk circumscribing their patient population unless they have to, since doing so by definition limits the potential sales of a new drug. Up to now, drug makers haven’t really faced much economic pressure to embrace personalized medicine, or “pharmacogenomics,” as it’s technically known. With pipelines drying up and the patent environment getting a lot harsher for the me-too drugs drug giants have long relied on, however, they may soon have little choice.

(Brief aside: Pharmacogenomics, of course, is also the answer to the oft-touted assertion that me-too drugs — meaning a variety of drugs that all target the same biological mechanism, such as the half-dozen statins approved to lower cholesterol — aren’t the waste that drug-industry critics often assert. This argument holds that patients who, for instance, don’t respond to one statin might actually benefit from a different one. The short and simple response is, Where’s the proof? If the makers of statins, or of the depressants known as SSRIs, really want to know which patients their drugs work best in, it’s certainly within their ability to find out. The fact that no one is conducting such tests tells you quite a bit of what you need to know about decision-making in the drug industry.)

UPDATE: Apropos of nothing, I just stumbled across this Reuters story describing a Royal Society report on personalized medicine. The bottom line:

“Personalized medicines show promise but they have undoubtedly been over-hyped,” said David Weatherall, who chairs the working group that produced the report.

UPDATE REDUX: For more on the FDA’s big push behind personalized medicine, see this more recent post.