Pathway Genomics is preparing to offer breast cancer screening including BRCA1/2
By Chris Chan

Advocates for breast cancer patients are ecstatic about the Supreme Court ruling that ended a patent on genetic screening tests for a breast cancer gene.

Now San Diego company Pathway Genomics is preparing to offer a more affordable test to patients. Angelina Jolie tested positive for a genetic mutation that makes breast and ovarian cancer extremely likely. And after the Supreme Court ruled that DNA tests for those mutations cannot be patented, testing will get cheaper.

That’s good news for cancer victim advocates who worry about women who are uninsured.

“These tests, these lifesaving tests will be much more affordable for all of us regardless of how much money is in your pocket.” said Laura Farmer Sherman from the Susan G. Komen chapter in San Diego.

The company Myriad Genetics held the patent for testing on what’s called the BRCA1 and BRCA2 genes, and charged any-where between $3,000-7,000.

After the Supreme Court ruling, local company Pathway Genomics announced that it will offer tests on those genes, and others will likely follow.

“It will result in other laboratories that have the capability of Pathway to offer these tests at a substantially lower price point,” said Jim Plante, the Pathway Genomics Founder and CEO.

Pathway Genomics would not say how much it will charge but promises it will be much less than $3,000. With an estimated 40,000 people expected to die of breast cancer this year, Pathway Genomics hopes the effects of cheaper genetic testing will beprofound.

“It could potentially save tens of thousands, if not hundreds of thousands of lives, said Plante.

Fact: America’s Finest City is the DNA sequencing capital of the world. (Who knew?)
BY TOM YORK

When San Diegan Brad Lally turned 45 last year, he decided his approaching middle age was the time to get a better handle on his health and fitness.

“I wanted to learn more about myself, and specifically, more about my body,” says the global development manager for a local scuba diving equipment company.

So Lally turned to cardiologist Samir Damani, who runs MD Revolution in La Jolla, a 21st-century medical practice specializing in genetic counseling.

Damani closely examined data from Lally’s DNA to see what genetic factors might impact his health, and set up a diet and exercise plan that fit his profile, as well as what he needs to look out for, such as various cancers and cardiovascular diseases.

“This is the way that medicine is going to be practiced in the future,” said Dr. Damani, who does take insurance and the cost of the programs is customized to the individuals’ needs.

DNA’s now big business, to say the least, and the concentration of both basic research and commercialization of that research has made San Diego the DNA capital of the world.

The region becoming the hub of the lucrative activity surrounding DNA, from research to manufacturing to patient care in the doctor’s office, should come as no surprise to local residents.

Indeed, BIOCOM, the local life sciences trade group, says the life sciences sector (which includes all the activity surrounding DNA R&D) accounts for more than 106,000 direct and indirect jobs, and pumps more than $12 billion annually into the local economy.

It all starts with research, which is where San Diego has a notable leg up on the rest of the planet.

San Diego serves as the home base for DNA pioneer Craig Venter, who was the first to sequence the human genome back in 2001, beating the lumbering Human Genome Project to the punch.

The rugged, 60-something Venter heads the eponymous nonprofit J. Craig Venter Institute, with 300 employees in La Jolla (and Rockville, Maryland), which will be moving its local operations to a more expansive 45,000-square-foot laboratory on the UCSD campus when construction is completed in 2013.

It’s become one of the go-to places for the latest research into the mysteries of the human genome.

Venter is also CEO at Synthetic Genomics Inc., the La Jolla-based privately held startup that is trying to create synthetic genes that can be put into industrial production to make such things as biofuels.

But that’s just the beginning.

Public company Illumina, Inc. is one of the global giants of the burgeoning DNA sequencing industry.

The San Diego company’s HiSeq brand machines have proven popular with government and academic research scientists as well as with commercial researchers, such as those in the pharmaceutical industry, and the company is working in a number of areas ranging from domestic plant research to farm animals.

The company is locked in a head-to-head market battle with Carlsbad-based Life Technologies Corporation for low-end ($125,000 or less) tabletop machines that can sequence important portions of a genome.

Life Technologies says it will start shipping its low-end sequencing competition later this year, which means that small clinics and laboratories will be able to afford such devices.

Indeed, such price drops puts the technology within reach of just about anyone who wants to know what they’re made of, at least big chunks of it.

Privately held BioNanomatrix Inc., which moved to San Diego from Philadelphia last year, has been on a five-year quest for the Holy Grail of genomics research: the ability to sequence the human genome for $100 or less in eight hours or less.

The company was on Technology Review magazine’s 2009 list of 10 emerging technologies that promise to change the way we live and do business.

Damani takes saliva samples from his inquisitive patients like Lally and sends them to one of two genetic testing laboratories he’s working with, Sorrento Valley’s Pathway Genomics Corporation, launched in 2009, or La Jolla’s Cypher Genomics Inc., spun off from the Scripps Health system last year.

The two labs then use saliva samples to peer into a patient’s DNA to determine such factors as propensity for certain diseases or how one responds to certain medications, or whether young couples are carriers of crippling genetic conditions that could show up in their offspring.

Other labs in the region offer similar services.

To be sure, critics say DNA testing is not quite ready for prime time. They argue the results are too imprecise, and can’t predict a person’s future health condition.

But Pathway Genomics founder and CEO James Plante says the tests can tell whether a patient is at a higher risk or lower risk for a wide variety of ailments, which is important data to have in someone’s medical record.

“It’s going to be in everyone’s medical record in the future,” he says.

Plante says growing demand will help keep San Diego in the forefront of DNA research and commercialization for years to come, and bolster its fast-growing reputation in the new field of health informatics.

“We’re just in the beginning stages,” he says. “The industry has lots of room to grow, and San Diego is sure to grow with it.”

Pathway Fit Test Results Include Exercise Strengths And Weaknesses, Eating Behavior

SAN DIEGO – A new fitness test created by a local company reveals more insight into your health than ever before.

Carmel Valley resident Michael Casler said he knew he had to get in shape.

“For me, my blood pressure started to get to a point where I needed to do something about it and really, it was driven by my weight,” he said.

Casler tried several diets but found he could not keep the results. He said a new test, the Pathway Fit, helped get him on track.

Here is how the test works: participants give a saliva sample in a tube. The sample goes to a lab and then 80 to 100 genes are examined. DNA is extracted. The test results can tell participants everything from exercise strengths and weaknesses, vitamins that they are lacking and eating behavior.

“The diet type for me is a Mediterranean diet,” said Casler. “As a business man, I know you can manage what you can’t measure and this report really helped me to identify specifically what I needed to work on.”

Olympic athletes have also used the test. Chula Vista resident and two-time Olympian high jumper Jamie Nieto recently took the Pathway Fit test, which was developed by Sorrento Valley-based Pathway Genomics.

“We’ve had a number of athletes take our tests,” said Dr. Michael Nova, who is with Pathway Genomics. “They want to learn these kinds of things and how to tailor their training programs better.”

Doctors remind those looking for better health that the Pathway Fit test is only the first step of many.

“So much of what chronic disease is about is behavior change and if we’re going to induce behavior change, you have to give all the information you possibly can to the patient,” said Dr. Samir Damani.

Casler has lost more than 30 pounds in the past four and a half months. He said that is thanks to the test results but more importantly, the hard work after he got them.

“Dr. Damani said I added about 10 years to my life,” he said. “I hope they’re good years.”

The test costs about $400 and is available only through a physician.

THE DNA DIETING METHOD IS THE LATEST CRAZE IN THE WEIGHT-LOSS WORLD. ITS CLAIM: THE SECRET TO A BETTER BODY IS INSIDE EACH OF US—LITERALLY.

THE PROMISE OF MINING OUR GENETIC CODE TO PREVENT DISEASE
(see: the Human Genome Project) is taking a back seat to the breakthrough the fitness-obsessed have been waiting for: using our genes to fight fat. Although science has demonstrated that low-carb diets (Dr. Atkins is the forefather) and low-fat diets (pushed hardest by Dr. Dean Ornish) can be effective, research also shows they don’t work equally well for everybody. A Stanford study suggests that DNA may be a big piece of the one-size-doesn’t-fit-all puzzle: Subjects who ate a diet tailored to their genetic type lost twice as much weight as those whose diets and genes were not in sync. If having your genes analyzed to slim down sounds like science fiction to you, consider these three accessible and increasingly popular new ways to get diet and fitness advice based on your DNA.

AT THE DOCTOR’S OFFICE

THE CONCEPT

The San Diego–based lab Pathway Genomics has crunched the academic-research literature and come up with a procedure that looks at 80 genetic markers that affect the way the body processes carbs, fats, and protein and how it will likely respond to exercise. You hand your trainer a test tube of saliva and $400 and complete a lifestyle-and-health questionnaire, then Pathway sends the customized diet-and-exercise report to your doctor. The company recommends one of four diets: low-fat, low-carb, Mediterranean (heavy on the “good” fats found in fish and olive oil), and balanced (a generic healthy diet). You (or your doctor) can discuss the results with a Pathway genetic counselor or nutritionist, for no extra charge.

THE PLAN

About 30 percent of Pathway’s clients are prescribed a low-fat regimen: Because their bodies don’t do a good job of breaking down and processing fats, they’re put on a diet that skimps on animal fats, dairy, and fried foods, which should decrease the amount of LDL, a.k.a. bad cholesterol. They pick up the caloric slack with fruits, vegetables, and whole grains. Low-carb candidates (another 30 percent of Pathway clients) don’t efficiently chop up complex carbohydrates to burn as energy, which means some of the carbs are converted into fat. This group is advised to steer clear of breads, cereals, and grains and close the caloric gap with lean, clean protein (fish, poultry), fruits, and non-starchy veggies. The Mediter-ranean diet is tailored to the 20 percent of clients whose genes don’t point them toward low-fat or low-carb diets but predispose them to receive a greater-than-average health boost from good-for-you fats, which raise their HDL levels—hence the plan’s emphasis on fish, nuts, and olive oil. The remaining 20 percent of people are put on Pathway’s balanced diet, because their genes have no telling variations. This all-purpose, textbook healthy plan loads up on brightly colored produce (carrots to cantaloupe, blueberries to broccoli), whole grains like quinoa and brown rice, fish, beans, and lean poultry.

AT THE GYM

THE CONCEPT

At Equinox health clubs in Los Angeles’ Century City and Greenwich, Connecticut (and coming eventually to most of the chain’s gyms across the country), you produce $300 and a test tube of saliva. Your sample is sent to the L.A.-based preventive-medicine company Existence Genetics, which looks for variations in your genes that indicate everything from your chances of developing arthritis to your risk of toppling over from a heart attack on the treadmill. The results help you choose the right diet-and-work- out regimen.

THE PLAN

The gym will recommend a customized training-diet program. Surprisingly, it’s Equinox’s younger, seemingly in-the-know clientele who are the most in the dark. “We find that our younger males are the ones with the least sophisticated knowledge relative to nutrition,” says Matt Berenc, fitness manager at the Century City club. “So we spend a lot of time working with this assessment to show them how to eat right, be it low-carb or low-fat,” Berenc says. “People will join a gym, will have goals—whether it’s to lose weight or get healthy. This gives them a little more kick in the butt.”

AT HOME

THE CONCEPT

In his new book, The Hunter/Farmer Diet Solution, Dr. Mark Liponis, medical director for the Canyon Ranch spas, has outlined a low-tech way to make the low-carb/low-fat call. He discerns your genetic type with routine annual lab tests and by eyeballing body shape, which he believes can reveal your evolutionary history. If you’re a “hunter,” you carry your weight in your belly, mostly because you process sugar slowly, which allowed your ancestors to retain their blood-sugar levels, and thus their energy, between kills. The results of your annual physical will probably include higher-than-average triglycerides. But if you have more “farmer” genes, you tend to pack pounds on your thighs and buttocks, even though you’re a doctor’s-office high performer (healthy cholesterol, triglyceride, and blood-sugar readings). Your ancestors’ bodies adapted over millennia to handle grains and cereals in a way that quickly converts carbs into energy.

THE PLAN

To lose weight, hunters need to cut back on refined carbs, which keep blood- sugar and insulin levels too high and send you down the pre-diabetic path. “If your ancestors couldn’t hunt it or forage it, don’t eat it,” Liponis says. Stay on the hunter schedule—eating fewer and bigger meals (read: when you get a kill). Farmer types, on the other hand, need to avoid overdoing high-calorie, artery-clog-ging animal fats, eating baked potatoes instead of fries, broiled chicken and fish instead of fried. They can graze as often as they like (granolas, berries, and nonfat yogurt are perfect) to boost energy levels.

by Joel Stein
Time Magazine, February 2014

Some of my genes predict athleticism. I have apparently nurtured the other ones.

I have come to accept that I am never going to compete in the Winter Olympics. This is is largely because I have never tried any of the sports. In fact, I have avoided all athletic activities of any kind for my entire life. I’ve always assumed that through no fault of my own, I was born without the genes that would make me able to ski and then stop skiing and shoot things, or to steer a bobsled after a giant man pushed us downhill.

To find out if I was right, Pathway Genomics, which uses a spit sample to deliver nutrition and exercise recommendations tailored to your genes, compared my DNA with that of Olympic gold medalist Sergei Bubka, the greatest pole vaulter of all time. I was guessing that of our approximately 20,000 proteincoding genes, most of mine would be too covered in fat for Pathway to read.

I went over my results with a Pathway doctor and found out, to my great disappointment, that Bubka and I were created similarly. We both have the “speed gene,” a variation of AcTN3, which is found in fasttwitch muscle fibers. Bubka uses it to generate speed on the track, and I use it to type really fast. We also both lack a gene that would show we’re prone to injury, as well as one that would give us the increased aerobic capacity of an endurance athlete. We both have a gene that probably leads to overeating, a tendency that I have controlled through will power and that Bubka controlled by growing up with Ukrainian food. The main difference between us is that I figured out that writing is much easier than propelling myself two stories in the air by running as fast as I can and shoving a stiff fiberglass pole into a metal box.

But when I looked more closely at our results, I saw that the gene INSIG2 shows that strength training is very effective for Bubka and not at all for me, which I have somehow intuited all these years and therefore avoided picking up and putting down heavy things. “Sergei is in a sense gifted when it comes to constant pressure and constant pressure on muscles. This is consistent with Olympic athletes,” said Jim Plante, the CEO and founder of Pathway. Bubka also gets a hugely advanced benefit from endurance training. I don’t get the same results, though I do get a higher-than-average benefit from the training, along with, apparently, a gene that allows me to forget I ever learned that fact, so I can continue to not go to the gym without feeling extra guilty.

I called Bubka in Sochi, where he is attending the Olympics as an IOC executive board member and president of the National Olympic Committee in Ukraine, so I could compare our youths and find out where someone with my excellent genes had gone wrong. Bubka was at a loud party right before the opening ceremony, and hehas a pretty thick accent, but I’m positive that when I asked him how Sochi was, he said, “It’s really nice. Great food. Excellent villages.” Having grown up in the Soviet Union, Bubka probably doesn’t define nice in a way that includes things such as bathrooms or doorknobs.

Bubka wasn’t surprised by his genetic results, since he’s always been better at shortterm, strength-oriented sports. “I was fastest and strongest of all my friends. I played sports most of the time with older guys,” he told me. When he was just 10, an older friend named Slava insisted that his pole-vaulting coach let Bubka try the sport, even though Bubka was considered way too young. When I tried pole vaulting two years ago with Olympian Brad Walker, I could neither clear the lowest level nor get Walker to stop making fun of me.

Genetic testing of athletic ability, Bubka said, should be administered to child athletes, as Uzbekistan has announced it will start doing, so that kids won’t waste time and money pursuing the wrong sport for their ability. I thought this idea was problematic in that someone might have used testing results to make me play a sport.

As much as genes do matter, Bubka said, the key to Olympic success is that “you need to have character to go to your goal, to do your work, to be a hard worker.” Actually, however, Pathway told me, though it isn’t part of the results they normally give, that both Bubka and I have a version of the DRD2 gene, which suggests that we respond positively to rewards, learn from mistakes, can be obsessive and have a low risk of addiction. Other genotypes that are even less well understood might indicate that we both are particularly driven. So in a way, I am more impressive than Bubka because I have had to work hard to fight my genes in order to be as lazy as I am. One day, I hope, the Olympics will recognize that as medal-worthy.

Joseph Hooper, Men’s Journal, October 2013

“These tests give people a better idea of where they are and where they need to be. It’s a probabilistic look at your health that is a critical component of anintegrated approach to wellness.”
Dr. Samir Damani Founder and CEO of MD Revolution

DIY DNA testing

…Ten years ago, the Human Genome Project deciphered the entire human DNA code at a cost of about $3 billion. What no one dreamed at the time was that the technology would quickly become so accessible andso cheap.

What Our Genes Tell Us

…In the case of San Diego-based Pathway Genomics, a doctor orders the test, receives the results electronically, and interprets them for the patient, usually with the help of a script providedby Pathway.

Genes for the Gym

With Pathway Fit, Pathway has gone the farthest in creatively interpreting genomic data to make it practical, accessible, and even gym-ready. Starting with a pilot program planned for this fall at six Equinox gyms in the San Francisco Bay Area, Los Angeles, and Dallas, you can bring the results from the Pathway Fit Report to a specially prepped Equinox trainer who will help you figure out the healthiest ways to eat and work out. It’s a lively grab bag that looks into your genes for things like food cravings, the risk of having lower levels of various vitamins (A, B2, B6, B12, C, D, and E), and some common food sensitivities. Then there are the questions about the most effective fitness regimen: Are you likely, genetically speaking, to be the sort of person who readily puts on muscle from weight training, or, conversely, will aerobic endurance work efficiently tune up your metabolism? Odds are experience has already given you answers here, but some of the other tests may prove useful, like one that looks at your propensity for Achilles tendinopathy (which will make you want to start stretching your calves daily) or your body-mass response to exercise (which could give you a hint about the best strategy to shed those last 10 pounds).

The part of Pathway Fit that has attracted the most attention draws on genetics to personalize nutrition advice. The panel will, in theory, put to rest the controversy that has launched a host of diet books: Should you be on a low-fat, lowcarb, or Mediterranean diet to stay healthy and lose weight?

For its part, Pathway cherry-picks 79 genetic markers that it matches against data from population studies. People with one genotype are more likely to have higher than average “good” HDL cholesterol when they eat less animal fat. If you share that genetic profile, it may be evidence that you would do best with a low-fat diet. Your genetic variations might instead match those in a population who eat a lot of the monounsaturated fats found in avocados and olive oil and tend to be thinner. In this case, your results will push you toward a Mediterranean diet.

by Claire Atkinson

SANTA MONICA, CA – June 12, 2013 – Movie producer Ryan Kavanaugh wanted to upend all the rules of Tinseltown when he established Relativity Media 10 years ago.

Now he wants to cure cancer.

The bubbly 39-year-old billionaire threw a benefi t on Wednesday for his latest investment, Pathway Genomics.

At the benefi t, held at Kavanaugh’s Santa Monica, Calif., airport hangar, Ke$ha performed and the movie mogul and former hedge-fund investor mingled with the likes of models Amber Valletta and Alessandra Ambrosio.

Whether it’s charity events, medical investments or models, Kavanaugh has become quite the master of cause marketing.

He’s invested tens of millions of dollars in the privately held San Diego biotech fi rm, one of many non-movie-business companies he’s been pouring his cash into.

Kavanaugh acquired a dog-food company, FreeHand, in 2013 with singer and friend, Michael Bublé, to go along with stakes in Vapor Corp., an e-cigarette fi rm, a digital ad fi rm that greets airport travelers in their native languages with duty-free off ers and Shoutz, a fi rm developing the global lottery business into the mobile era.

Whether in his personal portfolio or at Relativity, diversifi cation is the name of the game for Kavanaugh.

Before and after the Pathway fundraiser, Kavanaugh has been hypnotizing East Coast hedge funds and private-equity fi rms with plans to take his studio public, Hollywood fi nancing sources said.

The studio is working with Jeff eries to close a $1 billion pre-IPO placement early next week, sources told The Post. The placement calls for investors to see a public fl oat of between 20 percent and 30 percent of the company within 12 months.

The IPO will value the fi rm at between $6 billion and $10 billion, sources tell The Post. Kavanaugh, reached Thursday by The Post, declined comment. Though there is no pure publicly held Hollywood entity that lines up like Relativity, LionsGate is a similar beast.

But the obsession of Kavanaugh and others inside Relativity is to diversify the studio enough so that its shares don’t swing wildly on every movie release’s success or disappointment.

Currently, 60 percent of Relativity Media’s revenue comes from theatrical releases, sources said. But selling that mix to Wall Street investors — with its volatile nature — is no easy task.

So Kavanaugh is out to diversify his studio, sources told The Post.

By this time next year, sources familiar with the company said, the movie/non-movie revenue mix will move from 60/40 to closer to 50/50.

One plan to diversify includes a Relativity over-the-top platform — called RelaTV — where it would air its own original movies, TV shows and digital video, The Post has learned.

While the studio recently sold rights to its content to Netfl ix, that deal is non-exclusive.

• Relativity has also pushed hard into other non-movie sectors, like:
• Relativity TV, which makes reality shows for Food Network, OWN and GSN.
• MadVine, a new unit aimed at bringing advertiser dollars direct to its projects.
• Relativity Digital, which creates digital video vignettes.
• Relativity Sports that has relationships with a host of athletes, including NBA stars Dwight Howard and Amar’e Stoudemire, according to the fi rm’s Web site.
• Relativity Music, which releases soundtracks from the company’s movies.

Movies carrying Ryan Kavanaugh’s producer credit have averaged $47.6 million per release, according to Boxoffi ce-mojo.com.

Those set to benefi t from the IPO are Relativity Media’s current backers, including Ron Burkle’s Yucaipa Cos. and Kavanaugh’s original partner, Paul Singer’s Elliott Management.

Other lesser-known investors include: Jim Breyer, the CEO of Breyer Capital; Colbeck Capital; Softbank; Falcon Investments and China’s biggest bank, ICBC.

Relativity’s IPO won’t be the only one for investors to consider in the coming year.

MGM Studios, which creates the James Bond movies, is expected to go public after fi ling regulatory documents.

And there is also talk of WME/Silver Lake taking a merged WME and IMG Worldwide public in the years to come.

For Kavanaugh, however, Relativity will be just one of a number of chips on the poker table — but it will be his most important.

Presented by Relativity Media, Pathway Genomics, and Evian, the evening raised funds to provide affordable hereditary breast cancer testing and to eradicate the disease.

Barker Hangar in Santa Monica, Calif. was abuzz last night as the stars gathered to support the fight against breast cancer. Jaimie Alexander, Kellan Lutz, Jessica Roffey, Sophia Bush, and Emmanuelle Chriqui (pictured) were joined by Amber Valetta, Alessandra Ambrosio, Adrian Grenier, Busy Philipps, Jordana Brewster, and more at the Pathway to the Cures for Breast Cancer: A Fundraiser Benefiting Susan G. Komen event. Presented by Relativity Media, Pathway Genomics, and Evian, the evening raised funds to provide affordable hereditary breast cancer testing and to eradicate the disease. During the party, Pathway announced their plans to donate $10 million in BRCA genetic tests for women who can’t afford the test.

“It’s nice to come out in support of such an important initiative. The fact that 1 in 8 women is affected by breast cancer in their life is not an acceptable statistic,” Bush tells InStyle. “When companies choose to be proactive I’m just incredibly grateful because they’re going to save lives.” Chriqui also expressed the significance of showing up for the event. “Susan G. Komen has done so much for breast cancer awareness, so you never need to twist my arm to come and support their cause,” the actress says.For the occasion, the space was transformed into a luxe living room where guests could snap pictures in an Instagram photo booth, get their groove on, and snack on small bites like local handmade toffees and delicious charcuterie and cheeses. To top off the evening, Kesha gave a glitter-filled performance of several of her hits including “Timber” and “Your Love is My Drug,” which got everyone dancing. “I loved seeing Kesha, I was right up against the stage.” Valetta says. “I knew all the words to the first song!”

During the party, Pathway announced their plans to donate $10 million in BRCA genetic tests for women who can’t afford the test.

Despite the fun atmosphere, guests were really there to support the worthy cause. “I was really excited to hear what these two organization are doing. Both my mom and two grandmothers all had breast cancer,” Valetta shares. “Beside prevention and self-checking and doing your mammograms, the biggest way to help is by making genetic testing available for everybody, which is what this group is aiming to do.”