genetic testing

Improving Quantitative Evidence for Genetic Tests: Carlos Araya, Invitae

Warning: the first part of this story can sound quite typical. Three co-founders with backgrounds in genomics and AI found a Stanford spinout. Their goal: to bring the tools of AI and computational modeling to unlock the medical secrets of the genome and deliver those to patients. They call this company, Jungla—Spanish for “jungle”—naming not only their adventure, but the whole problem. Then things get interesting.

For their first beta testing, they go around the genetic testing industry looking for partners. Basically what they hear back, is we don’t need that. However, they don’t hear the real reason why these companies don’t need their product. The real reason is because it offers a level of quality and standardization for genetic testing that is not currently required by the industry. In fact it shows “just how vulnerable the industry is.”

But one company—one of the bigger ones, one of the more innovate in the field—said yes, we want to partner. That company was Invitae. And a year later, Invitae would buy out Jungla.

Our guest today is Carlos Araya, the CEO and co-founder of Jungla and now acting as Head of Functional Modeling at Invitae.

It’s the story of one scientist's journey from academia, driven because of a personal family loss, into entrepreneurship, and the story of one company and then one bigger company each saying, “everything can be done better."







Gene and Tonic Predictions for 2019

Oops.  We still had some champaign around.  Our look to the year ahead.


January 6th  The best selling non-fiction book on Amazon over the holidays has some strong mature genetics related material in it.   The second chapter of  Advice for Generation Z  is entitled,  “Don’t Take that Cyanide Pill Just Yet: Genetic Tests Are for Fun, Not for Real.”

February 12th  The Oxford English Dictionary adds “Crispred babies” to the lexicon.

Connecting the Dots for a Community of Rare Disease Patients: Terri Klein, MPS Society

The MPS Society is a rare organization. Not just because it is an umbrella for the rare diseases that have in common lysosomal storage malfunction. But because it is one of the largest rare disease organizations in the world.

Terri Klein is the CEO leading the MPS Society. She says the group has over three thousand members on their roster. This brings some strength and resources in an area where low numbers intensifies an uphill battle.

Her job, she says, is to find those researchers out there working on the various MPS diseases--Hunter’s, Sanfillippo syndrome and about a dozen others--and make sure any and all science toward understanding, therapy and cures gets shared and developed. She "connects the dots" between research, funding, trial experts, parents and patients. Beyond the science and medicine, Terri says about half of her budget goes to care of patients.

So what is the state of existing therapies for these diseases now, and how close are we today to gene editing and gene therapy cures?

Terri has been instrumental in the creation of ConnectMPS, a very successful disease registry for MPS patients. What are her thoughts on how to make rare disease registers more impactful?

Pharma Stepping Up, Footing the Bill for Genetic Testing & Counseling: Jordanna Mora, Alnylam

It seems to be human nature to value and pay up to hundreds of thousands of dollars for a little white pill that we can drop on the floor--and granted, can do wonders for us, but we want to pay nothing or very little to be told what is wrong with us so that we might know which little white pill to use in the first place.

So let's talk today about the The Alnylam Act, a program to shake up the business model in diagnostics and genetic testing on behalf of patients. The Alnylam Act is what it looks like when a drug company gets proactive and says, hey, we will step in and pay for patients to be genetically tested and counseled for the diseases on which we are working.

“We did this to reduce barriers to genetic testing—and the delays are often pretty long in rare diseases--so that individuals can make more informed decisions about their health.”

That’s today’s guest, Associate Director of Medical Affairs at Alnylam Pharmaceuticals, Jordanna Mora. And just to say it again, you understood her right. Her company, Alnylam, is paying for patients to be genetically tested and counseled.

Is Jordanna hearing any pushback over conflict of interest? After all, the patients who would be testing positive might be candidates for Alnylam’s drug.

The therapeutic we are talking about here is not on the market yet. In theory, it is set to be approved this August, and would be the first of the RNAi drugs. It will be an exciting day for the company, for patients, and for the drug development industry as a new class of treatments is born.

After years of seeing the diagnostics industry struggle to win reimbursement for their innovations, it's refreshing to hear about a drug company filling in the precision medicine gap for the good of patients, many who get misdiagnosed or wait way too long for a diagnosis. Will the Alnylam Act be a model for other drug companies?

“There are a number of companies doing very similar programs, and I think its fantastic,” says Jordanna.

We go for just over 15 min.





“It’s tailwind for us.”




The Global Business of Reproductive Genetic Testing with Gary Harton, Igenomix

Reproductive testing is one of the hottest fields in which genetics is going mainstream, a field hurdling us rapidly into the future. It’s an area we’ll be following closely in 2018.

Gary Harton serves as the Chief Operating Officer in the US for Igenomix, a company in the reproductive testing space with a vast global presence. The company has labs in the US, Japan, India, Turkey, Rome, Brazil, Mexico, Canada, and are headquartered in Valencia, Spain.

This international operation across so many cultures and national borders has its logistical and regulatory challenges, but it also offers the company an opportunity to introduce tests to cultures which are early adopters in a field fraught with big ethical and cultural decisions. With these more open cultures, the company can develop new tests and supporting clinical data.

The company’s most common test is preimplantation genetic screening (PGS) where embryos are checked during an IVF cycle for chromosomal abnormalities. According to Gary the test has gone mainstream in the US, but not in Europe. Yet in Europe, there can be wide variability. Spain and Italy tend to be early adopters and open to new testing technologies, whereas France is highly regulated.

One of Igenomix's newer tests is preimplantation genetic diagnosis (PGD). This offers parents who have a disease such as Huntington’s or cystic fibrosis--or are disease carriers--to eliminate that disease from their embryos through genetic testing. There is widespread support for PGD being used for this purpose. However the test can also be used for enhancements, or the grey area between disease and enhancements. Here, of course, decisions get much more complicated. For example, Gary says that recently the company had a request from deaf parents to select for deafness with their embryos. Should the company offer such a test?

How does Igenomix decide which traits to select for? Are there governing regulatory bodies that issue guidelines? A year ago we interviewed Hank Greely, author of The End of Sex, who argued that in 20-40 years parents would not use sex to reproduce. Does Gary agree with Hank's bold prediction?

We also talk with Gary about some less thorny issues. Years ago, the industry used FISH technology for testing then switched to arrays. Now most everything is done with NGS. How has NGS and new automated liquid handling technologies impacted the field? Has this raised the quality of testing?

It's a rare glimpse into life for some pioneers taking genetics into the future, and Gary is open and transparent.

Gene and Tonic, July 8, 2016: 49ers Going into Genetic Testing

Just two years at their new home in Silicon Valley and not far down the road from 23andMe, the San Francisco 49ers are offering their fans genetic testing and the chance to donate blood to advance human genome research.

Announcing a partnership with the company ORIG3N, the 49er Chief Operating Officer, Ethan Casson, says that “this is the first agreement of its kind where a major sports organization can give back to the human genome some of what the genome has given to professional football players.”

In Partnership with IBM’s Watson, Pathway Genomics Reinvents Itself

Direct-to-consumer (DTC) genetic testing has had a bumpy ride.

Back in 2010, Pathway Genomics and Walgreens made a deal to sell DTC genetic tests in thousands of Walgreens drugstores. Within 48 hours of the deal being announced, it collapsed. The FDA sent a letter to Pathway basically asking them what the hell they were doing. Walgreens quickly elected to put the kibosh on the partnership.

Since then, Pathway has reinvented itself as an “information technology company with a genetic testing lab on the side,” according to today's guest, Ardy Arianpour, Pathway’s Chief Commercial Officer.

Late last year Pathway announced a partnership to use IBM’s supercomputer, Watson, to power a new “killer app” called Panorama. This will be a “smart" app available later this year, Ardy says, that will incorporate data from wearables and biomedical literature (through Watson), and be able to recommend certain genetic tests that the company will offer.

However, this time Pathway is being more careful about selling the genetic tests. While the app will be available to every consumer, all genetic tests provided by Pathway must be ordered by a physician. The app becomes then really an educational tool for consumers which might lead them into discussions with their doctors. Ardy says Pathway is developing a separate app for physicians as well.

It's a new day for DTC genetic testing. The FDA just approved for the first time a DTC test offered by 23andMe. Might Pathway's Panorama app with accompanying tests find the right balance between protection of the consumer and the freedom to access our own genetic data?

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