genetic testing


Limited Genetic Diversity Affects Us All

Diversity’s in the news these days. It's not just political correctness. Let’s look deeper into our field at how limited diversity in genetics is affecting all of us.

If you are a member of a minority population and you go into a cancer clinic seeking help, some of the genetic tests on offer may not work for you because of your ethnic background. Not only is this wrong on a social justice level. It turns out it's just bad science.

Because limited populations have been studied, scientists had labeled certain mutations disease causing, but when they went to larger more inclusive populations, “they realized, in fact, these were common non-disease causing mutations in other populations. And so all those people were misclassified with respect to their disease risk. Scientists made an error. And those kinds of errors affect all populations. It’s not just minorities that will benefit from this information. All populations will benefit when we have better data.”

That’s oncology Professor Tim Rebbeck from Harvard and Dana Farber speaking with us on today's show.

But let’s go back to the member of the minority population walking into the breast cancer clinic. There are polygenic risk score tests available and listed just for people of European ancestry.

“This is not ideal on so many levels. Aside from the clinical justice standpoint of offering intervention to one group, but not another group . . .” exclaims the other guest on today’s program, Sheila Rajagopal, an oncologist and clinical instructor at the University of Chicago. She goes on to provide more scientific imperatives for the importance of gathering more diverse data, particularly the challenging new PRS testing.

So where are we today? What are clinics doing to deal with this in real time? What is the scientific community doing at a larger research scale? These are the tough questions for Sheila and Tim on today’s program.

Source: NIHMS

Bob Nussbaum on the State of Genetic Testing: 2020 Edition

From a career at NIH where he was Chief of the Genetic Disease Branch to academic Chief of Medical Genetics at UCSF to his current business title of Chief Medical Officer at InVitae, Bob Nussbaum has been a central figure in the field of genetic testing. A chief among chiefs. Today he gives our State of Genetic Testing: 2020 Edition.

Our approach is to ask Bob to weigh into the recent debates that have come up this past year. And they can be summarized into one question. Even one word. "Expanded."

What are Bob’s thoughts on expanded breast cancer panels? Should the NCCN guidelines be adjusted? Costs have come down—thanks in large measures to his company, Invitae. And the sheer number of good quality tests has gone way up.

What about expanded carrier screening?

What about the role of germline testing when a person has had somatic testing?

Is "expanded" even the right word?

Here’s Bob on the field today:

“It’s probably underdeveloped. There’s not gonna be a blockbuster test like there’s a blockbuster drug. There’s not going to be a secret sauce that one company has that another doesn’t have. Testing at this point involves service. It’s a service industry.”

August 2020 Review: Radical Shift on LDT Policy, First Pan-Cancer Liquid Biopsies, and New Alzheimer’s Test

After a long break, the world's first genomics pundits are back for the season. And they are calm and collected in the face of the strorm on Pennsylvania Ave. We're sixty days from an election. How serious should we be taking politicization of the COVID vaccine, this radical shift on LDTs at the FDA?

We also discuss some regular approvals and on rejection that sent the industry reeling with disappointment. Then it's on to Laura's, Nathan's, and Theral's picks for science of the month.

Welcome back!

The Pros and Cons of Expanded Carrier Screening with Mary Norton, UCSF

Mary Norton is a perinatologist and clinical geneticist at UCSF who says that in the age when we are diagnosing ever more rare diseases, adding to the carrier screening panel can be a good thing, but it’s complicated.

But it can be a good thing.

But it’s complicated.

Traditionally carrier screening was limited to ethnic groups, Mary tells us at the beginning of today’s interview, but has now been expanded to what’s called universal screening. The question for OB/Gyns like her is calling the limits on the panel. And it’s not just docs, labs or scientists who are savvy as to the latest conditions studied. Today’s patients expect the full treatment. Explaining that more is not always better can be a tough sell.

90% Go Undiagnosed, Says Geisinger’s Amy Sturm of FH Patients

More than one in two hundred people have an inherited form of heart disease. But most don’t know it.

Often on Mendelspod we talk about cancer genomics, but in the area of cardio, too, genetic testing can save lives.

Amy Sturm is the Director of Genomic Counseling and Screening Program at Geisinger Health Systems. There she has led the effort to return the results of cardio genetic tests to over 1,000 patients.

FH, or familial hypercholesterolemia—Amy says we need to get used to saying it out to spread awareness—is the most common inherited predisposition for heart disease. Over 90% of those with the FH variant go undiagnosed.

What does it mean for one's health if one has this gene? What are Amy’s pioneering studies at Geisinger revealing as they diagnose more and more cases and report results back to patients? How does cascade testing work where family members are notified and sometimes tested? And finally, what are Amy’s thoughts on the new polygenic risk scores that are coming out in the field of cardio genetics?

It’s an area of genetics ripe for its own Anjelina Jolie moment, says Amy.

Learning from the Field's Mistakes, Ancestry.com Rolls out Physician Ordered Health Testing

Just in time for Black Friday, Ancestry.com has launched new health testing. Thanksgiving week (the company calls the shopping holidays the “Turkey Five”) has been kind to what is the largest DNA testing company in the world. Back in 2017, their ancestry test competed with the Instapot for Amazon’s top sellers on the biggest shopping day of the year. To date Ancestry has sold over 15 million DNA tests.

Ancestry’s approach with the health testing shows that they have learned from the field's fumbles: the new tests, which will deliver “actionable health and wellness reports,” will be available to consumers but ordered by an independent physicians network and supported within the health ecosystem.

Sarah South is here to talk about the new rollout. She's the VP of Laboratory Science at Ancestry DNA. Her CV itself gives a clue as to the smart way Ancestry is going about launching this product. She was previously the VP of Clinical Lab Operations at 23andMe and before that the Lab Director at ARUP Laboratories.

She argues that there is a level for what she calls "opportunistic" testing between the more comprehensive "rule out" testing that clinical labs do, and the level of . . . well, doing nothing.

“We don’t need to have everything in the “rule out” bucket. There are times when I might like to have an “opportunistic” finding. I'm not currently experiencing any symptoms. I don’t know of a strong family history. But I know that there are things that may be subclinical right now. And if I knew about them, I could do something about them. For example, our hereditary hemochromoatosis offering, or the predisposition to develop iron overload. Most individuals are subclinical until they are in their 40s or 50s. But the risk is that if you wait until you are clearly having clinical symptoms, the damage to the liver may be irreversible. ”

Sarah gives other examples of the actionable health variants as well as wellness offerings.

What about the charge often put to 23andMe that these tests are not complete enough but give consumers the impression that they have been completely tested, such as for BRCA. Sarah is on to the answer before Theral can ask it.

She also anticipates the future of health testing in the age of polygenic risk scores.

Join us now for our first interview with Ancestry.com.

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."

Why Isn’t Personalized Medicine Being Mentioned by the Presidential Contenders? Ed Abrahams on Drug Pricing, Genetic Testing, and the State of the Industry in 2019

Ed Abrahams has a message for Nancy Pelosi about HR 3. That’s the new bill in the House to reduce drug pricing.

Ed is the President of the Personalized Medicine Coalition, an advocacy organization in Washington representing our industry which will soon announce a new caucus in congress devoted to personalized medicine. Ed joins us today and says to Pelosi, there’s a better way, a more American way to reduce drug costs.

The argument is not new. Personalized medicine will reduce costs if we encourage it to play out. The industry hasn't been around long enough to have yet made the difference. We're just at the beginning of this new era. The name 'personalized medicine' itself is only about twenty years old, Ed points out. What is new is a "value-sharing" pricing model which guarantees that innovation remains strong while making sure that patients have access to new therapies. Ed advocates for this new model and others like it on today's program.

"We need innovative ways of looking at drug pricing. It's a paradigm shift," he says. "And it's happening, but it's happening too slow and below the surface so that the public, as reflected in the Republican and Democratic parties, is unaware that there is a solution outside of price controls."

During an election cycle there’s bound to be a lot of noise on the topic, but for anyone who is serious about real solutions to healthcare, Ed’s organization does some terrific work and represents all the groups involved. Their annual conference takes place in Boston this November 13-14. Today Ed gives a preview of the topics which include drug pricing, but also our annual roundup of new therapies and an in-depth look at the year in genetic testing.

Gene and Tonic Predictions for 2019

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

2019

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?



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