genomic medicine


A New Way for DTC? Nathan Pearson, Root Deep Insight

You know him, but do you know what he does for a day job?

Over the past two years, Nathan Pearson has dazzled us with his broad knowledge of the genomics space on our regular monthly reviews. Today we’re talking to Nathan about his new company that he soft launched last December, Root Deep Insight, a venture into what he calls “direct-to-lay folk genetics.”

Nathan had a not undramatic debut in our field on the TEDMED stage with Ozzy and Sharon Osbourne interpreting their genome when he was at Knome. He would go on to become a lead scientist at Ingenuity and then a director of public outreach for the New York Genome Center.

In our show today, Nathan traces back his passion for unleashing the power of the genome to his childhood when he lost his mother to leukemia. He feels that had his mother had access to the greatly expanded bone marrow donor registries and involved patient data sharing options that we see today, the possibilities for her would have been much different. He’s driven by those possibilities for other patients.

Nathan is a bone marrow donor volunteer. And he found a few years back that he can ask for his genomic data back from the registry. Particularly his HLA data. All bone marrow donors can. But this data comes back undecipherable. Enter Root Deep Insight. Their vision is to make all this free data not only available but readable and valuable to the donors, or those who might volunteer to be donors.

Is this DTC? Yes, a new kind. First of all, it’s free.

“We’re learning the lessons from consumer genomics. HLA can already tell you really fun things, not just about your ancestry—and it really goes quite deep there—but important things about potential drug responses, for example.”

We get to other questions. What role does the genomicist play in society today? Do they look at the rest of us as just walking data points? And what are Nathan’s thoughts on the new generation of block chain companies such as Nebula and Luna?

It’s Nathan Pearson for an hour.

Genetic Testing in the Age of Trump: Hank Greely, Stanford

"In a world turned upside down, this is an area where I don’t think he’s had much effect. I don’t think he knows how to spell “DNA.”"

So begins Hank Greely in today’s interview on genetic testing in the age of Trump. Hank is a Professor of Law and, by courtesy, Professor of Genetics at Stanford.

The first order of business today is the boom in DTC testing. Hank is actually pretty cool with this, including the new DTC BRCA testing. He expresses some concern with Sema4’s recent newborn screening panel which he calls “quasi DTC." He is very happy with the current FDA director and thinks that the FDA is treating DTC the way they would have in the previous administration.

“There’s been an evolution, not a revolution."

So what’s turning Hank’s crank these days? Well, remember that article out in Tech Review a few weeks back about our genes predicting our intelligence? Hank is starting to wonder if the science really is that good. No. Really. He’s also feeling a bit chagrined about liking the bio hacker more than he should.

He’s funny. He’s thoughtful. And he’s on your speakers right now. Hank Greely for 36 min. Enjoy.

Eric Schadt and Sema4 Try the Consumer Model with Newborn Screening Panel

"We like to refer to it as consumer initiated, but physician supervised,” says Eric Schadt today when asked if his new test is direct-to-consumer.

Eric is the Dean for Precision Medicine at the Icahn School of Medicine at Mount Sinai in New York and since 2016 has served as CEO of Sema4, a spinoff that he founded out of the Mount Sinai Health System. Sema4 launched a newborn screening panel, Sema4 Natalis, in February of this year covering over 190 disorders.

With 400 people already employed, Sema4 is based largely on genetic testing, data science, bioinformatics, and software development teams that were built up at Mount Sinai prior to the spinout. New panels will be marketed directly to parents around the country, many of whom have already bought other prenatal screening tests from Sema4.

From 2011 to 2017, Eric served as the Founding Director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai. He says he founded Sema4 to achieve a greater scale than could be had within a single hospital system. For him and Sema4, the end game is to "partner with" tens of millions of patients for ongoing studies. He calls it his "growth hack" strategy.

The Natalis panel is a practical place to start. Many of the additional rare childhood disorders that expand the panel beyond the conventional heel prick testing of 30-50 disorders are the result of new research and the latest technology and are a no brainer. This will bring some uniformity across states. And the new testing can be done from a cheek swab rather than the more invasive heel prick.

Still, some argue, Sema4 Natalis really amounts to doing research on parents. For the panel includes cancer risk tests as well.

Does Eric plan to do any follow up studies with parents? Mount Sinai is the sole owner of Sema4. Has any other major healthcare provider made a play similar to this?

State of Sequencing 2018 with Keith Robison, Omics! Omics! Blogger

Sequencing geeks are fresh off the trail from AGBT, and it’s time for our annual look at the sequencing tools space. This year we sit down with the longtime Omics! Omics! blogger, Keith Robison, who not only can answer all your questions about the topic, he even knows which sequencer you’re using right now, and in which department.

Keith jauntily runs through the Big 3--Illumina, Pac-Bio, and Oxford Nanopore--and has a few odds and ends to say about the "niche developers."

We finish by asking Keith what new trends and new instruments he's looking at. He says his son is a senior in high school where Keith has offered to go in and demonstrate the MinIon nanopore sequencer.

"Imagine if the next generation of kids all learns sequencing on this little device. It starts becoming a practical reality where kids in high school--even middle school--learn sequencing and then learn data analysis."

The Flongle Generation, anyone?

Direct RNA-Seq Project Shows Nanopore Sequencing Can Reveal New Insights into Basic Biology: Winston Timp, JHU

Nanopore sequencing has arrived. Passing test after test this past year--including one we discuss today--this technology which was being hyped decades ago is delivering on its promise.

Winston Timp joins us today. He's an assistant professor at Johns Hopkins and one of the leaders on a recent large scale project to directly sequence RNA on an array of nanopores. Winston's is the first in a series of shows we've lined up with users of Oxford Nanopore's technology.

Why RNA-seq? Hasn’t this been done for years?

Yes, says Winston, but in the past no one has been looking at the RNA itself. They’re usually making cDNA from the RNA and sequencing that.

“One of the big advantages to nanopore sequencing, is that you can characterize any polymer you can put in the pore.”

Nanopore sequencing is polymer agnostic.

So what good does it do to look at the RNA directly? Ever heard of epitranscriptomics? Winston has worked for a while on DNA methylation in his lab. Now he’s looking at RNA methylation. Not only is he seeing basic biology that we've never seen before (unique isoforms, exon connectivity that has been imputed by informatics but never seen directly), he’s coming up with new translational questions for health and disease.

When we started Mendelspod seven years ago, the next gen sequencing race was in full swing. It was all about the push to bring down the price of sequencing. The lower cost brought an excitement to the world of biology with all the new projects it made possible. But we found out there were was a major limitation to the technology. Read length. Over the past couple years, PacBio paved a whole new world with their long reads that enabled many new genomic projects. BioNano gave us the big picture with their optical mapping. Today users of nanopore sequencing are generating reads of 1 megabase and the versatility of the nanopore is giving scientists even newer views of biological activity. The race is still very much on.

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.

The State of Genomics 2018 with Nathan, Laura, and Misha

Our first show of the year is an outlook on genomics for 2018. To do this we’re joined by our regular commentators, Nathan Pearson and Laura Hercher, and also by a special guest to mix things up a bit, Misha Angrist, Associate Professor at Duke University and Editor in Chief of Genome Magazine.

Misha wrote a seminal book on the rise of next gen sequencing and personal genomics (Here is Human Being: At the Dawn of Personal Genomics). After working at Knome, Ingenuity, and the New York Genome Center, Nathan recently founded his own company, Root, which works closely with tissue donor registries to give back DNA information to consumers for free. Laura is recognized as a leader in the field of genetic counseling, being a counselor herself and training many of today's working counselors.

Join us as we ask, where are we in genomics today?

Homo Sapiens (D)Evolves into Homo Medicus

A well known science and medical author, Wades Tudeep, has proposed an upgrade to a famous Shakespeare quote from Hamlet:

“What a piece of work is a man! How noble in reason, how infinite in faculty! In form and moving how express and admirable!  In action how like an Angel!  In apprehension how like a god! . . . [proposed addition] . . . In DNA, what an  encyclopedia of disease!"

Hank Greely on “The End of Sex" and Other Stuff

Each year at this time we bring on a guest who is somewhat out of the way of our normal lineup, for example, a science fiction writer or a philosopher. Today Theral interviews a law professor who loves to philosophize and write about the impact of biotechnology on our lives now and in the near future. His newest book out this year, “The End of Sex and the Future of Human Reproduction,” is another comprehensive and provocative example of what has made Stanford’s Hank Greely such an in-demand speaker both to scientist and non-scientist audiences alike.

“My prediction in the book is that in twenty to forty years, most people with good healthcare will conceive their children in a lab using stem cell derived eggs--and sometimes sperm—and then do whole genome sequencing preimplantation genetic diagnosis and pick the embryo they want,” says Hank at the outset of today’s extended interview.

Whereas sci-fi writers and the mainstream press often play into what Hank calls "our need for scary bedtime stories," he seeks to understand and elucidate the actual--and less dramatic--"muddling through" of new technologies into our lives.

In addition to discussing the book, we talk with Hank about his relationship to his colleague scientists at Stanford, what he thinks is the breakthrough technology of 2016, and the future of the FDA in the era of Trump.

What Does the Election Mean for Genomics? November 2016 with Nathan and Laura

While everyone is asking what will become of Obamacare, we ask our regular commentators, Nathan Pearson and Laura Hercher, specifically about genomics and medicine.

Nathan begins by saying that data scientists everywhere should be humbled. Does the failure to predict the election send out warnings about big data predictions in genomics?

Laura points out that Obamacare covers many of the new genetic tests which have become available in the past decade, such as screening tests for hereditary breast and ovarian cancer syndrome and lynch syndrome. Coverage for these tests is now up in the air.

"It is cruelly absurd to talk about the value to the human race of identifying the people with these syndromes if we don't then give them the ability to act on the information," she says.

No matter what happens to Obamacare, isn't there bipartisan support for genetic testing and for research funding? (See the passage yesterday of the 21st Century Cures Act.)

Both Nathan and Laura agree that genomic medicine will continue apace. However, they worry that under a Trump administration the less fortunate will become even more vulnerable and have less access to improvements in healthcare. They point to an area of testing that is already highly politicized: prenatal screening. Will women lose access to testing in an era that reverses gains made in women's reproductive rights?

We finish with a local election in the Florida Keyes where residents approved the use of Oxitec's genetically modified mosquitos. Fear, Laura points out, can quickly change suspicion into acceptance.



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