genomic medicine


Genomics and the 2018 Election

The last two years have had us on edge.  It had scientists marching in the street.  That was unprecedented.

So what does last week’s election mean for the genomics community?

Scientists can focus on science

A friend of mine put it this way, “When Obama was in office, I realized I’d been like a cat, relaxed and having my nap in the afternoon. When Trump was elected, I felt like a mouse, always on edge.”

Who Is Misleading Whom About Precision Medicine?

This month the New York Times put out an opinion article that was a reprint from Kaiser Health News written by Liz Szabo positing big doubts about the project of precision medicine. For the Times, it came with the title, “Are We Being Misled About Precision Medicine?” Unfortunately this piece does exactly what it warns against. It misleads.

Putting the headline in question form, rather than declaratory, reveals an insecure thesis. Why not just say it?

It’s the Social Factors, Stupid! Lisa Suennen on Healthcare, Her Career, Digital Health Investing, and . . . Just Being Herself

She's been a highly sought after venture funder and knowledge broker in the field of digital health. STAT News wrote that upwards of 1,500 pitches crossed her desk last year at GE Ventures. But as of a couple weeks ago, it's a desk at which she's no longer sitting. So what's she up to next?

No, we did not get a scoop here, though we do feel important. This interview was scheduled long before the healthcare venture capitalist, podcaster, blogger extraordinaire made her big break recently with GE. And in fact we’ve always known her for her own brand that goes beyond any employer, that of Lisa Suennen.

August 2018 Review with Nathan and Laura: The polygenic month

It’s our first show back after the summer break, and nothing has got us all buzzing about genomics again like a polygenic risk score. It even has Laura Hercher talking about the Human Genome Project doing some delivering, god forbid.

CRISPR has had a rough summer. But still . . . it is CRISPR.

Is Burning Man still cool, we were asked last weekend. Don't know. Don't care. We asked back, is 23andMe still cool?

Then we found sort of an answer in an old rag purchased last week down at the end of the street: "They rode into town on the cool train. They've been shoot'n it up out here in the Wild West makin' trouble for the sheriff. But now they've become one of the big corporations who hire their own guards to watch o'er their stage coach. They're makin' woopy with the big guys."

Surely it's talking about 23andMe.

Laura says 23andMe's heyday is past. Nathan says, no, their best is yet to come. And then he immediately gets excited about Neanderthals and Denisovan's having a love child 50,000 years ago.

Non sequitur?

An International Perspective on How to Improve Biobanking with Kirstin Goldring

For the next episode in our summer series on human tissue sample quality and biobanking, we turn to a veteran biobanker in the U.K. who managed several projects there including the U.K. Parkisons’ Disease Society Brain Bank at Imperial College.

Today we talk to Kirstin Goldring, Principal Scientist at Astra Zeneca where she’s in charge of Human Biological Sample Strategy and Governance. Kirstin is a counselor at the European Society for Biopreservation and Biobanking and also a member of ISBER or the International Society for Biorepositories.

So far, in the U.S. biobanks are not regulated. In the U.K., they have what is called the Human Tissue Authority or HTA. Kirstin explains that the HTA is really some light governance that leaves a lot open to the biobanks as to how they go about maintaining standards. Could the program be a model for us here in the U.S.?

What has been Kirstin's overall take away on the field after managing different projects in various locations? Are we getting any better at sample quality?

A Seqster Preview with Founder Ardy Arianpour

As long as we’ve been doing clinical genetics, the goal has been to marry up the genetic data with phenotypic data in the electronic medical records. This has been achieved with some success and with a few of the best genetic markers at some of the leading healthcare providers: Geisinger, Rady Children's, Brigham and Women’s—to name a few. But it hasn’t happened at scale, at least not in this country. Some of the national health services around the world are making the dream more of a reality, for example in Iceland and the U.K.

There is a movement, however, growing particularly strong in the current politics of deregulation for consumers to do it themselves by managing their own EHRs, genetic, and fitness data together in an online account similar to their financial accounts. Today we talk with Ardy Arianpour, the Co-founder and CEO of Seqster.com, a site recently out of stealth now offering such a service to early access customers.

If the business model of sites like Seqster is dependent on big pharma buying up the collected data in high numbers for their own purposes, what will make a certain platform "the one" or one of "the chosen few?" Indeed, as more and more private companies swarm to be this service and gather our private medical data, what will give us consumers the trust to take part?

“It’s already happening unidentified. So why not be fully transparent: involve the participants, the users, the patients so that they can collect, use and share their data on their own terms? All we’ve done [at Seqster] is created a technology that has that mission for its members,” says Ardy.

Followers of Mendelspod may remember hearing Ardy on the program from his days as Chief Strategy Officer at Pathway Genomics. Prior to that he served as Senior Vice President at Ambry Genetics which last year sold to Konica for $1 billion.

Detective Stories from the Genomic War Room with Ramesh Hariharan

A book like this only comes around once in a while—one never knows from which corner. This time it was written by the CTO of a next gen sequencing data analytics company.

“Every one of these cases was intense. It was just so fascinating that I had to put it down in a book and tell the story. There’s so much in biology that boggles your mind and makes you wonder.”

So says Ramesh Hariharan, author of Genomic Quirks: The Search for Spelling Errors. His new book tells the stories of nine cases he worked on first hand analyzing patient genomes. From the mystery of the author’s own color blindness to a rare childhood disease that took a couple’s two children and left them wondering whether to have another to a daunting instance of abdominal cancer, Ramesh reveals the interplay of three modern industries working at the their pinnacle: molecular biology, clinical medicine, and data analytics.

What makes the book so special is being with a passionate technologist as he discovers his own gift as a writer, to be there when he realizes he can bring the rest of us along on a journey filled with many fantastical twists and turns, dead ends and eureka moments, uncovering the long kept secrets of the human genome. This is different from the product of journalists who get it all second hand. Ramesh's book is personal, a labor of love, rare.

Does it all make him bullish on genomic medicine for the future? He says we’re running out of ideas.

I Won’t Rest Until We Have Quality Standards in Place for Biospecimens: Carolyn Compton, ASU

She’s a force of nature, and she’s back on Mendelspod. A decade ago, Carolyn Compton was hired by the NCI to solve a problem that has plagued the world of not just cancer research, but all of biomedical research. To this day, there are no standards in place for the acquisition, collection, storage, and delivery of human biological samples used for research. The leader of the NIH has acknowledged that this is a major part of biology’s non-reproducibility problem.

Yet Carolyn couldn’t solve it at the NCI. It took going to Arizona state where as part of the National Biomarker Development Alliance, she brought all of the stakeholders, government institutions, patients, private companies, and perhaps most importantly, the professional organizations such as CAP or the College of American Pathologists together, to put what in today’s program she calls “a basic floor” in place.

It was like the story of the blind men and the elephant.

"Despite the backgrounds of this broad swath of stakeholders who came to the conference—patients and regulators and scientists and physicians—they all had a certain knowledge of what was important. They all had knowledge of a certain part of the elephant, but they didn’t see the big picture until we came together. And what we came up with was astoundingly cohesive,” she says.

What has happened since? What changes has Carolyn seen toward the adoption of better standards and improving this immense problem that she simply calls, “garbage in, garbage out.”

We come in at around 25 min today.

You can find Carolyn’s referenced (free) article for Pathologist Magazine here.

May 2018 with Nathan and Laura: The Free Exome, California Database, and Mosaicism

Nathan Pearson and Laura Hercher are back for a look over a busy month of headlines.

May took us into the era of the free genome as Geisinger planted the genomic medicine flag on an even higher peak. And did you know California was keeping a genetic database for every baby born?

Meh. . . says Laura. Every state does it. Old news.

And mosaicism is old scientific news, says Nathan, but he likes the way Carl Zimmer brings it to light in a new book. Nathan and Laura then go above and beyond with their own elucidation.

It’s our final month-in-review before the break. Happy summertime!

Has Diagnostic Testing Plateaued? Alka Chaubey, Greenwood Genetic Center

If you’ve been in the field of genetic testing then you know about the Greenwood Genetic Center. With an address on Mendel Circle in Greenwood, South Carolina, this non profit diagnostic testing laboratory has basically written the book on diagnosing and understanding genetic disorders. Chances are, too, that you know the director of their cytogenetics lab and our guest today, Alka Chaubey. Her hunger for meeting new people and learning new science is matched only by her desire to share the Greenwood legacy.

The last time Alka joined us we talked about success stories in diagnostics. Today we’re talking about the limitations that our field is facing.

“If you look cumulatively at scientific discovery, definitely that is moving. But if you look sequentially at patient samples coming into our diagnostic lab, has our diagnostic yield increased? That number has not really made significant progress,” she says.

Now for the $64 million question, right? What can be done improve that number?

The Greenwood Genetic Center has a new program, TGEM (Technology and Genomics Enhancing Medicine) to spur innovation and partnership with technology companies. Alka talks specifically today about one of the six current initiatives in the program to bring BioNano Genomics' mapping technology into the lab’s clinical workflow.

We’ve talked with many scientists on the program lately about the new discoveries in structural variation. Alka's a clinical lab director who is not waiting for any dust to settle on those discoveries before making use of them in her lab. She’s already working on de novo mapping at the clinical level.

“This gives us way higher resolution than karyotyping. So we think that in combination with whole genome sequencing—because whole genome mapping is not a sequencing assay—this will give us more structural variation answers which we think play a significant role in that bucket of undiagnosed cases.”

We land the aircraft today at 23 minutes.

Editor's Note: Since this podcast was recorded, Alka took a new position at Perkin Elmer.



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