clinical genome

The Roller Coaster of Clinical Genomics with Tim McDaniel

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.


Tim McDaniels, PhD, Director of Scientific Research at Illumina
Bio and Contact Info

Listen (5:07) Mom diagnosed with rare T-cell cancer

Listen (7:50) Path to genome sequencing

Listen (5:56) Finding two key genes leads to unusual treatment

Listen (5:30) Regression, then reoccurence

Listen (4:54) How has this changed your view of health?

Today's story is a roller coaster of a ride. So far genomic medicine continues to be about those patients who by chance come across someone with knowledge of the latest in genomics.

Tim McDaniel is a Director of Scientific Research at Illumina, and so was in a unique position when his mother was diagnosed with a rare T-cell cancer. In the beginning of her illness, which first manifested as a nasty skin rash, Tim's mother, Beth, was in that "wilderness of rare illnesses." Her chance upon a doctor who had some experience with her cancer was just the beginning of this up and down tale. Tim attended the AGBT conference in Marcos Island, FL as part of his job at Illumina. There a new world opened up to him as he sat in on the presentation of an exciting story of genomic medicine. He encouraged his mother to have her genome sequenced which led to some helpful findings.

The plot of today's show, along with Tim's natural talent for storytelling will keep you on the edge of your seat.

Eric Topol and His "Creative Destruction"

Podcast brought to you by: The Burrill and Buck Aging Conference Explore how innovative approaches from regenerative medicine to digital health stand to change our notion of what it means to grow old.


Eric Topol, MD, Cardiologist, Genetic Researcher, and Technologist Bio and Contact Info

Listen (6:22) Patient stories heard at Future of Genomic Medicine Conference

Listen (4:34) Medical community's response to book

Listen (6:02) "I just wish I could go back and start medical school again"

Listen (4:30) Eradicate fee for service

Listen (3:05) Craig Venter: Quality of sequencing has gone down

Listen (4:29) "De"personalized medicine?

Listen (0:58) Excited about rollout of sensors

Eric Topol joins us to discuss what was perhaps the most talked about book in the life sciences in 2012, his "The Creative Destruction of Medicine." In his book, Topol tells of the now arriving era of individualized medicine and the rise of "homo digitus," or digital man. In today's show, Topol dives into some key topics from the book such as how to deal with misaligned incentives in healthcare. "I just wish I could go back and start medical school again because this is truly an era . . a renaissance, an enlightenment in the medical space," says Topol when asked about what he advises young people.

Dr. Topol recently hosted the Future of Genomic Medicine Conference at The Scripps in San Diego, and he begins the interview giving some highlights of patient stories.

Message from a Patient: Whole Genome Sequencing Not Clinical Yet

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Guests: Jay Lake, Sci-Fi Author Bio and Contact Info

Joseph Edward Lake, US Ambassador Bio and Contact Info

Listen (6:05) The term patient implies waiting - and waiting kills

Listen (3:34) The medical bureaucracy very challenging for a patient

Listen (7:30) Health is a privilege

Listen (10:46) Whole genome sequencing not clinical yet

Listen (2:13) Who is creating the future?

Today we begin a series, The Age of the Engaged Patient. Jay Lake is a sci-fi writer and compulsive blogger. He is also a patient. He joins us for today's program with his father, Joe, to talk about his struggle with colon and lung cancer. As is often the case with patient stories, patient can imply a team working together for the health of one individual.

Jake is very open about his cancer and his life as a patient. He blogs often about his daily medical experiences and has built up a large following in addition to his sci-fi fan base. "If I can use my storytelling skills to explain cancer, then I've beaten the disease," he exclaims in the interview. What do Jay and his dad think about the term patient? And what message does he have for our audience of life science researchers? Jay recounts his adventure with whole genome sequencing and is honest about how "painful and difficult" this aspect of his treatment has been.

Ingenuity Nabs Genome Scientist, Nathan Pearson

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Nathan Pearson, PhD, Principle Genome Scientist, Ingenuity Systems Bio and Contact Info

Chapters: (Advance the marker)

0:42 What does it mean that you left Knome for Ingenuity?

7:02 How important is it that we have common ontologies?

13:00 What is your first goal at Ingenuity?

15:24 What will it take to get the ultimate end user buying?

18:54 Is sequencing good enough?

20:48 Where will Ingenuity make most headway going forward?

26:50 Thoughts on ENCODE and junk/not junk?

31:35 BONUS A student of Jonathan Eisen

Long time player in bioinformatics and database cultivation, Ingenuity Systems recently announced a new Principal Genome Scientist, Nathan Pearson. Nathan is known for joining Ozzy Osbourne and his wife on stage for a TED talk after interpreting the rock star's genome at Knome. What does this move mean for Ingenuity and for Knome? As I wrote in a recent blog, Pearson feels he'll make more headway moving to a platform further upstream. "For me," he says in the interview, "it's a chance to put my shoulder behind a platform that has a really high ceiling for bringing genomes into everyone's life in a more substantive way". Though new on the job, Pearson is comfortable explaining his first goal at Ingenuity, and tackling the big question of what will it take to get the end user, i.e., patients in the clinic, buying genomic medicine. At the end we catch Nathan talking about the person who influenced him to be a scientist, evolutionary biologist, Jonathan Eisen.

Looking at the Big Picture in Bioinformatics with Christophe Lambert, Golden Helix

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. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing


Christophe Lambert, PhD , CEO, Golden Helix, Inc Bio and Contact Info

Listen (6:56) Beware the lure of solving tough problems for a small market

Listen (8:32) Is Illumina competing with their customers?

Listen (9:37) If the end user isn't buying, no one is selling

Listen (6:36) Learning from our GWAS mistakes

Listen (4:14) Where has Golden Helix found success?

Today we transition from our series on sequencing to one on bioinformatics. Christophe Lambert is the CEO of Golden Helix, a bioinformatics company based in Bozeman, Montana. With some degrees in computer science, Lambert saw early on the potential for IT in bio and began Golden Helix back in 1998, the same year Ingenuity Systems was founded. A research internship led to some funding from Glaxo Welcome and Lambert says he "started writing code in his bedroom" with no one to talk to but his wife.

Lambert's fourteen years in the business combined with his ability to think systematically has given him an insightful perspective on the industry. He's one of the few in this exploding field who acknowledges that the industry is quite small, not yet really making it to the clinic. "When the end user is not buying, no one is selling," he says in today's show. Lambert's impulse is to always look at the macro picture, probing why the science isn't there yet and what societal issues are holding back genomic medicine. I tried to pull him back a bit and get more information on Golden Helix, but half way through the interview, I just went with him. I highly recommend his blog at This Montana Canadian has something to say.

Father/Scientist Finds Gene Responsible for Daughter's Unknown Syndrome: Hugh Rienhoff Talks Personal Genomics

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.


Hugh Rienhoff, MD, Founder of Bio and Contact Info

Listen (6:44) Gene linked to daughter's unknown syndrome found

Listen (10:33) DNA sequencing now a first line test

Listen (1:42) What is your ultimate goal in this quest?

Listen (6:40) The father vs the scientist

Listen (4:56) Rewards and frustrations

Listen (4:37) How would you characterize your relationship with DNA?

Today's show is a bit of a scoop. Hugh Reinhoff is a biotech entrepreneur and physician. He is also a parent who has been on a special odyssey to find the genetic cause of a so far undiagnosed syndrome in his daughter Beatrice. Hugh made headlines around the world in 2007 when he set up a site to connect with other parents on similar odysseys. Over the years, we've read about Hugh in various articles and books as a lone parent/scientist up in his attic poring over the millions and millions of nucleotides making up his young daughter's genome.

What we didn't know when we contacted Hugh for the interview, was that he has now found the gene he finds "largely if not solely responsible" for Beatrice's syndrome. And his results have not yet been published. Hugh talks about how far DNA sequencing has come in the last six years and agrees that it is now a "first line test." As a geneticist and physician, Rienhoff was in a special position when it became evident his daughter Beatrice was obviously different. He admits in today's show that sometimes the father has been at odds with his role as scientist and physician. What has he learned as a father as a result of this unique odyssey, what has been the biggest frustration along the way, and what is his ultimate goal? Hugh's story is that of a pioneer in the Wild West of Personal Genomics.

Have We Been Missing the Big Picture in NGS? Erik Holmlin, CEO, BioNano Genomics

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.


Erik Holmlin, PhD, CEO, BioNano Genomics Bio and Contact Info

Listen (4:46) There is a lot of information lost with short read technology

Listen (5:06) What is an example of the practical impact of structural perspective?

Listen (8:49) Is it possible to have one platform that is good at short read and structural view?

Listen (11:28) From the clinic back to the tools space to persue the bottleneck

Listen (1:40) Thoughts on Moleculo

With all the advancement in next gen sequencing, have we actually been missing something important? Erik Holmlin thinks so. He's the CEO of BioNano Genomics, and he's left a career delivering diagnostics to the clinic to go back into the tools space and develop a new sequencing technology that would give a better structural view of the human genome. "I believe, broadly speaking, that the bottleneck in genomic medicine is unique and clinically significant genomic content. And the reason we don't have that is we don't have all the tools that scientists need. So I'm trying to develop those tools." That is a bold statement. In today's interview, I ask Holmlin if there is a new NGS Gospel to be spread?

The Snyderome

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours. With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow up.


Mike Snyder, PhD, Director, Stanford Center for Genomics and Personalized Medicine Bio and Contact Info

Chapters: (Advance the marker)

0:42 An update on iPOP

9:02 A model for the clinic?

15:39 How has the project impacted your personal life?

20:46 What is your definition for 'health?'

27:55 Power to the patient

30:11 BONUS: Thoughts on the George Church media flap about cloning Neanderthals

When Mike Snyder gets a cold, the world knows. Hundreds if not thousands of data points change in his body. Snyder, Professor of Genetics at Stanford Medical School, is perhaps the most biologically tracked person on the planet. In our last interview, Mike shared the results of a study that he's calling iPOP, or integrated personal omics profiling. The study achieved recognition around the world for predicting that he had Type 2 Diabetes. At the time he was showing no symptoms. This would not have been caught by any doctor. It was found by tracking his 'omes.' When he went into the clinic to check, his blood glucose level was indeed in disease range, and he immediately went on a strict diet and exercise regime.

In this interview, we follow up with Snyder a year later. He is still tracking his biology, collecting 40,000 data points 20 times in the last 14 months. And he has kept to his strict diet and increased exercise plan. Mike talks about what the study could mean looking forward to using this kind of data in the clinic and also how the study has impacted his personal life. For Mike, health has become a set of data points watched over time. The study has now increased to looking at his microbiome, and ten new subjects are being enrolled for similar tracking. Will the 'Synderome' become the model for omics in the clinic?

Speeding Data Transfer with Dawei Lin, UC Davis

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Dawei Lin, PhD, Director of the Bioinformatics Core at UC Davis Genome Center Bio and Contact Info

Chapters: (Advance the marker)

0:50 Set up first bioinformatics server in China

3:15 From 26 hrs to 30 seconds: a new high speed connection with China

11:52 Training the next generation of bioinformaticians

25:47 Empowering the masses to understand their own biological data

30:02 BGI and genomics in China

35:15 Know thyself

37:43 EXTRA: Molecular modeling with legos

Dawei Lin set up the first bioinformatics server in China back in 1995. And things have come full circle this past summer, as he was involved in setting up a new high speed connection between China and the Genome Center at UC Davis where he is Director of the Bioinformatics Core. Dawei worked with BGI to set up the connection. We ask him about the company and about genomics in China.

It's Dawei's passion to know himself that brought him to working with biological data.

Genomics Around the World with Chris Barbazette, Affymetrix

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1:08 Population specific genomics

7:03 Personalized medicine and diagnostics abroad

16:15 Agbio

20:02 Are arrays still more widespread than sequencing worldwide?

27:11 What's the most obscure place where you've promoted arrays?

31:00 Personal path to international markets

34:57 Worst airport story ever

Chris Barbazette is Affymetrix's VP for International Markets. He travels the equivalent of the distance around the globe each month. He joins us to talk about what's going on in genomics in such places as Saudi Arabia and China. Are arrays still the most important genomic technology abroad? Where's the most obscure place he's been for work? These are some of the questions we ask in this fun overview.