genomic medicine


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.

Guests:

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.

A Great Time to Be in Biology: Steve Quake, Stanford

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

Guests:

Steve Quake, PhD, Professor, Bioengineering, Stanford
Bio and Contact Info

Listen (4:45) Bringing physics to biology

Listen (6:28) New technology driving the study of single cells

Listen (4:30) A great time to be in biology

Listen (4:32) Thoughts on privacy and incidental findings

Listen (4:05) What is holding back the adoption of genomic medicine?

Asked about how he comes up with so many inventions, today's guest, Steve Quake, replies that he is "impatient." It's a quick answer that leaves a lasting sting. Last year when Steve won the Lemelsen-MIT award for being such a mad-inventor, Jim Plummer, dean of the Stanford School of Engineering, wrote of Steve: “It is important to remember that, at just 43 years old, Steve Quake has introduced a number of inventions, any one of which most people would consider a lifetime achievement — and there’s more to come. The true measure of the man, however, is less in his remarkable productivity, but in the profound reach of his inventions".

Beginning with a discussion about the technology Steve developed and commercialized to drive the study of single cell genomics, our interview continues on into the realm of genomic medicine and and the future of biology. Is Steve a believer that we'll be living to 200 yrs old anytime soon? And what are his thoughts on the issue of incidental findings? Listen to Steve's latest ideas in today's program.

NOTE: Since this interview was taped, Steve was elected to the National Academy of Sciences. http://engineering.stanford.edu/research-profile/quake-elected-national-...

After Buyout, Cliff Reid, Complete Genomics Stay on Track

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

Guests:

Cliff Reid, PhD, CEO, Complete Genomics Bio and Contact Info

Listen (3:32) Audience questions about Long Fragment Read technology

Listen (3:53) From 200 to 5000 people

Listen (4:11) How do you respond to national security questions?

Listen (4:39) Genomic tests will be commodotized like computers

Listen (7:38) Thoughts on bioinformatics

Listen (2:44) Conversation of bioethics being changed by Facebook generation

Listen (2:51) Future role at the company

In March of 2006, Cliff Reid teamed up with Rade Drmanac and John Curson and founded a company to commercialize a new DNA sequencing platform. But rather than make another sequencing tool and sell it, the company, known as Complete Genomics, would use a different model. They would be devoted entirely to sequencing human genomes as a service. In February of 2009 the company announced its first human genome. By the end of '09, Complete had sequenced 50 human genomes. And in the 3rd quarter of 2010, they sequenced and analyzed 300 human genomes. In 2012, BGI, or Beijing Genomics Institute, offered to purchase Complete for $117 million, and after clearing regulatory hurdles in the US and China, on March 18th the acquisition of Complete was complete.

CEO, Cliff Reid, joins us today in one of his first interviews after the buyout sounding as enthusiastic and on track as he did in our earlier interview. He admits there's a joke in his family that "the fourth time is the charm," because he was involved with two other startups that were ahead of their time. Cliff will be staying on as CEO with the same vision of advancing clinical genome sequencing. He says the company will be commercializing their LFR or Long Fragment Read technology, and he answers questions from our audience about when and how. Acknowledging that the company didn't have the staying power to get to the clinical market and were squeezed out of the research market by an unforeseen preference for exome sequencing, Cliff is still bullish that the price of genome tests must continue to come down further to make a difference in healthcare around the world.

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

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

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

Guest:

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 http://blog.goldenhelix.com/?author=5. This Montana Canadian has something to say.

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.

Guest:

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.

Guest:

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?

Time to Rethink Cancer Therapy?

In an earlier post, I wondered a bit about the ultimate causes of cancer. For the last several decades cancer has been labeled as a genetic disease, an idea which we have chased with great fervor. Yet, It feels to me sometimes as though the evolving story of the causes of cancer is like a hall of mirrors in an amusement park in that there seems to be an ever receding chain of causal genetic alterations fueling cancer’s inexorable progression.



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