personal genomics

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.

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.

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?

DTC Genomics: Opportunity Lost?

Once I warmed up to the idea of startup companies offering to sequence the DNA of anyone capable of ordering from, I began to look forward to what might come of this nascent industry. Enabling individuals to have their DNA sequenced certainly seemed like an out-of-the-box idea at the time and I wondered if a so-called paradigm shift might arise from placing genetic information, unfiltered and unadvised, in the hands of its owner.

I had(and still have) two chief hopes for "paradigm shifts" that might come from throwing the genetics box wide open:

Best of Mendelspod 2012

Thank you to all our 2012 sponsors and underwriters! Your support enables us to tell some great stories from the front row of a fascinating, ever unfolding industry.

Our final show of 2012 is a compilation of highlights from throughout the year. If you remember, it started off with some great buzz about sequencing. Both our series on sequencing and what to do with all the data is represented. 23andMe’s Anne Wojcicki came on the program to talk about her direct to consumer approach. This year we spent time with some folks who are attempting to shake up the industry and we’ve included two of them in today’s show. Finally we end with a selection from our series, Science and the 2102 Election.

(See Guests for speakers' bios.)

Listen (2:09) Paul Billings talks up the Ion Proton from CES in Vegas

Listen (8:37) Sultan Meghji weighs in on Roche bid for Illumina and the future of genomics

Listen (3:12) Anne Wojcicki answers questions from the audience

Listen (8:28) Big Pharma's Apostle of Innovation speaks out

Listen (4:56) Bill Frezza insists that the life sciences need a Grand Awakening

Listen (2:10) Chris Mooney: if scientists are the new world rulers, they don't know it

Listen (:48) Year end note to our audience

Happy New Year! from the Mendelspod Team