genomic medicine


Stefan Roever Talks the Future of Next Gen Sequencing

Guest:

Stefan Roever, CEO, Genia

Bio and Contact Info

Listen (7:34) Update on Genia technology

Listen (3:31) How will you compete with Illumina?

Listen (7:52) How will genomics scale in the clinic?

Listen (3:52) Encouraged to see nanopore sequencing now go commercial

Listen (3:26) Archaic regulatory environment holding back genomic medicine

Listen (5:10) Are you a believer in the DTC space?

Stefan Rover is the CEO of Genia Technologies, where he and his team are working on the next NGS technology. This space has become dominated by Illumina, who this year announced they had achieved the important benchmark of the "$1,000 genome." Stefan and Genia aim for the "$100 genome." In today's interview, we ask Stefan just what it will take for a new technology to break in to the sequencing market.

Beginning with an update on Genia's nanopore based sequencing, Stefan then goes on to talk about how NGS will scale in the clinic.

"Ultimately you don't want a doctor or the clinic to worry about how much does the instrument cost, how many reagents to order, and at what cost, etc," says Stefan. "All they want to do is provide a test and get an answer. And handling things like analysis in the cloud, or patient confidentiality, or integration with payer reimbursement systems---all of that is something that can be handled in a cloud service that can be integrated with the instrument."

Stefan says that the biggest challenge for genomic medicine is our regulatory system, which he calls "archaic." Speaking directly about the FDA's recent clamp down on 23andMe, he favors a system where there are competing regulatory agencies and where the market itself is allowed to raise the value of genomic tests.

Stefan says he's "absolutely" a believer in the DTC genomics space. Consumers own their genomic data and should be able to access it freely, he contends.

"The consumer should be able to go to any service they want and ask any question they want regarding their data."

The discussion about regulation with Stefan provides a preview into our upcoming series, Regulation and Genomic Medicine, where we'll be interviewing Cliff Reid of Complete Genomics, Anne Wojcicki of 23andMe, Alberto Gutierrez of the FDA, among others.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Bioinformatics Pioneer, Martin Reese, on Scaling Up Human Genome Interpretation

Guest: Martin Reese, Co-founder, President & CSO, Omicia

Bio and Contact Info

Chapters: (Advance the marker)

0:40 How did you get started in bioinformatics?

3:04 What is the biggest challenge with human genome interpretation?

8:01 Diagnosing Ogden Syndrome

13:30 What sets Omicia apart?

18:08 Who is ordering your tests?

23:29 FDA letter to 23andMe unfortunate

25:47 What's your main objective for 2014?

Martin Reese's career in bioinformatics began in 1993 when he attended a lecture in Heidelberg, Germany entitled "Genome Informatics." Reese, a German, then switched his studies from medical informatics to bioinformatics and moved to Berkeley where he worked on assembling the genome for the Human Genome Project. In 1996, he started a company with his Ph D advisor, David Haussler (of Genome Browser fame), called Neomorphic, part of the first commercialization of bioinformatics.

Martin is now the president of Omicia, a company he founded to take on the challenge of scaling up human genome interpretation.

How far have we come in the clinical interpretation space? Martin says that in 2013, 80% of human genome interpretation was done for research and 20% for the clinic. In the next 3-5 years, he predicts those percentages will switch to 20% for research and 80% clinical.

Martin says that one of the biggest challenges for human genome interpretation is easy-to-use visualization tools. For this reason, he's been a fan of the DTC company, 23andMe, and felt that the FDA's letter to the company was "very unfortunate."

"[23andMe] educated the whole population about genetics," he says in the interview, "and they tried to make the reports easily understandable and manageable by a regular person. . . . The easier we make the reports, the better doctors can understand them."

Just who is ordering reports from Omicia, and what is the company's objective in the year ahead? Join us for an insider's take on clinical genomics.

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The Clinical Sequencer

A Feburary 7th article in the online version of Nature magazine began with the line, "Genomics finally came of age as a clinical discipline on November 19, 2013, when the US Food and Drug Administration (FDA) approved Illumina's MiSeqDx next-generation sequencing (NGS) system for clinical use."   

Now, some may argue with this and say genomics was coming of age with the BRCA test from Myriad back in the nineties, or with the use of NGS for cancer treatment, or the rise of prenatal diagnostics.

Noam Chomsky on Language and the Study of Biology

Guest:

Noam Chomsky, Professor of Linguistics, MIT

Bio and Contact Info

Listen (6:34) Reductionism? Not so fast

Listen (3:10) How does a scientist come up with better questions?

Listen (2:54) Do we need new metaphors in biology?

Listen (5:29) Are data scientists getting enough basic science?

Listen (5:13) Does science have a PR problem?

Listen (2:07) How does a culture go about solving ethical issues?

Our guest today is the intellectual giant, Noam Chomsky. He is widely known as the "father of linguistics," and joins us for our Philosophy of Science series.

If linguistics is the scientific study of language, the purpose of today's interview is to talk about the language of scientific study.

We begin with the question of reductionism and whether the study of biology is being limited by a method of inquiry developed with physics and chemistry. (See earlier interview with John Dupre.) Chomsky urges caution.

"If you look at the history of the hard sciences, it has not been consistently reductionist by any means," he says.

Using examples from the history of chemistry, Chomsky points out that though there were attempts to use principles of physics to study chemistry, it often didn't pan out. By the time you get to the twentieth century, there was a real break between chemistry and physics. With the work of Linus Pauling came about the unification of physics and chemistry. But "this is not reductionism," he insists. Chomsky says it may turn out the same for biology. That biology must be studied in its own way "with an eye to unification" and this unification may or may not be reductionist.

What about our overly gene-centric notion of biology which is now being replaced by systems biology?

"What should be done in science is to pursue all directions and see which ones work out," he suggests.

Chomsky is surrounded at MIT with data scientists. Does he think that "code writers" who are increasingly taking over biology with their ability to mine huge data sets are trained enough in basic biology?

An outspoken activist, Chomsky doesn't shy away from a discussion of the politics of science. Is science suffering from a PR problem in the US? And if so, what can be done about it?

We conclude with a discussion of the murky area of bioethics in which Chomsky says "there are no algorithms to tell you how to proceed."

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Illumina Dominates NGS with Still Much Room for Improvement

Guest:

Shawn Baker, Chief Scientific Officer, AllSeq

Bio and Contact Info

Listen (3:39) #AGBT14: to tweet or not to tweet

Listen (6:23) Illumina solidifies dominance

Listen (6:07) The Wizard of Oxford?

Listen (4:21) Qiagen with a killer workflow

Listen (2:21) Genapsys teases

Listen (1:07) Affy founder with a new technology

Listen (2:26) Aw shucks - a new reference genome

Listen (4:49) Where to from here?

Today we begin our annual sequencing series with Shawn Baker, Chief Scientific Officer at AllSeq.

In today's interview Shawn links highlights of last week's AGBT conference with the overall trends in the sequencing space. If last year was all about "long read" technology, Shawn says this year is about Illumina's total domination.

Yet there are newcomers. Qiagen is set to introduce a sequencer designed for clinical use. After picking up bioinformatics platforms, CLC Bio and Ingenuity last year, "Qiagen will have the workflow, start-to-finish, that no one else has these days," says Shawn.

The upstart Genapsys, funded by the Russian tech investor Yuri Milner, presented at AGBT with a teaser on their new sequencer with the footprint of an iPad. And Affymetrix founder, Steve Fodor, introduced a new company with a product that will integrate with NGS.

It's one of the hottest technologies in our business, and Shawn, who maintains an up-to-date Knowledge Bank at AllSeq.com, can talk about it like no one else. Presenting NGS 2014.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Antireductionism and Biology: An Interview with John Dupre, Philosopher of Biology

Guest:

John Dupre, Professor, University of Exeter

Bio and Contact Info

Listen (2:19) Why should scientists think about philosophy?

Listen (8:47) Antireductionism

Listen (6:04) Have molecular biologists suffered from reductionism?

Listen (9:20) Underestimating the problems of biology

Listen (2:01) Are biologists getting the message?

Listen (5:29) Do you think much about the GMO controversy?

When a researcher is doing basic science, what is meant by that? Indeed, what is science? Ernest Rutherford, a British chemist and physicist at the turn of the 20th century remarked, “all science is either physics or stamp collecting." Is this true? Can all science be reduced to physics or does a discipline such as biology need to be studied in its own way? We can ask more specific questions pertaining to life science. What is a genome? And is the tree of life really a tree? And furthermore, are these questions really that interesting?

Here to answer these questions and kick off a new series, "Philosophy of Science," is John Dupre, a philosopher of biology and professor at the University of Exeter in Southern England. John is an antireductionist. In today's interview he argues that molecular biologists have been limited by a system of science inherited from physicists and other scientists that has been overly reductionist. For example, he says that biologists have relied too much on certain models of the cell without remembering that these are abstract models.

"The real nature of the parts is really shaped by the sort of system that it's participating in," he says.

It's true that we've recently seen biologists become more concerned with "systems" and move away from the overly gene-centric view of biology. The power of new tools and cheap computing are now opening up new possibilities to look at the vast network of connections that transpire in biology. However, John questions whether the new systems biologists aren't just more reductionists working at large.

Should scientists be studying philosophy? John answers, " . . . some scientists need to think more about what they're doing than they're often given time to do."

We finish with a question about the public controversy over GMOs.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Why Scientists Should Study Philosophy

Since the first human genome was sequenced, there has been disappointment in and with the life science community over the fact that we haven’t figured out more of the big biology problems.  Cancer, for instance.  Oh, there’s been rapid technological progress.  Illumina announced this year that the human genome that cost $3 billion to sequence originally can now be done for the cost of a root canal, or $1,000.  

So why the disappointment?  Why were scientific expectations so high?  



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