genomic medicine

Classes for the school year begin this week at Stanford University. New to the faculty is Carolyn Bertozzi, an American chemist who made her name across the bay at Berkeley and was wooed to Stanford by a chance to do research and teach chemistry in a new interdisciplinary institute known as ChEM-H. The institute will bring chemists, engineers, biologists and medical doctors together to understand life at a chemical level. We’ve often heard of biology and engineering institutes, or bringing bio and IT. This institute ups the ante and includes chemistry and medicine.

Carolyn is an outspoken scientist who feels that chemistry gets short shrift in a time when biology is considered the queen of the sciences. She points out that the National Insittues of Health tend to be lead and run by biologists. We usually call it biomedical research, not chemical-biomedical research. And yet, she argues, it is chemistry that will give us the answers going forward.

“This is a bit of semantics, but I’d say that what we don’t understand about biology is what happens at the level of molecules. What we don’t understand about biology is the chemistry of it. It is hard to see. You need a different set of tools and technology to see what happens at the molecular scale. And that is the chemistry,” says Carolyn in today’s interview.

Does Carolyn think there’s too much hype around genomics? Would she like to see a revival of chemistry?

As the editor-in-chief of a new open access journal, ACS Central Science, Carolyn will be publishing much more on the topic, making louder and prouder the voice of the chemist.

Diagnostics can be a tough business. The FDA is making a strong push to bring more oversight. Obtaining reimbursement can be outright Sisyphean. And clinicians are slow on the uptake. All of which makes today’s story so good.

Located at 106 Gregor Mendel Circle in Greenwood, SC, the Greenwood Genetic Center became the first lab to partner with Affymetrix to commercialize their recently FDA cleared CytoScan Dx assay. This test is the first-- and so far the only--FDA cleared whole genome test to aid in the post-natal diagnostic evaluation of constitutional disorders, such as developmental delay.

In today’s interview, Alka Chaubey, director of the cytogenetics lab at GGC, explains why this array-based test has become so successful.

It’s taken some time, but the NCI is finally sponsoring a big time clinical trial for cancer where the patients are organized by the genomic pathway that defines their cancer rather than the organ type.

"Instead of being a breast cancer trial, or a colorectal cancer trial, or the usual construct that’s been used, this one is obtaining biopsy specimens from patients with a whole variety of differing tumor types, evaluating them with a standardized platform to identify abnormalities, and then linking those abnormalities to arms in the trial with drugs targeted to those abnormalities. This is a completely new way of doing a clinical trial and becomes an important step in moving forward a precision medicine cancer therapy approach,” says today's guest, Stanley Hamilton, head of Pathology and Laboratory Medicine at MD Anderson Cancer Center.

How are the four centers participating in the trial going about selecting patients for this new trial? And what pathways does Stanley foresee dominating the trial?

Stanley’s lab has chosen to use Thermo Fisher’s Ion sequencers to characterize the patients’ genomic pathways. Why? Find out the answer to these questions in today’s interview with one of the leading PI’s for this unique clinical trial.

Nathan Pearson, formerly a genome scientist at Ingenuity and Knome, has been doing public outreach for genomics at the New York Genome Center for about a year now. In today’s interview, Nathan says he always wanted to be able to speak directly to the larger public about the great science he’s been involved in.

“Ever since graduate school, I’ve wanted to take insights from our field to the public more directly. Not just through the ivory tower--the education system that is set up to train scientists—but to help other people out there who won’t be professional scientists. They can benefit from the insights that science brings societally, and can also increasingly contribute to those insights by investing their own data on behalf of science," he says at the outset of today's show.

Nathan offers first an overview of the mission at the NY Genome Center and lists examples of their collaboration projects. Then the interview runs a bit like a review of genomic medicine as of summer 2015.

What are Nathan’s thoughts on the debate over how much of the genome is functional? What is Nathan doing to reach out to the general public? And is he concerned about the ‘hyperbolome,' or the over hyping of genomic discoveries and technologies?

Matt Might came knocking on the door of genomic medicine out of pure necessity. After a four year diagnostic odyssey that led them to Duke University, Matt and his wife, Cristina, finally found out through exome sequencing that their son, Bertrand, was suffering from a rare disease known as NGLY1 deficiency. That was three years ago.

In today’s interview, we focus on what Matt did after he received this diagnosis. Through various means, mostly involving the internet, he has been able to connect with the parents of thirty seven other children with the same rare disease. As the group of patients grows, so do the options for studying the disease and for developing a therapy.

Since the president launched his Precision Medicine Initiative, we've heard from a new round of critics that genomics research just isn’t paying off. Matt’s story contradicts these criticisms.

In fact, he comes right out and says he’s on a campaign "to end the phrase, ‘non actionable.’” To Matt--who’s career has been in computer engineering--science is medicine. Matt’s connection with the rare disease community was kicked off with a personal blog he wrote that went viral, Hunting Down My Son’s Killer. Matt says with Google, blogging, and social media parents everywhere can do science. 

Prior to recording this interview, Matt was at the White House for a couple weeks helping out with the president’s new initiative. What is his take on that, and, as an outsider, what is the number one thing he would change about biomedical research?

Last year, pharma giant Roche went on a buying spree, picking up one company after another. In December, when it was announced they had bought out Bina Technologies, many of us were playing catch up. Who is Bina, and how do they fit in the overall bioinformatics space?

Today we hear from Bina's CEO, Narges Bani Asadi. As with many new bioinformatics companies, Bina has changed their service and product since they spun out of Stanford and UC Berkeley four years ago. Narges says that the biggest demand from customers is to provide a comprehensive solution for the entire organization. Often, she says, she encounters brilliant bioinformaticians working at customer organizations who are completely overwhelmed by all of the various informatics tools available. Many of these tools are offered free over the internet, and, she says, it’s creating “open source overload.”

Bina has been a very ambitious company from the start, working to provide NGS users with a comprehensive informatics solution, from beefy, fast infrastructure to an interface for the various kinds of users in an organization, to high powered analytics. And Narges is excited about the Roche buyout, saying that it will speed up their plans. Indeed, just providing bioinformatics solutions to Roche in both their drug and diagnostic divisions is already a huge project.

What was Bina doing so well that attracted Roche, and what will the future NGS informatics ecosystem look like? Join us for an inside look at the world of bioinformatics with one of the space’s most dynamic leaders.

In the second part of our interview with Tim Triche, Director of the Personalized Medicine Center at Children’s Hospital Los Angeles, Tim says that micro arrays are still a vital technology for today’s cancer researcher. Making use of both next-gen sequencing and arrays for his research, Tim confirms that arrays still have advantages in the clinic as well, such as quicker turn around time. 

Tim also weighs in on some ongoing questions about whether poor biospecimen quality is hampering research efforts and whether genomic medicine is paying off for patients. 

Go to Part 1:  Want Answers? Look to the Non-Coding Region of the Genome, Says Cancer Researcher, Tim Triche

Listen to Tim Triche from Children's Hospital Los Angeles for very long and you’ll get excited again about cancer research. I couldn’t stop listening. Which is why his interview is being published in two parts.

Now sure, like other guests we’ve had on the show, Tim calls this the “absolute golden age of biomedical research.” But Tim has a unique story. He has been, and is still - though less so now, he says - an outlier in cancer genomics. Whereas most cancer researchers talk about genes, Tim is more interested in non-coding RNA.

An avid user of microarrays, Tim begins Part 1 of the interview with a reference back to “a very interesting experiment” done at the Affymetrix research lab when the first arrays were being designed. The Affy research team put (nearly) the entire stretch of chromosome 21 onto a wafer, and in a “beautiful Science paper” showed the importance of the non-coding or inter-genic region of the genome.

Using the Affymetrix Exon array that was developed as a result of the experiment, Tim has continually demonstrated that there are indeed useful diagnostic and prognostic cancer biomarkers to be found in the non-coding RNA.

And speaking of technology from the early 2000’s, Tim argues that we should reconsider GWAS studies. Perhaps there are still some simple answers to be found when considering the whole genome and not just genes.

In Part 2, Tim vows the incredible staying power of the array technology in the clinic as well as research. He also responds to recent skepticism over whether the age of genomics is delivering on its promise.

Editor's Note:  In this interview, Tim refers to an older generation Affymetrix array (GeneChip^(R) Exon 1.0 ST Array).  The newest array (GeneChip^(R) Human Transcriptome Array 2.0) is able to measure gene and exon level expression of coding and long non-coding RNA with the ability to detect alternative splicing events.

When science journalist Ivan Oransky co-founded Retraction Watch, a blog with the express purpose of making scientific retractions more public, he didn’t think he would be posting much.

“Adam Marcus, my co-founder, was quoted as saying, ‘yeah, we figured we’d post periodically, our mothers would read it, they’d be very happy, nobody would read it other than them.’ Obviously that hasn’t been the case,” says Oransky in this first of a series of podcasts on scientific integrity.

Now putting out almost a post a day and funded in party by a grant from the MacArthur Foundation, the blog has revealed - and no doubt helped drive - a boom in retractions the last few years.

What is leading to so much bad research, and just how is Oransky’s blog keeping scientists honest?

Oranksy points to science career pressures and financial incentives as part of the problem. He also explores the issue of cell line authentication, a particular quality concern in cancer research.

We couldn't resist the chance to pull this veteran journalist into our recent debate over whether the genomics revolution is delivering on its promise.   

And finally, Oransky was at the now infamous woman's luncheon in South Korea last month when a nobel laureate, Tim Hunt, blew the crowd away . . .  and not with brilliance.

Pharma companies have always had their chief medical officers (CMOs). Now, as the diagnostics industry grows, many kinds of life science companies are filling this important position as well. Sequencing tool makers, direct-to-consumer firms, bioinformatics companies—they’re all appointing CMOs.

Paul Billings was the first and only CMO at Life Technologies before they got bought out by Thermo Fisher. Now he’s filling that role at Omicia, the genome interpretation company where he manages clinical cases and the transmission of information to doctors and patients. He also handles regulatory issues and clinical trial selection. And, as eloquently demonstrated in today's show, he represents his company externally, a vital and delicate function in a rapidly changing, heavily regulated industry.

This position gives Paul a clear window into some of the most important topics and debates we’ve discussed on the program: patient consent, direct-to-consumer testing, the use of arrays vs. sequencing, and the regulation of laboratory developed tests (LDTs).