genomic medicine


A Diagnostic Success Story with Alka Chaubey, Greenwood Genetic Center

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.

Is This the Future of Clinical Trials for Cancer? Stanley Hamilton on the NCI’s New MATCH Trial

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.

New York Genome Center’s Nathan Pearson on Public Outreach for Genomics

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?

Father of Child with Rare Disease Says Science Equals Medicine

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?

Bina CEO Details Secret to Success in NGS Informatics

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.

Cancer Researcher Tim Triche on the Staying Power of Microarrays

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

 

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.

Ivan Oransky on Today's Retraction Boom

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.

 

Participation in Genomics Research a 21st Century Public Good, Says Paul Billings of Omicia

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).

Gene and Tonic: The Tenth Commandment of Science, Icelandic Treasure, and TechBio Babies

We were off last week, so there’s plenty to talk about.

The big news has been about human germline modification.  Do you know about this?  MIT’s Tech Review put out an article early in the month that was kind of an expose suggesting that scientists around the world are beginning to modify the human germline.  Now, this is not the germs you pick up in a public restroom.  No, we’re talking the reproductive cells, our sperm and eggs.  We’ve been changing human genes before, it’s called gene therapy,  but never the germline because then the changes get passed on to future generations.   So it could be a good thing.  But it might be really bad.  Someone might make a mistake and create a new disease. 

And this danger has the scientific community up in arms.  Two groups of scientists took to the prestigious journals last week with papers, one in Science Magazine, the other in Nature.  

The Nature paper came out and said flatly:  Do not modify the human germline.  The Science Magazine paper, however was more . . . you might say optimistic.  This paper said let’s be careful.    If the authors of the Nature paper were setting themselves up as God  writing one of the holy Ten Commandments of Life Science with His finger: Thou Shalt Not Modify the Human Germline, then the authors of the Science paper were playing the loving gentle father who takes his son aside one day, and puts his arm around his shoulder, and says, son, or daughter, there’s something I should tell you about the world.  Just because you can fly a plane, doesn’t mean you should fly it into the side of a mountain.  And son, or daughter, looks dad back in the eye, and says,  but dad, no one would do that.

Speaking of cold mountains in Europe.  A treasure trove of genomic data was released out of Iceland this week.  Huh? Iceland?  Well yeah, after going bankrupt, the country may have just found their next big hidden natural resource:  genomic data. 

This is a treasure for two reasons:  first, the homogenous nature of the population.  There’s not much genetic mixing going on . . . because who the hell wants to  go and live on Iceland?

And two:  in hoping to benefit from this new natural resource, the citizens have been very willing to consent.  

So we’re seeing some cool stuff in this week's publication of the data.  There's been discovery of new disease causing genes.   For example, the MYLF gene was found in only eight people, and all eight have early onset atrial fibrillation.  There’s also a rare mutation that influences the thyroid.

Unfortunately, they haven’t found the gene yet that explains why someone would want to live on the North Pole.

Daniel MacArthur--he’s a geneticist at Mass General who’s in charge of the genomic data for the whole world--he says the work is very impressive, but completely unfair. He says deCODE, the company that generated the data, has now managed to get more genetic data than he has, and he’s funded by the Broad!  It’s just completely unfair.

No he didn’t say that.  

People in cold country are not the only ones being sequenced.  A report out of Saudi Arabia this week says that marriages are being called off due to genetic incompatibility!  One Saudi prince said that before he takes that fourth wife, he wants to be sure this time that she has no 'dominant' genes.

Speaking of arranged marriages, we attended the Techonomy Bio conference this week.  It’s an attempt to bring together tech and bio folks and see what happens.  One of the pairings was Marc Benioff, you know the tech billionaire and  CEO of Salesforce, interviewing Susan Desmond Hellman, the CEO of the Gates Foundation.  Benioff told Sue that he loved what she’s done with her bio, and Sue told Benioff she loves what he’s done with his tech.  And then they kissed.

No they didn’t.  They’re married--to other people.  But wouldn’t it be great to have one of these tech moguls marry a biotechie and then have techbio babies.  Benioff said that the place where tech and bio will meet is in digital health.  So they would be digital health babies.  But not everyone is on board with that.  One of the most tweeted lines of the day came from an investor, Greg Simon, who said he wasn’t convinced.  He said, “wearing your Fitibit into Dunkin Donuts does not a digital health revolution make.”

And that’s our show for March 27th.  Have a great weekend everyone.

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