arrays

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.

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.

Jeremy Koenig is a molecular biologist and an athlete. His interest in both led him to found a new direct-to-consumer genetic testing company called Athletigen.

Still it its early days, the company has curated several genetic markers which tell about a person’s athleticism. With their first report now available, the company makes it super easy to get started if you have already used 23andMe’s service. The athletigen.com portal will link in to 23andMe and retrieve your raw data. Within minutes you can be looking into whether you’re more of a power or endurance athlete, or whether your body will respond well to the paleo diet, among other predispositions. The report is free.

So how will the company make money, we ask Jeremy, who is also CEO. And, being a Canadian company, what regulatory hurdles does the company face? The DTC genetic testing space has been a treacherous one. The winners have been those companies which offer non health related products, such as genetic ancestry or paternity, or those which have sold large data sets to big pharma.

In today's show, Jeremy points out that the human body is the ultimate technology, and that athletes push this technology to its limits. Athletes can learn from their genes. And the rest of us can learn from studies of athletes and their genes. Will the field of sports genetics take off and open up new possibilities for research and precision medicine?

“One of the things my coach said to me as an athlete in college - I was a hundred meter sprinter - he’d say, 'Jeremy, we are all wearing different bodies, and you need to embrace yours. Don’t think that you need to do what the best sprinters in the world are doing right now. You need to do what’s good for Jeremy.' I think everyone needs to take stock of their own DNA,” says Jeremy.

Go about anywhere in the life science industry, and you’ll run into someone who once worked at Affymetrix. Since the founding of Affymetrix and the development of what’s come to be known simply as the Affy chip, the company’s history has been intertwined with that of biotech and the genomics revolution. But what has become of the company today?

In the present heyday of DNA sequencing, some have predicted the death of Affy’s chip or microarray, a platform celebrated in it’s time for the ability to see thousands of genes in one assay. But a recent deal with the prenatal diagnostics company, Ariosa, signals that the array is anything but dead.

Today we talk with Affymetrix CEO, Frank Witney, who has engineered a certain comeback for the company. In the Fall of 2013, Affy's stock hit a low point of $3.01 per share. They had just purchased eBioscience for their flow cytometry technology in an effort to diversify. But Affymetrix was dangerously low on cash. Since then, though, the stock price has quadrupled and quarterly earnings are consistently beating analysts' expectations.

What happened? What is the future of arrays? Will they actually come behind sequencing and be the main workhorse for translating genomics into the clinic?