Exomes Are a Transition Test
At the heart of the move towards precision medicine, is the ability to make powerful diagnoses to pinpoint exactly what is at the route of a patient’s troubles. One of the central technologies being used for this is Next Generation Sequencing. At this year’s American Society of Human Genetics, we caught up with Haim Neerman, CEO of Variantyx. As a company, Variantyx have been working with clinicians, labs, and hospitals, to enable fast and accurate diagnosis at a reduced cost. Read on to find out why the clinic is making the move to whole genome sequencing.
FLG: Why is whole exome sequencing becoming more widely accepted as a diagnostic test?
HN: If you look at it from the payer’s perspective, exomes provide a much faster diagnosis at a much lower overall cost than the standard protocols being used today. With the maturity in the technology, drops in sequencing price and better quality, exomes are becoming the first line of diagnosis in hospitals. However, we believe that exomes are a transition test. In a few more years, labs will be screening whole genomes rather than exomes. For now, the preference is largely due to costs.
FLG: What makes whole genome sequencing more attractive?
HN: It provides comprehensive coverage of both coding and non-coding regions and the ability to identify more than just small sequence variations – including structural variants. You can detect deletions, duplications, inversions, trinucleotide repeat expansions and mitochondrial variants … You can’t do that with exome sequencing. It’s practically all genetic tests in one.
Today, whole genome sequencing costs about 1,300 USD. The price has dropped rapidly over the last few years. Illumina is talking about eventually getting that price down to as low as 100 USD. At those prices, you can sequence everything, do the analysis, and have a very affordable test. As whole genome sequencing identifies most genetic variations, we believe many of the other tests, including panels and exomes, will become obsolete in a few years.
FLG: You recently launched Variantyx Unity™, a WGS-based test that combines multiple genomic diagnostic tests into a single test that identifies small sequence changes, structural variants, trinucleotide repeat expansions and mitochondrial variants. How did that go?
HN: We launched at the NSGC (National Society of Genetic Counselors) conference in September. We’ve run about 100 samples, and the diagnostic yield is amazing. We might have gotten a little bit lucky, but the yield is up at 70%. You typically see diagnostic yields of around 40% in exomes, so it definitely reinforces the advantages of whole genome sequencing. It covers more, saves time and money, makes it easier for payers, and reduces the diagnostic odyssey for the patients.
FLG: How does the Genomic Intelligence® platform work as part of this?
HN: Genomic Intelligence® is the proprietary software platform that we’ve built. It’s clinically validated to identify and annotate the different types of variants which are then interpreted and selected for clinical reporting by our medical geneticists. It is a clinical platform intended for clinical use. Whenever we update the algorithms or annotation sources, we calibrate it against the data from a few thousand samples we’ve already sequenced. In addition to using the platform to directly support our Variantyx Unity™ test, some of our customers use the platform as a service to perform their own tests and diagnoses. So it also works for labs and hospitals that want to do the testing work in-house.
FLG: How do you see the field progressing over the next 5-10 years?
HN: It’s difficult to predict the future. In an ideal world, every new-born baby will be sequenced, and the data will follow them for their entire life. Diet, exercise, pharmacogenomics… it will be used for wellness as well as for diagnosis and treatment. That’s not as far away in the future as some people think. We’re almost there. It’s an exciting space to be in. I’m looking forward to the development of the industry and Variantyx along with it.