Ion Community

Ion PGM Dr. James Watson Healthcare Grant

Dr. John Iafrate, Director, Massachusetts General Hospital's Diagnostic Molecular Pathology Laboratory
Dr. Long Phi Le, Clinical Pathology Resident/Molecular Fellow, Massachusetts General Hospital

Share

Drs. Iafrate and Le propose using Ion technology in broad-based tumor diagnosis, prognosis, and treatment stratification. The Ion PGM's short run times and direct sequence data make it practical for the clinic.

The Diagnostic Molecular Pathology Laboratory is a clinical service laboratory offering specialized molecular DNA testing focused on tumor diagnostics. The laboratory currently performs various testing for cancer gene mutations based on PCR, sequencing, SNaPshot technology, and FISH.

Question & Answer

Your Ion PGM Sequencer Grant application proposes a broad-based cancer genotyping initiative in a clinical setting. What are you doing in this area currently?

Dr. John Iafrate:  If you are a cancer patient coming now to Massachusetts General Hospital, an initial cancer diagnosis would first be established based on histological review by a pathologist. In the current era of genetics, we realize that the classification of tumors based solely on microscopic diagnosis is not sufficient. We would want to know more about the mutation profile of the tumor and perhaps identify its Achilles Heel, or weak point, for the purpose of targeting the mutations in what is known as personalized cancer therapy.

To characterize tumors at the genetic level, most labs use low-throughput, traditional sequencing methods such as Sanger sequencing to examine one or two point mutations. Last year we launched an assay based on the SNaPshot technology from Applied Biosystems to test about 100 most common cancer mutations all at once. Based on the findings, we can tell patients in more detail about the molecular subtype of their cancer. This information may be used to inform patients about their prognosis or to match patients with targeted treatment. Our goal is to apply this clinical test for all cancer patients.

What advantage does Ion Torrent offer you over these technologies?

Dr. John Iafrate:  The SNaPshot assay we are using as well as other conventional genotyping techniques cannot provide us the amount and type of data that we need for comprehensive genotyping. There are just too many genes and too many mutations to use an approach which detects hot spot mutations. There are several very large genes that are important in cancer. PTEN for instance, which when mutated activates an important cancer pathway, is too large to be analyzed using a point mutation assay.

So what we need is more comprehensive sequencing for cancer. But performing Sanger sequencing on, let's say, 1,000 to 2,000 exons, which is really what we are considering to be the minimal cancer gene subset, would be an engineering feat and inefficient. It would also be very expensive. So over the past few months we've been exploring the idea of next generation sequencing, which would allow us to achieve deep sequencing of critical cancer gene targets. We think that next-generation sequencing, and hopefully the Ion Torrent system, will allow us to obtain a fully comprehensive cancer genotype profile, so that we can find the vast majority of mutations that could possibly be causing the tumor.

Ion Torrent stood out to us immediately as possibly having a number of key advantages. First, the short run time is critical in the clinical arena for quick turnaround time. Second, the simplicity of the data, which is direct sequence data rather than image-based data, makes the bioinformatics challenge seemingly much simpler for a clinical lab. Third, the low cost of the technology would allow us to scale up our operation for high volume testing. The clear dedication of the company towards making this type of technology more widely available to the clinical lab also appealed to us. So when we thought about the ability for clinical application, ease of use, plug-and-play potential of the instrument, price point, and philosophy of the company, it just seemed like a perfect solution.

Where is your project going from here?

Dr. Long Le:  Using the Ion Torrent PGM Sequencer, our proposal is to develop and validate a sensitive, broad-based cancer genotyping assay that would be applied within the constraints of a clinical setting for all tumors.

The next six to 12 months will encompass the validation stage where we finalize the targets that we're interested in and narrow down our choice of target enrichment. Following that will be validation in terms of comparing our samples of known mutation status with the Ion Torrent data. We need to determine the sensitivity and specificity of the technology and make sure that it's compatible with clinical testing, that is, of good enough quality to be documented in a patient's chart.

In the next year or two, we would plan for a clinical launch. We anticipate a fantastic reception from our clinicians who would apply the comprehensive genotype profile in the management of their patients. What has not been mentioned are the possible clinical correlations that may arise. Data will be generated that may help plan novel clinical trials based on newly defined targets or stratify patients based on prognostic information. These are the rewards that would be reaped in the two- to three-year range and beyond.

I would like to add one comment. Our work is specific with regard to the cancer field, but should this technology work for us at the clinical level, it is going to change genetic diagnostics in other fields as well. In pediatric patients with constitutional disorders, next generation sequencing of implicated genes in inherited diseases would be more affordable where it's currently costing a whole lot of money to do Sanger sequencing. Imagine a panel of all the relevant genetic targets for a certain syndrome, and imagine sequencing all of the genes of that syndrome for the price of what it costs right now to sequence a few exons and to be able to do that with a 1-2 hour run. That's exciting.

Share