Next-Generation Sequencing for Sarcoma

Mrinal M. Gounder, MD

Today we are joined by Dr. Mrinal M. Gounder, a medical oncologist who specializes in the treatment of patients with soft tissue or bone sarcomas at Memorial Sloan Kettering Cancer Center (MSKCC) in New York City. Dr. Gounder presented an analysis he and his colleagues undertook to understand the impact of next-generation sequencing on diagnosing sarcomas and identifying therapy options for patients at the recently held American Society of Clinical Oncology (ASCO) annual meeting that took place in Chicago in early June.

-Interviewed by Anna Azvolinsky

OncoTherapy Network: First, can you talk about the way that most sarcomas are diagnosed, and the challenges of making an accurate diagnosis?

Dr. Gounder: The diagnosis of sarcomas really follows the same principles that pathologists use to diagnose any other cancer-knowing the history of the patient, the presentation, and their age. All of this is combined with standard techniques where a biopsy or occasionally an entire grossly resected tumor is first evaluated under light microscopy. This is followed by a number of different stains as well as immunohistochemistry to look for certain types of protein expressions; when they are in the ballpark of what the diagnosis may be, they use molecular testing such as FISH [fluorescent in situ hybridization] or RT-PCR [reverse transcriptase polymerase chain reaction] for a few limited genes to further confirm the diagnosis.

In terms of the second part of your question, diagnostically, this is a very tricky disease to diagnose accurately. The main reason is that sarcomas are just 1% of all of the cancers diagnosed annually. So the annual incidence of this disease in the United States is only about 10,000 to 15,000 patients. The word “sarcomas” encompasses anywhere from 50 to 70 different histologies, which are all completely unique, have unique natural histories, molecular biology, presentation, and response to treatment and prognosis. So, the challenge of diagnosing 70 different histologies that encompass only 1% of all cancers is a daunting task. This is particularly challenging for many of the community pathologists that don’t see sarcomas very frequently. To understand and know the nuances of the 70 different sarcoma histologies is something that requires a lot of evaluation and experience; even at the large centers that have dedicated sarcoma pathologists, there is quite a bit of confusion in making the right diagnosis. So the rarity of the disease, as well as the vast number of different histologies that encompass this one term, certainly makes this a diagnostically challenging group of cancers.

OncoTherapy Network: So where does next-generation sequencing come in? How is it currently used as a research tool for understanding sarcomas? Is it used at all in the clinic now?

Dr. Gounder: The simple answer is that next-generation sequencing has really taken off in the last 5 years or so. There are multiple private companies that offer this platform to evaluate hundreds of genes that may be aberrant, including fusions in all cancers. Next-generation sequencing itself is not approved in either soft tissue or bone sarcoma for any particular gene to serve as a biomarker or to make a particular diagnosis. Having said that, at this point, individuals who have the resources or have insurance companies that are willing to pay some or all of the cost associated with next generation sequencing do go ahead and have their tumor sequenced. So to answer your question, this is not Food and Drug Administration (FDA) approved; there is currently no FDA-approved biomarker to do routine next-generation sequencing in the clinic but we do use it when patients or the insurance companies pay for it.

OncoTherapy Network: Can you tell us briefly about the design of your study and how next-generation sequencing is and can be used to diagnose sarcomas?

Dr. Gounder: Sure. This is a retrospective study and at MSKCC, we actually partnered with a private company called Foundation Medicine (Cambridge, MA) that does genomic sequencing and profiling as part of a platform that they offer to patients. We looked at the sequencing information on about 5,750 patients who were sequenced with a diagnosis of soft tissue or bone sarcoma over the last 4 or 5 years. There were two important questions we wanted to ask. We just didn’t want to look at the genomic landscape of soft sarcoma and the different histologies because that sort of work has been done and reported over the last decade or so. The question we really wanted to ask is: Does genomic profiling of sarcoma patients make a difference in their diagnosis or does it make a difference in terms of their treatment, or even in their prognosis? In order to answer that question, we really needed to have clinical outcomes on patients. Following IRB approval, we looked at about 120 patients at MSKCC who underwent genomic profiling using the Foundation Medicine platform and we reviewed their clinical outcomes. We looked at a very small portion of the whole cohort (5,750 patients)-about 2%-and asked the question of whether genomic profiling can help in the management of patients from a diagnostic as well as a therapeutic perspective.

OncoTherapy Network: What were the most important findings from the study?

Dr. Gounder: We had some really profoundly surprising and important findings. So the first thing is, as I mentioned, that the diagnosis of sarcomas is really challenging. This large cohort of 5,750 patients is worldwide, so what we are seeing is real-world diagnosis and practice and not just patients who are seen at large tertiary academic centers. When we looked at the pathology report and diagnosis that was issued for the patient and compared it with the genomic profiling that happened down the road, we noticed there were a significant number of mistakes that had occurred. In total, about 8% of all patients had either an incorrect diagnosis or very high suspicion of an incorrect diagnosis, or there were opportunities where the genetic term “sarcoma” could have been further refined and a specific histology could have been assigned if the information from genomic profiling was utilized at the time of initial diagnosis. That percentage (8%) of errors or opportunities for further refinement is a really high number for any cancer, and the nuances between these different histologies really make a big difference. The natural history of each of these histologies is different, as is the molecular biology, and thus the treatments and prognosis are sometimes different. Therefore, making an accurate diagnosis down to the exact type of sarcoma is really essential. In some instances, the diagnosis is so off that patients who are supposed to get life-saving chemotherapy are not, and others are getting unnecessary chemotherapy because the diagnosis is incorrect. We are further looking into this in terms of the clinical trials outcomes and we will be part of the manuscript that is in preparation.

Another major aspect that we wanted to understand was what are the therapeutic opportunities in doing genomic profiling? We found that using current technologies, we were unable to find any actionable mutations in about 40% of all sarcomas. But the remaining patients had multiple types of actionable mutations for which current FDA-approved drugs or clinical trials could be used. We categorized these sarcomas into three different categories: 1) evidence where there is an FDA-approved drug for an FDA-recognized biomarker; 2) evident where there is an FDA-approved biomarker for an FDA-approved drug, but in a different indication; and 3) novel or emerging mutations to which there are investigational drugs that are currently in clinical trials as part of NCI-MATCH [National Institutes of Health Molecular Analysis for Therapy Choice] study or the ASCO TAPUR [American Society of Clinical Oncology Targeted Agent and Profiling Utilization Registry] trial, for example. The third category accounted for the vast majority of cases. We were also able to find several mutations that conferred resistance to certain drugs, so in the absence of that knowledge, patients would have been exposed to drugs that they would not have benefited from. This is particularly important in certain diseases such as gastrointestinal stromal tumors and liposarcoma, for example.

In addition, we were able to look at the tumor mutational burden across the entire cohort of 5,750 patients and we found that the mutational burden of sarcoma was quite low (in the range of 2.5). But when we analyzed the data slightly differently, we found that there was certainly a tail where patients had a tumor mutation burden greater than 6, so we analyzed this differently by looking at tumor mutation burden greater than 10. These are arbitrarily picked numbers, but we found that about 5% of patients who had high tumor mutation burden would most likely benefit from current immunotherapy drugs.

Lastly, what was really surprising is that we found a remarkably high number of patients who harbored germline mutations, on the order of 9% or so. In clinical practice, none of the sarcoma healthcare workers really anticipate that the percentage of patients with germline mutations would be that high. So this certainly calls into question how we should change our practice and to be able to have discussions of germline testing of patients as well as their families moving forward. In some ways this is a paradigm shift of how we need to adjust the care of sarcoma patients moving forward. There are also several actionable fusions which have so far been unrecognized, as well as many other new genes and mechanisms of action that emerged in this work.

OncoTherapy Network: Thank you so much for joining us today Dr. Gounder.

Dr. Gounder: Thank you.