Memorial Sloan Kettering Cancer Center study points to expanded genomic screening that aims to benefit children and young adults

NEW YORK, May 18, 2022 – New findings from researchers at Memorial Sloan Kettering Cancer Center (MSK) and published today in the journal Nature Communications report the results of using a comprehensive sequencing approach on 114 pediatric patients, adolescents and young adults with solid tumors. The researchers found that their approach identified at least one additional oncogenic variant associated with cancer in 54% of patients (62 out of 114), compared to the current standard gene sequencing test MSK-IMPACTa. Of these, 33 patients had one or more findings that were of direct clinical relevance or potentially actionable.

DNA sequencing tests that look for mutations in cancer-associated genes have become standard of care at major centers, including at MSK. The MSK test, called MSK IMPACT®, can detect mutations in more than 500 cancer-related genes. From this information, doctors can then determine if an available drug might benefit a particular patient, based on the genetic profile of the tumor.

This cancer gene panel approach works very well for adults with common types of cancer, such as breast, colorectal, lung, and prostate cancer. But for rare cancers in children and young adults, these panel tests haven’t been as helpful in matching patients to appropriate therapies. Indeed, as researchers are beginning to realize, the types of mutations that cause tumors in young patients tend to be different from those in adult patients.

“Adult cancers are usually caused by a permanent accumulation of mutations due to exposure to things like sunlight, cigarette smoke and carcinogens in food,” explains the doctor-researcher. Andrew Kung, who is director of MSK’s Department of Pediatrics and who studies the molecular causes of childhood cancers. “These mutations are usually what are called point mutations – where a single letter of DNA is changed in a gene.”

“With pediatric cancers,” he continues, “motor mutations tend to be structural changes affecting entire sections of chromosomes. These are often located outside the boundaries of known cancer genes, where they go undetected. by existing tests.

To better visualize these structural variants, researchers need a way to read not only changes to the spelling of particular “words” or cancer genes, but also the organization of those words in the context of paragraphs. and chapters. That’s what a technique called whole-genome DNA and RNA sequencing offers, and Dr. Kung and his colleagues believe it can make a big difference in the care of children with cancer.

“Everyone agrees that whole genome sequencing will eventually become the go-to diagnostic test for profiling tumors,” says computational oncologist MSK Elli Papaemmanuil. “But several obstacles stood in the way.”

Most important, she says, is being able to make sense of the vast amount of data that comes from sequencing the billions of letters of DNA that make up an entire genome – identifying and, relatedly, conveying clinically relevant information to physicians in a delay that could help with care decision-making. In the published research, researchers have refined the analysis of this data to be accomplished in days, compared to standard approaches that require weeks or months.

Not yet a replacement for further testing

The researchers point out that the new platform does not currently replace panel-based assays, such as MSK-IMPACT, which work well to capture relevant mutations in adult patients with common tumors – and have made a difference in their results.

“What we’re trying to do is bring a more holistic approach to pediatric patients and other people with rare cancers, a minority of whom benefit from panel-based testing,” says Dr. Kung. “We want to make precision medicine more inclusive and a possibility for every cancer patient.”

The study authors say the benefits for pediatric patients are so compelling that this type of test is now being made available to all MSK pediatric patients through philanthropic funding.

Funding for this study was provided by the Olayan Fund for Pediatric Precision Cancer Medicine. Memorial Sloan Kettering Cancer Center has intellectual property rights and financial interests in Isabl Inc., the company providing the technology described in this article. Drs. Papaemmanuil and Kung have intellectual property rights related to the technology. Dr. Papaemmanuil is co-founder of Isabl Inc., is CEO of Isabl Inc. and owns shares in the company. Dr. Kung is co-founder of Isabl Inc., sits on the board of directors of Isabl Inc. and owns shares in the company.

About Memorial Sloan Kettering Cancer Center (MSK)

As the oldest and largest private cancer center in the world, Memorial Sloan Kettering Cancer Center has dedicated more than 135 years to exceptional patient care, influential educational programs and innovative research to uncover strategies more effective in preventing, controlling and ultimately curing cancer. MSK is home to more than 20,000 doctors, scientists, nurses and staff united by a relentless dedication to beating cancer. Today, we are one of 52 National Cancer Institute-designated comprehensive cancer centers, with cutting-edge science and technology supporting groundbreaking clinical studies, personalized treatment, and compassionate care for our patients. We also train the next generation of clinical and scientific leaders in oncology through our ever-evolving educational programs here and around the world. Year after year, we are ranked among the top two cancer hospitals in the country, consistently recognized for our expertise in adult and pediatric oncology specialties.

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