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With $1.5M Grant, Columbia University to Extend Pediatric Precision Cancer Program Across NYC

NEW YORK (GenomeWeb) – With a $1.5 million grant from the Sohn Conference Foundation, Columbia University Medical Center is aiming to make genome sequencing more accessible to pediatric cancer patients in New York City.

The funds, which will be dispersed over three years, will enable the university to provide genomic analysis and expertise to pediatric cancer patients across NYC hospitals.

As sequencing technologies become cheaper, genomic analysis is becoming standard care in oncology, particularly in hard-to-solve cases and rare cancer types. Moreover, programs like the newly launched Sohn Precision Medicine Program are in line with national research initiatives, such as President Barack Obama's Precision Medicine Initiative initiated last year and Vice President Joe Biden's "moonshot" to cure cancer announced this week.

However, insurers pay for genomic testing — particularly the kind of whole-exome and RNA sequencing that will performed within the Sohn Precision Medicine Program — in very limited settings, often making such interventions financially out of reach for many patients and families.

"Why is this kind of testing not being done for every child with cancer? The reason for it is that the technology is so new that it is currently not covered by insurance companies," Andrew Kung, chief of the pediatric hematology division and stem cell transplantation at Columbia University Medical Center (CUMC), said today at an event announcing receipt of the grant.

He's hopeful the funds from Sohn Conference Foundation will make a difference in this regard. The aim will be to make genomic sequencing available at no cost to children who reside in New York City, are 18 years old or younger, and have cancers with a 50 percent or greater chance of relapse.

The Sohn Conference Foundation was started 20 years ago in memory of Ira Sohn, a Wall Street trader who at 29 years old died from cancer. The foundation, started by Ira's friends and family members, raises money for pediatric cancer by hosting financial conferences and in this way has raised $65 million to date. The annual conferences in New York draw several thousand attendees from the financial community and other meetings are held around the world.

"Our stakeholders are financial professionals," and the funds raised through the conferences often fund the "long-term play" — to advance cutting-edge cancer research, support fellowships, and back technology programs, said Evan Sohn, VP of the foundation and Ira's brother. The $1.5 million the foundation is committing now will fuel the "short-term play," said Sohn, "to affect children's lives today."

Doctors are currently able to cure 80 percent of childhood cancer cases. "For the 20 percent of the patients not cured, it is still the fact that cancer is the leading cause of disease-related death in children," Kung said. "That's a loss that we've wanted to try to address in a more direct manner."

Kung leads the Precision in Pediatric Sequencing (PIPseq) program, which is trying to make a dent in that 20 percent statistic. Within PIPseq, launched two years ago at New York-Presbyterian/Columbia's Morgan Stanley Children's Hospital, researchers have been conducting comprehensive genomic analysis for every pediatric cancer patient. The program involves a group of 40 people with cross-discipline expertise in pediatric oncology, laboratory medicine, genomics, and bioinformatics.

The Sohn Precision Medicine Program will be an offshoot of PIPseq, where pediatric patients in NYC can have exome sequencing on tumor tissue and normal tissue, as well as RNA sequencing of their tumor. These three types of testing — enabling identification of germline variants, somatic variants, copy number abnormalities, translocations, and gene expression changes — have been cleared by the New York State Department of Health. "I think we are the only entity that has all three of those approved as a test," Kung told GenomeWeb.

This testing will allow doctors to move beyond older technologies, such as certain kinds of chromosomal analyses, karyotyping, and fluorescent in situ hybridization. Currently, the sequencing within PIPseq is performed on Illumina technology, but Kung is open to exploring other platforms.

"It is not the case that the [sequencing] technology has now allowed us to suddenly cure 100 percent of patients," he added in a speech. "But what I can tell you is that the result of this type of testing has been deeply impactful, including patients who are alive and well today only because of the kind of testing we do."

In addition to sequencing, pediatric patients seen within PIPseq at Columbia have mouse avatars created for them, where patients' tumors are modeled on mice, so that personalized treatments can be tested before they are given to children. For one toddler with a particularly aggressive fibrosarcoma, doctors were able to identify a novel gene implicated in the disease. They were then able to use avatars to test and select a chemotherapy regimen that benefitted the child.

Mouse avatars may not be routinely available for patients from other hospitals, Kung told GenomeWeb, "because you need to be able to get [the samples] into mice quickly." However, the sequencing and other expertise from PIPseq will be accessible to high-risk pediatric cancer patients treated at other hospitals across NYC.

A program like PIPseq requires a large infrastructure and community hospitals usually lack the resources to put such an effort in place. "This is not an infrastructure that can be or should be rebuilt at every hospital in the city," recognized Kung.

"There are a lot of specialized tests for which there are reference labs that have the experience [and] the quality control," he said. "So, the idea is to take the platform that we have in place and become a reference lab where other places can send samples."

Every year, between 150 and 200 new cancer patients are treated within PIPseq. Through the Sohn Precision Medicine Program, Kung's group will expect to sequence an additional 100 samples from high-risk patients.

Within the precision cancer program, physicians typically receive results from advanced sequencing tests in a few weeks. According to Kung, his program's goal is to eventually return all results back in three weeks. "That's a time frame that works well with a child that comes in and gets started on a standard therapy but then, eventually, relapses six months or a year down the road," he said. "We'll have all the information ready. If we wait until a patient relapses, three weeks is too long."

Ultimately, with the grant from Sohn, CUMC will attempt to lift the cost barriers to genome sequencing for patients and families that otherwise wouldn't be able to access such testing. Tom Maniatis, director of CUMC's Precision Medicine Initiative, acknowledged that, immediately following the completion of the Human Genome Project in 2001, the medical and research field didn't appreciate how complicated it would be to integrate complex genomic information into everyday medicine.

"We're at a very critical phase now where we need the resources to prove to everyone, including the insurance companies, that this method of diagnosis and treatment of cancer is the wave of the future and has to be funded by society," he said.

As reported by GenomeWeb in 2014, when PIPseq was launched, the cost of the exome and RNA sequencing being performed within the program was in the range of $6,000 to $10,000. The cost is less now — $5,000 to $7,000 — but insurance coverage remains challenging.

CUMC has been putting a lot of thought behind how to demonstrate the value of genomic analysis to payors and make access to advanced sequencing technologies more equitable. The university recently held workshops to discuss reimbursement challenges with leaders in the insurance industry and healthcare inequities with experts in the medical field. "What was clear from these conferences was that by seeding the initial studies to establish the feasibility, we will be able to do this," Maniatis said. "And this gift [from Sohn] really does this in a profound way."

Although the grant from Sohn will fund testing initially, Kung is hoping that the reimbursement situation will improve by the end of the three-year period. There are already some encouraging signs in this regard.

NantHealth this week announced that Philadelphia-based Independence Blue Cross has agreed to cover its GPS Cancer test, which involves whole-genome sequencing of tumor-normal samples, as well as RNA sequencing and quantitative protein analysis for certain cancers. The agreement extends testing coverage for certain cancers, such as rare tumor types, pediatric cancer, metastatic cancer of unknown primary, primary brain tumors, triple-negative breast cancer, and metastatic cancers unresponsive to conventional treatments.

"We have to demonstrate the value of doing this … in terms of the impact on the patient but also in terms of cost-effectiveness," Kung said, noting that the critical task for any precision medicine program right now is to prove that patients are better as a result of having access to sequencing technologies.

Maniatis admitted that although the technology has great promise and has helped many patients, given the complexity of the genome and human biology, an actionable outcome may not be achieved for every child sequenced. But "that's the wonderful thing about this technology," he said. "The more we learn, the more children will be saved in the future."