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MMRF to Bolster Recently Launched Clinical, Genomic Patient Data Registry With Immune Profiles

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NEW YORK – The Multiple Myeloma Research Foundation (MMRF) is piloting a new initiative called Immune Atlas to develop an immune profiling platform for use in myeloma research.

All of the data generated through the Immune Atlas will be aggregated into CureCloud, a centralized data repository that MMRF unveiled last month for aggregating and visualizing data gleaned from multiple myeloma patients.

CureCloud includes a patient registry containing clinical and genomic information from multiple myeloma patients. It will also hold and share data from several studies of multiple myeloma that MMRF has facilitated over the past decade through various partnerships.

The platform "will take all the preceding datasets that MMRF has constructed over the past 10 to 15 years and make that available under one umbrella," Steve Labkoff, MMRF's chief data officer, said in an interview. It is essentially "a sort of a library of datasets."

The proposed infrastructure will include data from MMRF's Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile, or CoMMpass, initiative, an ongoing study to identify molecular drivers of multiple myeloma. Launched in 2011, the longitudinal study is following more than 1,100 multiple myeloma patients and collecting clinical and genomic data prior to treatment as well as at key time points such as when patients relapse.

The platform will also provide access to data from a patient registry, which MMRF plans to launch this fall. The organization is currently inviting patients to contribute their clinical and genomic data to the registry. Eventually, they will collect immune data from participants as well. Participants are also invited to share information from their electronic health records (EHRs). Last year, MMRF completed a pilot study that enrolled 65 patients who consented to have their data included in the resource. The selected patients provided access to data from their EHRs, as well as blood samples for sequencing.

Meanwhile, last week MMRF disclosed its Immune Atlas pilot program, which will collect data from 20 cases, half of whom are rapid progressors and half of whom are patients with long-term sustained response/remission. The five centers involved in the pilot are Beth Israel Deaconess Medical Center, Emory University, Mayo Clinic Rochester, Mount Sinai School of Medicine, and Washington University. From the 20 samples provided, these partners will generate proteomic, single-cell RNA sequencing, and mass cytometry datasets, among others.

Meanwhile, once the Immune Atlas pilot is complete, "we want to profile all cases in CoMMpass to provide a rich immune view of the data" according to Anne Quinn Young, MMRF's chief marketing and development officer. This will "complement the one-of-a-kind genomic analyses done on the myeloma samples," she said in an email.

MMRF is working with several partners to develop CureCloud, including Broad Genomics, the Broad Data Science Platform, COTA, Tempus, EMSI Health, Prometheus Research, and PierianDx. The system will provide tools to answer "critical clinical questions while supporting the identification of new targets and care pathways," MMRF's Labkoff said in a statement. "It is thanks to the willingness of our partners and the MMRF's legacy data assets that we are able to collect and aggregate massive amounts of research and clinical data."

CureCloud is part of a three-year MMRF plan to provide mechanisms for patients to share their genomic, immune, and clinical data with relevant stakeholders including clinical researchers and physicians. Multiple myeloma is the second most common blood cancer. According to MMRF, an estimated 31,000 adults in the US will be diagnosed with the disease this year. An estimated 13,000 people are predicted to die from the disease.

In 2017, MMRF said it would invest $5 million over three years to boost precision medicine's profile among clinicians and patients. At that time, it launched the MMRF Answer Fund to come up with better ways to identify and treat patients at high risk for multiple myeloma.

Meanwhile, the foundation has participated in various research initiatives over the years focused on generating and sharing data related to multiple myeloma cases. In 2016, MMRF partnered with Memorial Sloan Kettering Cancer Center on a multiple myeloma clinical trial designed to identify and treat predictors of sustained minimal residual disease negativity using combination therapy and genetic sequencing.

That same year, the National Cancer Institute said that MMRF would contribute genomic and clinical data to the NCI Genomic Data Commons including information from its CoMMpass initiative. MMRF was also involved in the Molecular Profiling Initiative, which performed clinical-grade genomic sequencing on bone marrow and peripheral blood samples from 500 relapsed and refractory multiple myeloma patients. Data from both the NCI partnership and the MPI study will be included in CureCloud.

Ahead of the planned launch of the registry in the third or fourth quarter of 2019, MMRF is running a second pilot with 50 to 100 patients to work out any outstanding regulatory, legal, or computational issues and test different tools and workflows, according to Labkoff. The organization is recruiting patients for the pilot from beyond its own internal rosters but is also connecting with patients through social media and other outlets.

The registry will include abstracted EHR data from patients. In addition, a subset of patients in the registry will also have their full exomes sequenced from bone marrow biopsies, Labkoff said. MMRF will also collect immunologic and RNA sequence data from patients as well as patient-reported outcomes information and insurance claims data. The goal is to have "a truly 360 view of a patient that will include a variety of genomic and RNA sequence data," he said.

The foundation is also seeking financial support to build out the registry. Currently, it has raised sufficient funds from personal and philanthropic donations to perform genomic and immunologic sequencing on about 2,600 patients for the registry. The goal is to be able to collect this data from up to 5,000 patients as well as to support future data collection efforts, Labkoff said. "The plan is not to do one and done," he said. "When a patient has a relapse or recurrence or there's a change in the diagnosis, we want to get another specimen for more genomic and immunologic work."

MMRF's Young added that although the initial focus for this registry is patients with active disease, MMRF hopes that it will eventually be able to collect these kinds of data from any patients that are willing to share. "When we launched CoMMpass, … we put the data in the public domain [and] we thought that others would follow or we would be able to gain access to different datasets," she explained in an interview. "That didn't happen and so we had to go back to the drawing board." By working directly with patients to collect the information and using updated technologies, MMRF is able to gather the data needed for research and to do it at a lower cost than was previously possible, she said.

The registry also offers an opportunity for patients whose disease had not been diagnosed at the time the CoMMpass study was launched to contribute their data for research. Moreover, there are benefits to patients who opt to have their data included. For example, patients whose tumors can be sequenced, along with their clinicians, will receive feedback on their tumor types as part of their participation.

Labkoff said that the partners are "working on a way to provide patients with a perspective on the genetics of their disease." Specifically, "a fully CLIA-[certified] genomic test is being created that will, upon completion, provide a report about the somatic changes observed in free circulating tumor DNA," he said This proprietary 77-gene myeloma-specific assay is being created at the Broad Institute and is expected to launch in late 2019.

In addition, MMRF and its partners have plans to develop a patient portal that allows patients review their genomic data in the context of the rest of the individuals in the study group, Labkoff said. An early prototype of the portal is currently being tested using the CoMMpass data as a reference data set.

"Once we accrue enough patients to make the visualizations viable with CureCloud [Direct-To-Patient] Registry data, the plan is to transition to a more sophisticated visualization tool focused on the registry," he said. The data contained in the broader CureCloud infrastructure, meanwhile, is intended for use by cancer researchers in academia and industry who are seeking access to raw sequence, variant call lists, and so on.

CureCloud is being built on cloud infrastructure developed by the Broad Institute for storing and analyzing genomic data. It is an iteration of the FireCloud infrastructure which the Broad developed for use in the Cancer Genome Cloud pilots. Other partners on the project include researchers at Prometheus who are helping to architect the backend of the system, Labkoff said. Meanwhile, COTA is handling the data extraction from electronic health record systems. All of the data stored in the platform will be de-identified. The platform will also include tools that allow researchers to move data into virtual research buckets and run analysis algorithms on them.

COTA is providing clinical data support services to MMRF. Andrew Norden, COTA's chief medical officer, said that the company offers tools to simplify the task of analyzing oncology healthcare data and to enable clinical researchers to ask questions about their patient populations. For example, they can ask how many patients with a particular subtype of myeloma are going to be refracted, what sort of treatments those patients are receiving, and what their health outcomes look like.

Norden said that COTA has worked with data from multiple myeloma cases before and is familiar with the complexities of the information. "We happen to be partnered up with a number of providers who take care of large populations of patients with myeloma," he said. "We've also been motivated to develop expertise in myeloma because so many new drugs have been developed [for] myeloma in the past decade." COTA currently has partnerships with a number of pharma companies who are developing drugs in myeloma.

Trained experts at COTA will use detailed protocols and standard operating procedures to extract structured and unstructured information from the EHRs. They will then feed this information into a myeloma-specific model that includes all of the needed data elements as well as defined terms for describing the disease.

Prometheus CEO Leon Rozenblit said his company is advising the CureCloud partners on data engineering architecture and ways to combine data from various sources in sustainable and usable ways. It is also providing expertise on ways to negotiate some of the regulations and privacy matters associated with the project. "Most of the work has been developing documentation, architecture compliance and helping MMRF reach their goal." he explained in an interview. "The most challenging thing from our perspective is dealing with multiple data partners and thinking about what data standards need to apply across the board so that the data is usable and can be maintained in the long term."

Prometheus Research is a data science consultancy that offers tools to help customers create large-scale and highly curated data assets and resources. Earlier in the year, the company received nearly $1 million in funding from the National Institutes of Health to add new features to its Prometheus Research Exchange Database platform that will support observational research studies in autism cases. Prometheus' current customer base includes medical specialist societies and disease advocacy groups that are trying to create data assets for specific disease areas. The company is also the principal informatics partner for the American Urogynecologic Society and is contributing to the society's efforts to build a data registry.

In order to use CureCloud's data and resources, researchers will need to go through an application process and be approved to access data from both the patient registry and the broader CureCloud infrastructure. Labkoff said that MMRF has begun offering access to the datasets from its past and current research initiatives. Interested participants can reach out directly to the organization for more information.

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