New JCO PO Article Examines Genomic Data Workflows, Challenges, and Potential Solutions

October 2, 2019

A new JCO Precision Oncology (JCO PO) article co-authored by CancerLinQ® Deputy Medical Director Wendy Rubinstein, MD, PhD, FACMG, FACP, and CancerLinQ LLC Medical Director Robert S. Miller, MD, FACP, FASCO, examines next-generation sequencing in relation to how it can be implemented into the clinical workflow in a practice setting. The article, Next Generation Sequencing and the Clinical Oncology Workflow: Data Challenges, Proposed Solutions, and a Call to Action," was published in JCO PO on October 1.

While next-generation sequencing (NGS)—rapid sequencing of DNA and RNA—is being increasingly used in cancer treatment and care, and is a foundational aspect of precision oncology, how best to gather the molecular data, integrate them within electronic health records (EHRs), and actually use them in the practice setting remains a significant challenge. There are many challenges related to a lack of data standards and operability—how to input the data in a uniform way across practitioners and systems—and with the rapidly growing and evolving body of knowledge needed when caring for patients.

This article analyzes various genomic data workflows for managing NGS data and the problems that arise when there are inconsistent standards and sharing across systems and then proposes potential solutions for these challenges. These solutions include two ASCO initiatives, mCODE™ and CancerLinQ®:

  • mCODE, short for Minimal Common Oncology Data Elements, mCODE has assembled a core set of structured data elements for oncology EHRs to form the basic data that would populate all EHRs for patients with cancer. The data elements are intended to be sufficiently precise so that a query related to a particular patient would return a cohort of matched, de-identified patients from a larger database. This would facilitate cancer data interoperability and improve overall cancer data quality for patient care and research.
  • CancerLinQ is ASCO’s physician-led big data initiative, which analyzes real-world cancer care data from oncology practices of all sizes and types across the United States. Since 2017 CancerLinQ has been extracting high-value genomic information via user interface-assisted data abstraction; however, there is a significant genomic data gap in native EHRs. When data does exist, it is often unstructured. Though CancerLinQ has developed various technical solutions to structuring and re-structuring genomic data as it exists in EHRs, these would not be necessary if the originally structured data were provided.

The authors emphasize the increasingly key role that NGS plays in cancer care and thus the concurrent attention that should be placed on tools and systems to facilitate the influx of this critical data. “There is no dearth of [clinical decision support] tools to help translate patient data into quality care. Nor is there a lack of technical solutions to transmit, harmonize, curate, store, or otherwise manage data. Rather, operationalizing precision oncology is hampered by insufficient adoption of data standards and by failure to share data in computable formats. These problems are not primarily technical and solving them requires a will to action with social incentives and disincentives.”

Read the full JCO PO article.

JCO PO is a peer-reviewed, online-only, article-based journal publishing all types of clinical research (basket trials, exceptional response results, informatics, computational approaches, mechanism and evidence-based case reports, and small series of educational value) and extensive expert-driven commentary, editorials and reviews considering the challenges and value of targeted therapies based on genomic analyses.