Clinical genomics laboratories are increasingly looking to liquid biopsy cancer assays to complement their current solid tumor assays. Compared to their solid tumor assay counterparts, circulating tumor DNA (ctDNA) assays offer a different set of challenges to consider for clinical labs. One of the most important of which, is to develop a set of reagents that are appropriately validated to determine the critical performance of the assay across many parameters. The ctDNA targets of liquid biopsy assays are typically at much lower allelic frequencies and require a robust and reproducibly designed assay to consistently detect these important variants.
SeraCare’s new Seraseq™ Circulating Tumor Reference Materials
A 0.1% measurement requires a reasonable amount of input material
The field of circulating tumor DNA analysis (ctDNA, also sometimes called in a larger context “liquid biopsy”) holds great promise for monitoring response to cancer treatment, assisting therapeutic choice, monitoring recurrence, and for pre-cancer screening. As such there is a great amount of assay development and ongoing clinical trials; at ClinicalTrials.gov searching for the term "Circulating DNA" you can find over 180 open clinical trials for a wide range of tumor types and interventions.
"The most effective ways to use QC data to monitor the health of your NGS assay."
Previously, we wrote about some of the Quality Control challenges that clinical laboratories performing Next Generation Sequencing (NGS) face towards ensuring their assays are safe and effective for guiding medical management decisions. Reliable access to high quality reference materials is necessary to help overcome these challenges; however, it is not sufficient. Insights that reference materials provide into the health of an NGS assay are only as good as laboratories’ ability to use their QC data effectively.
With limited time and resources to collect, organize, access, and analyze QC metrics, laboratories may frequently rely on reference materials as binary indicators of Pass/Fail: As long as the expected endpoint results are obtained, an assay is considered to be performing well. The drawback of this approach is that it is reactive, rather than proactive: A sufficient number of failures must occur within a given timeframe before a troubleshooting investigation is performed. By the time a problem is recognized, resources have been wasted and turnaround times (TAT) delayed; in some cases, fidelity of patient results may even have been put at risk. Additional time and costs are then incurred as the investigation proceeds.
Specimen analysis by NGS yields a wealth of information in addition to endpoint variant calls that is indicative of assay performance. Data such as nucleic acid quantity and quality at different steps throughout the workflow (PDF) and sequencing library characteristics are generated every time a reference material is tested. However, these data must be carefully tracked and trended to allow use as highly informative QC parameters. For clinical laboratories whose primary focus is on patient testing and reporting, granular QC metrics may not be captured and reviewed as part of routine test monitoring.
Non-invasive prenatal screening (NIPS) is currently offered in over 80 countries, covering over 80 million annual births, with an estimated volume of over one million screening tests performed annually. First offered in 2011, there has been rapid adoption of these genomic tests in the marketplace.
Important information for assay development and review by the FDA
The presentations during the FDA-AACR Liquid Biopsies in Oncology Drug and Device Development Workshop on July 19, 2016 included several important pieces of information that will likely guide the development of assays and their review by the FDA.
Circulating tumor DNA, along with immunotherapy, are two major themes of #AACR16
At the American Association for Cancer Research conference recently held in New Orleans, LA (April 16 - April 20, 2016) one theme that generated considerable interest was circulating tumor DNA detection, sometimes called liquid biopsy (although that term also encompasses circulating tumor cells). A few of the ctDNA presentations are highlighted below.
Diagnosing inherited disease, processing FFPE samples, state-of-the-art oncology in North Carolina, and developments in circulating tumor DNA technology
We are living through a time of rapid change in the clinical genetics laboratory, though at times it may appear that change doesn’t occur fast enough given the challenges within the existing healthcare system. At the recent Molecular Medicine Tri-Conference held in San Francisco March 7 through 11 2016, here are a few summary highlights of the conference.
Poster Titled “New Technical Approach to Construct ctDNA Materials for use in Characterizing, Developing and Validating Plasma Assays”, available for download
The Keystone Symposia is an organization with 44 years of history on specialized topics across the fields of molecular and cellular biology. This week in Banff, Alberta, Canada is a Keystone Symposia conference called The Cancer Genome, along with a joint meeting on Genomics and Personalized Medicine. Their Twitter description (@KeystoneSymp) describes the Keystone organization as “A catalyst for accelerating life science discovery and connecting scientists within and across disciplines at symposia worldwide”.
How can you measure something without a ruler?
The science of metrology is tightly coupled with biological science, in tandem with biology becoming less descriptive and more quantitative over the past half-century. The US National Institute of Standards and Technology (NIST), an agency of the US Department of Commerce, has been established to ‘promote U.S. innovation and industrial competitiveness by advancing measurement science, standards and technology in ways that enhance economic security and improve our quality of life’.