We continue our series on molecular diagnostics. Previous articles covered: what you need to verify your molecular assay and the three major components of the verification process. FDA-cleared or FDA-approved tests have four performance characteristics that must be verified and documented: accuracy, precision, reportable range, and reference interval. Laboratory-developed tests and modified FDA-cleared or approved tests have two additional characteristics for verification (analytical sensitivity and analytical specificity). Now, it’s time to turn our attention to best practices for each of the performance characteristics. First up – accuracy and precision.
3 Important Stages of Assay Verification Molecular diagnostic tests are widely available in clinical microbiology laboratories now. It’s important to a lab’s success to understand the requirements before adding a new test. Protocols aren’t specified by regulators, so they vary by lab. The assay influences the controls and parameters, but the type of verification and its complexity are determined by lab directors. In a recent article, we took a look at what to verify. This is the first of several articles that will cover how to confirm a molecular assay performs as expected.
Qualitative tests produce binary results, usually positive or negative. This presents a challenge for serological testing, since most of it is qualitative. Positive or negative results are determined in relation to a threshold value or cutoff. This cutoff, the line between positive and negative, is the medical decision point. It’s critical that this point is consistently acc urate at the lower limits of detection, where positive becomes negative. Without precision at the lower levels of positive results, laboratories may not feel confident in the results they present. Do they have a higher number of false positives or false negatives than they should?
Adding a new molecular test to your lab? Make sure you understand the regulations that apply and the required performance characteristics. The following is the first in a series of articles on this topic that will include best practices. Before we dive into the how of verification for molecular diagnostic assays, let’s take a look at the what. Clinical laboratories performing an FDA-cleared or FDA-approved test must verify that the manufacturer’s performance characteristics can be met or exceeded Laboratories performing laboratory-developed tests (LDTs) and modified FDA-cleared or approved tests, must verify the same characteristics, plus determine analytical sensitivity and analytical specificity
Authors: Yves Konigshofer, PhD; Andrew Anfora, PhD; Omo Clement, PhD; and Krystyna Nahlik, PhD. LGC Clinical Diagnostics. Introduction Liquid biopsy methods developed for circulating tumor DNA (ctDNA) analysis in solid tumors are transforming clinical practice, allowing for non-invasive detection and assessment of earlier stages of disease, monitoring for resistance to therapy, and post-treatment monitoring for minimal residual disease (MRD) and recurrence of cancer. The presence of minimal residual disease may be prognostic in that is has been found to correlate with worse patient outcomes, so early and accurate measurement is crucial. ctDNA-based assays allow for the detection of MRD at earlier time points than standard clinical and imaging surveillance, and could allow for treatment modification based on real-time assessment of the tumor genomic landscape.
This is Part 1 of a 2-part blog reviewing the Genomic Testing webinar and panel discussion featuring Dara Aisner, MD PhD, George Green, PhD and Greg Tsongalis, PhD. With so much rich information, we will be posting two blogs. Part 1 will cover select important themes discussed by each speaker, and Part 2 will review the audience Q&A. Recently, I had the pleasure of participating in a webinar co-sponsored by LGC SeraCare and GenomeWeb. The topic was “Genomic Testing to Support New Therapies for Advanced Cancer”.
As an RNA virus, SARS-CoV-2's genome replication is innately error-prone such that mutations are expected (1). Every now and then, a mutation will provide an adaptive advantage (such as increased transmissibility or infectivity to a human host), and will be positively selected for in the population. This process drives viral genome evolution, and gives rise to the rich diversity of viral strains and lineages that we see. However, for SARS-CoV-2, the unexpected emergence of such diversity since late 2020 has led to considerable anxiety around the progression of disease, and the efficacy of diagnostics and vaccines to control its spread.
This is Part 3 in a 3-part Q&A blog series with a panel of liquid biopsy experts addressing many of the issues faced in developing and deploying NGS-based liquid biopsy assays for clinical applications in oncology. At a 2020 liquid biopsy webinar, Dr. Vollbrecht shared a molecular pathologist’s perspective on the current state of liquid biopsy. Laboratory processing and analysis of cfDNA samples is a multi-step process that requires a high degree of precision to achieve consistent results. Her presentation focused on pre-analytics variables, which are often left out of discussions and tend to focus on biochemical manipulation of isolated nucleic acids. Seemingly simple factors at the point of sample collection such as problems with blood test tube filling, storage and labelling are able to affect the cfDNA stability, abundance, and confound the reliability of final interpretation. Variation in sample treatment during laboratory processing, including but not limited to, cfDNA quantification and QC methodology are also amongst the challenges for liquid biopsy.
This is Part 2 in a 3-part Q&A with a panel of liquid biopsy experts addressing many of the issues faced in developing and deploying NGS-based liquid biopsy assays for clinical applications in oncology. At a 2020 liquid biopsy webinar, Professor Schuuring discussed the plethora of options available to detect low copy number mutations in plasma cfDNA of lung cancer patients. His research laboratory combines NGS, ddPCR, qPCR and mass spectrometry approaches to address three main applications: (1) primary diagnosis by detection of predictive mutations, (2) monitoring of treatment response based on changes in plasma mutant levels, and (3) detection of therapy resistance mechanisms.
This is Part 1 in a 3- series deep-dive Q&A with expert panelists addressing many of the issues faced in developing and deploying NGS-based liquid biopsy assays for clinical applications in oncology. At the 2020 liquid biopsy webinar, Professor Sandi Deans highlighted a recent EQA scheme aimed at evaluating the standard of cfDNA testing in NSCLS and CRC patients. It was driven by demand from participants themselves, as well as pharmaceutical companies, IVD manufacturers and IQNPath (International Quality Network for Pathology).