DNA methylation is an epigenetic mechanism modulating the function and expression of genes. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. Changes in DNA methylation are associated with numerous diseases and abnormal DNA methylation has been implicated as one of the mechanisms driving tumor onset, development, progression and recurrence. Identification of tumor-associated methylation patterns is of great diagnostic potential, especially for early detection of disease. In Part 2 of this two-part blog series, the article continues to review the methylated DNA biomarkers in plasma webinar. As a reminder, Part 1 covered the main themes discussed by our invited webinar speakers - click here to read that article. To conclude the recent webinar hosted by LGC Clinical Diagnostics and GenomeWeb, Dr. Yves Konigshofer talked about levels of evidence required for clinical diagnostics, from analytical validity through clinical validity and clinical utility. Reference materials can help prove analytical validity and assess the impact of pre-analytical factors. Methylation reference materials that he is currently developing at LGC CDx address the analytical validity of 5’methylcytosine measurements in cfDNA.
DNA methylation is an epigenetic mechanism modulating the function and expression of genes. DNA methylation regulates gene expression by recruiting proteins involved in gene repression or by inhibiting the binding of transcription factor(s) to DNA. Changes in DNA methylation are associated with numerous diseases and abnormal DNA methylation has been implicated as one of the mechanisms driving tumor onset, development, progression and recurrence. Identification of tumor-associated methylation patterns is of great diagnostic potential, especially for early detection of disease. Recently LGC Clinical Diagnostics had the pleasure to host a webinar, bringing together a panel of academic, clinical, and industry experts in the field of methylated DNA testing, who discussed the promises and challenges of early cancer screening and recent technological advances. It was a great opportunity to hear from the pioneer of prenatal cfDNA testing, Dennis Lo, MD, PhD, and an expert in computational cancer genomics analysis, Jimmy Lin, MD, PhD, MHS, as well as Yves Konigshofer, PhD, the head of technology development at LGC Clinical Diagnostics.
Our series on molecular diagnostics continues with a look at best practices for two performance characteristics – reportable range and reference interval. These two characteristics need to be verified and documented for FDA-cleared or FDA-approved tests, laboratory-developed tests, and modified FDA-cleared or approved tests.
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”.
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.