SeraCare’s clinical genomics technologies are developed to address challenges faced across the spectrum of NGS assays. From early development of assays – either IVD assay manufacturers or clinical labs building their own LDTs - there is a scarcity of characterized, complex, difficult variants to ensure the assay can robustly detect all the critical genomic variants in a patient sample. Using our highly characterized, reproducible, and GMP-grade NGS standards, laboratories have a wide range of analytical and clinical validation tools to deeply characterize assay performance such as LOD, linearity, specificity, sensitivity, and reproducibility.

Liquid biopsy requires better standardization to realize all the new possibilities for studying metastasis, heterogenicity, treatment efficacy, and disease recurrence. Furthermore, it is critical for clinicians to have confidence in liquid biopsy data to diagnose and treat patients. This is only achievable when consistent and high-quality data is generated at research and all clinical centers. The Liquid Biopsies course at EMBL Advanced Training Centre provides a unique practical training in best practices and pitfalls on the complete liquid biopsy workflow, from sample preparation to data analysis. The course is targeted for clinical laboratory and research scientists interested in learning all aspects of liquid biopsy testing.

There is that old adage that says the only thing that is constant is change. This is one of those universal truths we have all come to accept. Heck, even Dunkin' Donuts, widely credited as being the inventor of the word “Donut,” is dropping the word from their brand name. Blasphemy! But that is for another blog...

Recent clinical studies of immuno-oncology (I-O) checkpoint inhibitors have indicated that the tumor burden in a cancer patient’s genome may be predictive of positive response to I-O therapies such as Keytruda® and Opdivo®. The tumor mutational burden (TMB), that is, the number of mutations per megabase of sequenced tumor sample as determined by whole exome sequencing (WES), is currently the most promising biomarker for cancer patient selection and stratification in many clinical trials. Numerous clinical studies are underway to elucidate and validate the role of TMB in I-O treatment decision making and therapeutic response.

A recent study, published in the Journal of Molecular Diagnostics, describes a new, more sensitive Hepatitis B Virus (HBV) assay1. This study, led by Song-Mei Liu, MD, PhD, of the Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University in China, is particularly exciting because the new assay can be used to diagnose hepatocellular carcinoma (HCC) at an earlier stage and to manage antiviral HBV treatments more effectively. It also highlights the way innovative molecular diagnostics can play a synergistic role with the development of new pharmaceutical therapeutics.

One of several important steps in next-generation sequencing (NGS) is tuning the many options provided by mutation callers. Providing values for options configures the signal to noise ratio of the impending mutation calls. In theory, providing values that increase the stringency of mutation calls will reduce the number of false positive calls and thus enrich for true positives. In practice, increasing stringency can eliminate true positives.

Microsatellites are simple tandem repeats that are present at millions of sites in the human genome. Microsatellite Instability (MSI) is defined as a change of any length due to either insertion or deletion of repeating units in a microsatellite within a tumor compared with normal tissue.1 The molecular mechanism for the change in repeat length is slippage of nascent DNA strand with respect to the template strand during replication followed by failure to recognize the mismatch due to deficiency in mismatch repair genes.

While good progress has been made of late with more clarity around FDA requirements, as well as organizations such as CAP and AMP providing more 'meat' in their guidance to clinical laboratories, there still remains a ways to go before this modality of testing is more standardized and uniform across the various laboratories offering the testing--be it via commercially available IVD kits or multiple different LDTs providing similar performance characteristics.

In a recent post, we discussed key considerations for designing a robust next-generation sequencing (NGS)-based lung cancer assay. Putting those plans into action in the development phase brings forth a new set of challenges. Through our experience developing NGS reference materials and the relationships we’ve built with assay developers of all stripes, we’ve identified those important factors and ways to navigate them. But before you begin designing and optimizing your assay, you should become very familiar with binomial and Poisson distributions and their use because the outcome of many analytical steps can be modeled and explained with them.

On April 4th, 2018, a new outbreak of Ebola Virus Disease (EVD) occurred in Equateur Province in the Democratic Republic of the Congo. As of June 10th, there have been a total of 55 EVD cases and 28 deaths with a case fatality rate of 50.9%. Although the outbreak remains active, public health authorities have expressed cautious optimism because there have been no new cases in two of the three affected areas (Bikoro and Wangata zones) since May 17th, 2018 and the rate of new cases in the third affected zone (Iboko) has slowed.1