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.
An important goal in cancer disease management is early detection. When detected early, disease progression can be significantly mitigated with a plethora of options (targeted therapy, chemotherapy, surgery, etc.) available to medical practitioners, to afford progression free survival and a higher quality of life. A great promise of liquid biopsies is the possibility of early detection of cancer long before clear evidence of lesions and tumor growth observable by imaging or other techniques.1 As proxy for solid tissue biopsies, plasma-based liquid biopsy application is rapidly gaining traction in cancer disease diagnosis, progression, monitoring, and in predicting resistance to treatment options.2
Highly multiplexed reference materials are particularly valuable when developing and optimizing new NGS assays because they allow you to evaluate the performance of your assay across a large number of variants including different variant types (SNVs, indels, homopolymeric variants, etc.) and contexts. However, it can be frustrating when a variant in the reference material is not detected, or not detected at the expected variant allele frequency. Troubleshooting such issues can give new insight into the performance of the assay. Here we share some stories from Seraseq™ users where the lack of detection of one or more variants at the expected levels helped them improve their assay or set more appropriate QC thresholds.
Next-generation sequencing (NGS) allows deeper insights than ever before into the human genome and a host of diseases and conditions. So it makes sense that there is a worldwide movement to employ NGS in a growing number of applications. But as the saying goes, with great power comes great responsibility.
SeraCare Customer Poster Talk Video with Data Presented by Asuragen
Next-generation sequencing (NGS) of liquid biopsies offers a minimally invasive alternative to solid tissue biopsies and a more holistic profile of intra- and inter-tumoral heterogeneity for therapy selection and disease monitoring.
Watch the video and download this free poster to learn:
The ability to rapidly and effectively evaluate the performance of customized next-generation sequencing (NGS) panels is critical to provide high-quality sequencing solutions to customers. New England Biolabs®, together with Directed Genomics®, is developing a new offering, NEBNext Direct® Custom Ready Panels, which will allow researchers to select from a large library of genes for which baits have been developed and optimized, thus enabling rapid deployment of customized target-enrichment panels. Directed Genomics has been collaborating with SeraCare Life Sciences in order to streamline the optimization and characterization of NEBNext Direct target enrichment panels.
Assay development and optimization for clinical genetics is increasingly challenging. In an era of clinical genomics, new technologies and clinical utilities constantly call for newer and better performing assays. Having access to an abundant supply of relevant and reliable test material is critical for quick assay development and well-documented assay performance.
From extraction, to library prep, to sequencing, to the bioinformatics pipeline, there are countless points where something could go wrong.
Despite the absence of clear guidelines or firmly established best practices, next-generation sequencing (NGS) assays are becoming the method of choice for gene fusion detection.
This is significant because, although some of the cancers that contain fusion RNAs are rare, they’re now treatable thanks to new targeted therapies. If your assay can detect fusion RNAs, it can help profile tumors for important diagnostic, prognostic, and therapeutic targets, which can lead to improved patient outcomes.
The old FISH method limited you to one type of fusion variant at a time; it was effective, but also slow and cumbersome. With the latest NGS techniques, detecting fusion RNAs is more efficient than ever. It’s more sensitive and can detect multiple fusions in the same assay.
Nevertheless, it’s still challenging because of the complex workflows and the need to rigorously ensure performance across all fusion variants. From extraction, to library prep, to sequencing, to the bioinformatics pipeline, there are countless points where something could go wrong.