Diagnostic Precision

A SeraCare blog focused on precision medicine and advanced clinical diagnostics

Choose your Article Focus | NGS | Molecular & Serology

Diagnostic Testing Schemes for NTRK Cancers: All Roads Lead to NGS

Catagory: NGS, SeraSeq, NTRK, RNA fusion

Posted by Russell Garlick on Feb 12, 2020 12:13:31 PM
New treatment options for cancer patients with neurotrophic tyrosine kinase (NTRK) rearrangements are a tremendous success, demonstrating first-hand the importance of precision diagnostics. The FDA granted accelerated approval of Bayer's VITRAKVI (larotrectinib) for adult and pediatric solid tumors containing NTRK fusions1. The approval was one of the first tissue agnostic approvals based on genotyping results, and included patients with unresectable or metastatic cancer. For 12 cancer types, the overall response rate was 75% with 22% complete response and 53% partial response. In addition to VITRAKVI, Genentech's entrectinib has a "breakthrough" status and is being evaluated for the potential treatment of advanced or metastatic tumors that harbor NTRK or ROS1 gene rearrangements.
Read More

Multi-Lab Study of Fusion RNA Reference Standards for Targeted NGS

Catagory: NGS, reference materials, AACR, NTRK, RNA fusion

Posted by Andrew Anfora, PhD on Jan 28, 2020 11:45:00 AM
Sourcing assay validation samples as positive run controls or workflow controls in targeted NGS RNA fusion assays remains a challenge today. This is further exacerbated with clinical labs looking to provide validated NGS assays for patient stratification in a host of new drugs in clinical trials or newly approved targeting fusion genes, such as NTRK genes (Larotrectinib, Loxo/Bayer) and Entrectinib (Genentech/Roche) for rare cancers in adult and pediatric patients, and RET (Loxo/Lilly) for lung cancer. SeraCare produces several RNA fusion reference materials. This article describes the development and multi-laboratory evaluation of a pan-cancer multiplexed Fusion RNA reference standard for analysis of clinically relevant fusion genes in solid tumors. The evaluation was conducted at 5 different laboratories on different NGS platforms (amplicon- and hybridization capture-based) as well as at different RNA inputs within a platform. Results highlight the utility of this Fusion RNA reference material to support clinical NGS assays as positive controls in solid tumor cancer patient stratification for many of these fusion-based targeted therapies.
Read More

So Many Posters, So Little Time

Catagory: ctDNA, AACR, RNA fusion, TMB

Posted by Sam Blier on Jun 6, 2019 10:32:00 AM
Cancer research is purposely methodical and measured. So – somewhat paradoxically – it can be difficult to keep up with the steady stream of discoveries in the literature and presented at conferences like AACR. As a developer and manufacturer of platform-agnostic NGS reference standards, we’re in a unique position to collaborate with cancer genomics assay developers, laboratories, pharmaceutical companies, and other organizations invested in more precise and robust cancer tests.
Read More

Presenting NTRK Reference Materials for Global Assay Standardization at AACR 2019

Catagory: SeraSeq, AACR, NTRK, RNA fusion

Posted by Catherine Huang on Apr 8, 2019 3:00:00 PM
On the last morning of AACR 2019, I had the privilege of presenting a poster together with my colleague, Sebastian Bender from Bayer AG, in Berlin. Because of this, I didn’t have a chance to attend any talks, but I still wanted to finish out my blog series with highlights from each day of the conference.
Read More

NTRK Fusion Testing for New Therapies

Catagory: cancer, NTRK, RNA fusion

Posted by Omo Clement, Ph.D. on Feb 6, 2019 9:15:00 AM
Neurotrophic tyrosine receptor kinases (NTRK) can become abnormally fused to other genes resulting in growth signals that can lead to cancer in many organs of the human body. TRK gene fusion-based cancers are rare but present in pediatric and adult cancers such as lung, thyroid, colon, etc. (see, e.g., Figure 1).
Read More

Twists and Turns That Lead From “Curiosity Driven Research” To Innovative Diagnostics

Catagory: AACR, RNA fusion

Posted by Catherine Huang on May 8, 2018 8:15:00 AM
Jennifer Doudna is not a cancer biologist and joked that she might deliver her entire lecture at the 2018 AACR Annual Meeting without ever mentioning the word “cancer.” However, when presenting the Irving Weinstein Foundation Distinguished Lecture, she told a fascinating story about how curiosity regarding an interesting sequence motif in bacteria led to gene-editing tools, and how investigation of the mechanisms behind those tools may lead to innovative diagnostics for the future.
Read More

With so many options, how do you select the best NGS cancer assay?

Catagory: cancer, NGS, reference materials, RNA fusion

Posted by Catherine Huang on Jan 11, 2018 12:10:00 PM
Clinical labs must constantly evolve their test offerings in order to support the most recent advances in clinical care. For next-generation sequencing (NGS) tumor profiling assays, there are often multiple commercially available kits with similar claims for gene content and sensitivity, as well as customized solutions. How can you quickly perform an effective evaluation of available assay systems to make a data-driven choice?
Read More

3 Steps for Building a Bulletproof Clinical NGS Assay: Step 3

Catagory: NGS, qc management, RNA fusion

Posted by Russell Garlick on Dec 8, 2017 10:30:00 AM
What does it mean for an NGS assay to be bulletproof and why does your lab need it? In two previous blog articles (parts one and two), we’ve talked about the factors that go into making NGS assays that doctors can rely on to deliver targeted, lifesaving therapies to their patients. Bulletproof assays are the tests that make your lab a trusted name in the NGS field, a leader in a rapidly-growing market. But, as we’ve written, genetic sequencing is complex, expensive, and time-consuming. Therefore, finding ways to do it more efficiently, while maintaining the quality of your tests, is in the best interests of your lab and its customers. As a refresher, here are the three steps for building a bulletproof clinical NGS assay: Consulting with experts Outlining your validation and quality control (QC) strategies together Evaluating reference material options We’ve already covered the first two steps. In this article, we’ll look at the third one. Choosing the right reference material technology can help control the high validation and running costs of highly multiplexed assays.
Read More

Is Your NGS-Based Assay on the Right TRK?

Catagory: NGS, QC Management Software, qc management, reference materials, RNA fusion

Posted by Trevor Brown on Oct 9, 2017 2:13:00 PM
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.
Read More