Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

If I Call Out of Tune, Would Mutations Stand Up and Walk Out on Me?

Posted by Matthew Butler on Aug 9, 2018 10:15:00 AM

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.

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Topics: SeraSeq, NGS reference materials, Clinical NGS Assays

Microsatellite Instability Testing to Predict Immunotherapeutic Response: New Tools to Meet Testing Challenges

Posted by Catherine Huang on Jul 30, 2018 10:00:00 AM

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.

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Topics: Microsatellite Instability, microsatellite testing, MMR, MutS, MutL

A First of its Kind Survey to Assess the QC Habits of Labs Running Clinical NGS Assays

Posted by Trevor Brown on Jul 12, 2018 9:30:00 AM
 
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.
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Topics: QC Challenges, QC Reporting, assay performance, NGS reference materials, Clinical NGS Assays

Developing a Rock-Solid Lung Cancer Assay, Part 2

Posted by Yves Konigshofer on Jul 2, 2018 4:45:00 PM

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.

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Topics: assay development, Lung Cancer

Ebola Outbreak 2018: Diagnostics Again are Essential to Minimize Spread and to Control Disease

Posted by Catherine Huang on Jun 25, 2018 10:00:00 AM

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

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Topics: Accuplex, reference materials, ebola

How A New Generation of ctDNA Reference Standards Are Enabling the Promise of Precision Medicine

Posted by Omo Clement, Ph.D. on Jun 14, 2018 10:00:00 AM

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

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Topics: ctDNA, SeraSeq, NGS assays, liquid biopsy, ccfDNA, NGS reference materials, Clinical NGS Assays, Lung Cancer, colon cancer

FAQ: What to do when your NGS assay fails to detect a variant contained in Seraseq Reference Materials?

Posted by Catherine Huang on Jun 11, 2018 1:15:00 PM

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.

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Topics: SeraSeq, NGS reference materials, Clinical NGS Assays

Sensitive ctDNA Assays are Required for Minimal Residual Cancer Detection

Posted by Russell Garlick on May 29, 2018 3:10:00 PM

The 11th International Symposium on Minimal Residual Cancer was held this month and much of the conference was devoted to new minimally invasive methods for circulating tumor cell enrichment and or the analysis of circulating tumor DNA. Today’s clinical needs are to measure disease burden, track mutations over time, or to detect early resistance and all of these applications require extremely sensitive, robust assays.

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Topics: ctDNA, SeraSeq, DNA

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

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.

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Topics: DNA, fusion RNA, aacr

Next-Generation QC Precision Metrics for Next-Generation Sequencing

Introducing the SeraCare Confidence Score, a comprehensive precision metric designed for NGS assays

Posted by Lorn Davis on Apr 16, 2018 4:00:00 PM

Introduction

There is an even greater onus to track quality control metrics for NGS assays because of the number of steps and elements that must successfully work together to produce consistent results. The Standards and Guidelines for Validating NGS Bioinformatics, published in January by AMP and CAP, highlight the importance of tracking QC metrics over time because “trends in these metrics can indicate an emerging issue with an NGS process that has not yet manifested itself in failed tests.”

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Topics: NGS assays, QC Challenges, NGS Management Software, QC Management Software, bioinformatics, Quality Management Systems, Clinical NGS Assays, qc management, confidence score, SeraCare Confidence Score

 
 

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