Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

Building and Implementing Liquid Biopsy Assays with the Industry’s Most Patient-Like Reference Materials

Posted by Omo Clement, Ph.D. on Oct 24, 2018 9:00:00 AM

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.   

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Topics: reference materials, liquid biopsy, patient-like, SeraSeq, Clinical NGS Assays

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: Clinical NGS Assays, SeraSeq, NGS reference materials

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: Clinical NGS Assays, NGS reference materials, QC Challenges, QC Reporting, assay performance

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, ccfDNA, NGS assays, Clinical NGS Assays, liquid biopsy, NGS reference materials, 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: NGS reference materials, Clinical NGS Assays, SeraSeq

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

What Is The Difference Between Quality Control Software Like iQ NGS And LIMS?

Posted by Lorn Davis on Apr 6, 2018 8:00:00 AM

SeraCare Life Sciences, in partnership with GenomeWeb, recently offered this exciting on-demand webinar: 

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Topics: qc management, Clinical NGS Assays, QC Management Software, performance-based metrics, assay performance, QC Challenges

Developing a Rock-Solid Lung Cancer Assay

Posted by Yves Konigshofer on Mar 15, 2018 11:55:00 AM

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.



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Topics: Lung Cancer, NGS reference materials, standard operating procedures, reference materials, Clinical NGS Assays

CNVs and Tumor Profiling: New CNV Materials for Breast, Lung, and Brain Cancer

Posted by Dana Ruminski Lowe, Ph.D. on Feb 14, 2018 4:00:00 PM

Simply described, copy number variations (CNVs) are DNA segments present at a variable copy number in comparison to a normal genome. It was originally thought that a CNV consisted of a region of greater than 1 kilobases, however advances in technology have allowed for identification of CNVs as small as 50 basepairs1.

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Topics: Copy Number Variations (CNVs), biosynthetic reference materials, Lung Cancer, Brain Cancer, Breast Cancer, tumor profiling, Clinical NGS Assays

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

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?

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Topics: reference materials, Clinical NGS Assays, fusion RNA, next-generation sequencing, custom

 
 

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