Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

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

An Efficient and Ultrasensitive NGS Solution for Profiling ctDNA [Poster Talk Video]

Posted by Trevor Brown on Mar 5, 2018 8:28:14 AM

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:
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Topics: ctDNA, NGS assays, liquid biopsy, next gen sequencing, NGS reference materials

Reliable Interpretation of NGS Data: New Poster Talk Video

Posted by Cynthia Hendrickson, CEO Directed Genomics on Feb 1, 2018 8:00:00 AM

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. 

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Topics: NGS, SeraSeq, NGS assays, Variant Allele Frequencies, highly-multiplexed reference material, NGS reference materials, AMP2017, reference materials

The First Comprehensive Myeloid Cancer Reference Materials for NGS Assays

Evaluate your detection of key diagnostic, prognostic, and therapeutic markers

Posted by Ram Santhanam on Nov 8, 2017 4:30:00 PM

Myeloid cancers are “liquid” tumors that arise from the blood and bone marrow.  These diseases have undergone greater study and characterization than perhaps any other type of cancer, largely due to the ease of accessing these cancer cells via a blood draw rather than a tissue biopsy, as for solid tumors.  There are many different types and subtypes of these malignancies that are known to be caused by mutations in genes that encode proteins involved in cell signaling, transcription, epigenetic regulation, and splicing1

Before next-generation sequencing became available in the hematology/oncology clinic, high-resolution genetic analysis of myeloid cancers relied primarily upon site-specific methods such as Fluorescence in Situ Hybridization (FISH) and PCR-based assays.  And, while other methods such as karyotyping and array comparative genomic hybridization are indeed able to survey large genomic rearrangements and copy number changes across the entire genome, these methods lack the resolution required for detection of many mutations that are important for myeloid cancers.

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Topics: NGS, NGS assays, myeloid malignancies, myeloid cancer reference materials

Dr. Andrea Ferreira-Gonzalez on the Seven Benefits of Clinical Genomics Universal Standardization

The Chair of Molecular Diagnostics, Department of Pathology at Virginia Commonwealth University shares her success story

Posted by Dale Yuzuki on Jun 22, 2017 3:32:52 PM

 As a 25-year veteran of clinical molecular diagnostics, Dr. Andrea Ferreira-Gonzalez has seen many changes in genetic technologies used in the testing laboratory. With the advent of personalized medicine and using multi-gene NGS panels as a laboratory-developed test, Dr. Ferreira-Gonzalez and other experts have agreed to lend their expertise to the design of SeraCare’s reference materials.

 

She and other groups have participated in an interlaboratory test of standardized reference materials for detecting cancer somatic mutations, with results that will be published in the coming months.

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Topics: Reference Material, NGS assays, next gen sequencing, clinical genomics, laboratory training

Prevent Assay Drift In Your Clinical NGS Assay by Avoiding 2 Common Mistakes

Daily variations in your test performance can cause assay failure and may lead to false positives. Do you have the tools to detect them?

Posted by Trevor Brown on Apr 27, 2017 3:00:00 PM

 

Clinical NGS tests may be powerful diagnostic tools for your molecular pathology laboratory, but they remain complex amalgamations of different hardware, reagents, and software systems — often from several different vendors and with different levels of quality. Only one of these critical reagents or systems has to fail or underperform in an assay to cause performance drift.

If you don’t catch assay drift quickly enough, it can lead to assay failures such as false positives or unexpected changes to assay performance — such as those that impact limit of detection (LoD).

How can your lab protect itself better? Avoid these two common mistakes:

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Topics: NGS assays, Common Lab Mistakes, Assay Drift

Highlights from the Precision Medicine World Congress

Status of FDA regulation of laboratory developed tests, the promise of precision medicine, and a workshop about achieving accurate NGS laboratory test results

Posted by Russell Garlick on Feb 15, 2017 1:30:00 PM

On January 23-25, 2017 the Precision Medicine World Congress was held in Mountain View, California. The PWMC conference kicked off with Dr. Keith Yamamoto, Vice Chancellor for Science and Policy and Strategy UCSF, with Dr. Robert Califf, FDA Commissioner in a “fireside chat” format. Dr. Califf has been with the FDA for 2 years, has served as Commissioner for 11 months, but has resigned as of January 20th 2017. One of his important parting thoughts presented was how the FDA has been re-energized by the 21st Century Cures Act to hire new scientific talent to implement the President’s Precision Medicine and Cancer Moonshot plans.

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Topics: NGS assays, EGFR, re-validation, limit of detection, ngs validation, FDA Regualtions, Precision Medicine World Congress, mutations, cancer patients, clinical genomics

Multiplexed Reference Materials as Controls for Cardiomyopathy Diagnostic Next-Generation Sequencing

A Journal for Molecular Diagnostics article describing ‘an attractive addition to the repertoire of materials for the development, validation, and quality monitoring of clinical NGS assays’

Posted by Dale Yuzuki on Dec 13, 2016 11:01:00 AM

Hypertrophic Cardiomyopathy (HCM) is a disease where the heart muscle is enlarged and a significant cause of sudden cardiac death, and is frequently asymptomatic.  HCM is commonly caused by a mutation in one of nine heart muscle genes that comprise the sarcomere, and occurs at a prevalence of about 1 in 500 in the general population. HCM is the leading cause of cardiac death in young athletes in the United States.

Clinical genetic testing for mutations in the HCM-related genes has been ongoing for over a decade;  the GeneTest.org database reveals 105 laboratories offering some version of genetic testing.  While knowledge of prevalent pathogenic variants are available, the majority of variants remain private (that is, unpublished and not widely available). The move to NGS-based gene panels for HCM testing has lead to new challenges for test development, validation and routine quality control due to the inherent scarcity of samples, the cost of including numerous single mutations from these individual samples, and the lack of these materials for laboratories without a long history of testing.

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Topics: NGS assays, next gen sequencing, allele frequencies, Controls, Cardiomyopathy, DNA, Clinical Genetic Testing, multiplexed referenence materials, multiplexing

Clinical Laboratories: You Are Not Alone. (Part II)

"The most effective ways to use QC data to monitor the health of your NGS assay."

Posted by Matt Ryder on Dec 7, 2016 4:00:00 PM

Previously, we wrote about some of the Quality Control challenges that clinical laboratories performing Next Generation Sequencing (NGS) face towards ensuring their assays are safe and effective for guiding medical management decisions.  Reliable access to high quality reference materials is necessary to help overcome these challenges; however, it is not sufficient.  Insights that reference materials provide into the health of an NGS assay are only as good as laboratories’ ability to use their QC data effectively.

With limited time and resources to collect, organize, access, and analyze QC metrics, laboratories may frequently rely on reference materials as binary indicators of Pass/Fail:  As long as the expected endpoint results are obtained, an assay is considered to be performing well.  The drawback of this approach is that it is reactive, rather than proactive:  A sufficient number of failures must occur within a given timeframe before a troubleshooting investigation is performed.  By the time a problem is recognized, resources have been wasted and turnaround times (TAT) delayed; in some cases, fidelity of patient results may even have been put at risk.  Additional time and costs are then incurred as the investigation proceeds.

Specimen analysis by NGS yields a wealth of information in addition to endpoint variant calls that is indicative of assay performance.  Data such as nucleic acid quantity and quality at different steps throughout the workflow (PDF) and sequencing library characteristics are generated every time a reference material is tested.  However, these data must be carefully tracked and trended to allow use as highly informative QC parameters.  For clinical laboratories whose primary focus is on patient testing and reporting, granular QC metrics may not be captured and reviewed as part of routine test monitoring.

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Topics: NGS, ctDNA, Reference Material, NGS assays, Sequencing quality control, next gen sequencing, qcdata management, False Negative, False Positive, QC Challenges

Clinical Laboratories: You Are Not Alone.

“Ensure NGS-based tests for Personalized Medicine are safe and effective for guiding medical management decisions”

Posted by Matt Ryder on Nov 8, 2016 1:06:00 PM

Since the introduction of the GS20 in 2005 by 454 Life Sciences, Next Generation Sequencing (NGS) has found many applications in clinical diagnostics.  As a result of this transition from the long-held gold standard, Sanger sequencing, the primary challenge for clinical laboratories has shifted from data acquisition to ensuring these tests are safe and effective for guiding medical management decisions.

Many laboratories struggle to gain a thorough understanding of the analytic performance characteristics of their NGS tests.  The difficulty arises from the fact that these assays are comprised of highly complex, fragmented workflows, and have many different intended uses.  However, across the various practices currently used for NGS assay development, validation, and performance monitoring, there is a common goal: results must be as accurate, precise, and consistent as possible.

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Topics: NGS, Reference Material, NGS assays, amp2016, next gen sequencing, False Negative, False Positive

 
 

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