Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

Making the Shift from Technological Innovation to Operational Excellence: Delivering on the Promise Of Next-Generation Sequencing for Personalized Medicine

Posted by Peter Duncan on Apr 22, 2019 9:44:00 AM

As originally seen in The Journal of Precision Medicine March 2019.

Targeted therapies and now recently, immunotherapies, have demonstrated great promise towards increasing response rates, as well as duration of response for cancer patients. This is often achieved by understanding biomarkers associated with therapeutic response and then stratifying patients accordingly.
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Topics: NGS, Precision Medicine, next gen sequencing

AACR 2019 Day One Highlights: Next-Generation Car T Cells

Posted by Catherine Huang on Apr 2, 2019 12:10:00 PM

I’m excited to be at the Annual AACR meeting at the Georgia World Congress Center in Atlanta, GA. AACR is my favorite scientific meeting because each year I am inspired by the remarkable research presented and leave the conference feeling I’ve learned an incredible amount in just a few days.

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Topics: next gen sequencing, aacr

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

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: Cancer, NGS, next gen sequencing, fusion RNA, Clinical NGS Assays, reference materials

As to Myeloid Diseases, Make a Habit of Three Things

Use genetic information to treat, or at least to diagnose and to predict

Posted by Ram Santhanam on Dec 13, 2017 2:15:00 PM

Previously, we wrote about the unique capabilities that next-generation sequencing (NGS) offers the oncology clinic. NGS could mark the beginning of a shift away from “single-site” technologies such as FISH and PCR-based testing, in favor of comprehensive screening across many different targets at once.

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Topics: next gen sequencing, myeloid cancer reference materials

A New Focus on Implementing Clinical Genomics

Posted by Trevor Brown on Oct 20, 2017 11:02:24 AM

For many years, next-generation sequencing (NGS) made headlines with researchers promising unprecedented breakthroughs in medical diagnostics. But the clinical impact was always explained as being a few years and more large-scale studies away from reality. In 2010, forward-thinking academics forecasted whole-genome sequencing in a matter of hours for only $30 (right around that same time, a Stanford researcher sequenced his own genome for less than $50,000 – a record low at that point).

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Topics: Genomics, NGS, next gen sequencing, clinical genomics

This is the Number One Risk to Your Clinical Sequencing Assay

Critical missteps during the assay development phase can cause expensive delays and risk the quality of an assay. How can you be sure your bioinformatics pipeline is correctly calling variants?

Posted by Trevor Brown on Oct 17, 2017 11:00:00 AM

If you’re relying on remnant patient samples to tell you how well your lab's bioinformatics pipeline can call clinically important variants, you might be missing more than you realize.

In our experience, the bioinformatics pipeline can be the weakest link in assay development for many labs. Just because a variant is sequenced correctly doesn’t always mean that it will be called. And false-positives are just as bad.

  • Sometimes it’s an issue of allele frequency. For example, we’ve seen cases where labs could detect certain mutations at 10% allele frequency, but as soon as the frequency dropped to 7%, they stopped detecting it.
  • Other cases are caused by the complexity of the variant. For example, even at low allele frequencies, a lab may pick up relatively easy-to-detect single-nucleotide variants (SNVs) but can have problems with insertion/deletion (INDEL) calling errors.

In both examples, the mutations aren’t missed because of sequencing or library preparation problems. As we’ve witnessed time and time again, when labs optimize their bioinformatics pipelines, they start picking up the low-frequency and difficult-to-detect variants again.

The catch is, you first have to know you’re missing something. In assay development, what you don’t know can seriously weaken your test.

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Topics: next gen sequencing, allele frequencies, bioinformatics

Is Your NGS-Based Assay on the Right TRK?

From extraction, to library prep, to sequencing, to the bioinformatics pipeline, there are countless points where something could go wrong.

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.

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Topics: NGS assays, next gen sequencing, NGS reference materials, QC Management Software, fusion RNA, qc management, 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: NGS assays, next gen sequencing, clinical genomics, NGS reference materials

Real-World Needs for Genetic Testing Reference Materials

From troublesome mutations to FDA validation studies

Posted by Matt Ryder on Jun 1, 2017 9:09:00 AM

“Happy families are all alike; every unhappy family is unhappy in its own way.”

I have always thought the opening of Anna Karenina applies for many things beyond familial harmony (or lack thereof).  Certainly, in the world of molecular genetic diagnostics, conclusive results are usually obtained for most patients; however, there are times when a final result is more elusive than conclusive.  When this occurs, it may seem as though no two challenges are ever the same.

The following are real examples – presented in general terms for patient and institutional confidentiality – of difficult, unanticipated, and even bizarre cases I encountered during my time in clinical testing for predisposition to hereditary disease.  Each of these situations required extraordinary effort, dedicated time, and additional resources for resolution.  At the end of each day, satisfaction came from knowing that another problem solved was another patient helped in making life-altering medical management decisions.

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Topics: next gen sequencing, reference materials