Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

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-generation sequencing, myeloid cancer reference materials, myeloid, Myeloid diseases, targeted therapies

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

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.

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:

  1. Consulting with experts
  2. Outlining your validation and quality control (QC) strategies together
  3. 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.

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Topics: fusion RNA, Clinical NGS Assays, genetic sequencing, qc management

AMP 2017 Highlights: The Epigenetic Basis of Common Human Disease

Posted by Catherine Huang on Nov 30, 2017 1:30:00 PM

The Association for Molecular Pathology Meeting (AMP) was held this year in Salt Lake City, Utah on November 15-18.  For me, one of the highlights of this year’s meeting was the lecture given by Dr. Andy Feinberg, who is a professor at Johns Hopkins University School of Medicine Center for Epigenetics and the winner of the AMP award for Excellence in Molecular Genetics.

Dr. Feinberg spoke on “The Epigenetic Basis of Common Human Disease.”  He defined epigenetic changes as stable, heritable, modifications of the genome that are not based on actual sequence changes.  These epigenetic changes can be modifications of either the DNA, or the DNA associated factors that are maintained through cell division.  Examples include DNA methylation, particularly at CpG islands, histone tail modifications, nucleosome remodeling and changes in higher order chromatin structure (such as compaction). 

Stochasticity mosaic painting by Andy Feinberg, after a portrait of Conrad Waddington by Ruth Collet,
was featured on the cover of Nature Genetics May 2017 Volume 49 No 5
. 

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Topics: Genetics, AMP2017, Epigenetics, Molecular Genetics, Common Human Diseases

3 Steps for Building a Bulletproof Clinical NGS Assay: Step 2

Because NGS assays are so complex, involving a dizzying number of genes, mutation types, and options for sequencing and bioinformatics, the bulletproof assay is no easy feat. But it can be done.

Posted by Russell Garlick on Nov 14, 2017 1:00:00 PM

As the use of genetically targeted cancer therapies becomes mainstream, the demand for reliable NGS assays is skyrocketing. To help doctors personalize treatments to their patients’ genetic profiles – and to stand out from the competition – clinical laboratories like yours are constantly looking for ways to create more accurate, more comprehensive assays.

We call this the quest for the elusive “bulletproof” assay – one that exhibits the highest performance and reliability in delivering patient results. Because NGS assays are so complex, involving a dizzying number of genes, mutation types, and options for sequencing and bioinformatics, the bulletproof assay is no easy feat. But it can be done.

As we wrote in our last blog post, there are three key steps:

  1. Consulting with experts
  2. Outlining your validation and quality control (QC) strategies together
  3. Evaluate reference material options

In this article, we’ll discuss step two: strategically outlining the NGS assay validation study and QC plan together.

Doing the validation study and QC plan at the same time will give your lab the highest probability of achieving a functioning assay with high quality:

  • Validation results set assay performance
  • A well-designed QC management system will make sure the assay stays within specifications
  • QC tracking and trending will also provide early indicators of assay drift or potential failure
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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

3 Steps for Building a Bulletproof Clinical NGS Assay: Step 1

What do we mean by bulletproof? A bulletproof NGS assay is one that exhibits the highest performance and reliability in delivering patient results. If you want every assay your lab develops to be bulletproof, read on.

Posted by Russell Garlick on Oct 31, 2017 4:39:10 PM

As next-generation sequencing (NGS) has advanced and doctors have learned to match therapies to specific tumor genotypes, genetic profiling of newly diagnosed cancer has become standard practice.

As a clinical laboratory director or scientist, you want to make sure doctors and patients are working with the best diagnostic results. That means making strategic technology choices and sourcing decisions when choosing NGS assays, sequencing platforms, and bioinformatics pipelines. Often, the first decisions you make are the most important, as they have lasting effects on patient care and your lab’s ability to compete in the exploding NGS market.

But adopting an NGS technology is not like adopting any other new method for a clinical lab – not when you consider the number of genes and gene regions that are sequenced, the complexity of types of driver mutations, and the myriad of sequencing schemes and bioinformatics platforms available.

Because creating a new NGS assay is so complex, it will take us three blog articles to explain all the factors that should play into your decision-making process. As you’ll learn, there are three critical steps for building a “bulletproof” NGS assay:

  1. Consult with experts
  2. Outline your validation and quality control (QC) strategies together
  3. Evaluate reference material options

What do we mean by bulletproof? A bulletproof NGS assay is one that exhibits the highest performance and reliability in delivering patient results. If you want every assay your lab develops to be bulletproof, read on.

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Clinical NGS Assay Developers: Eliminate Your Specimen Search Headaches

Posted by Trevor Brown on Oct 24, 2017 1:10:53 PM

There comes a point during the development of every NGS assay at which you want to make sure it will reliably detect everything you say it can. You want its real-world performance to match your claims.

That means fine-tuning your development protocol — from specimen handling, to nucleic acid extraction, to library prep — against a range of variants and allele frequencies to make sure your early-stage assay picks them all up.

Only after doing so can you move the assay on to the costly validation phase.

Naturally, to replicate real-world scenarios, many developers instinctually turn to real patient samples.

But the truth is, if you’re only subjecting your assay to the patient samples your lab has on-hand — or even ones you procure from colleagues or biobanks — you’re not exposing your assay to a wide enough range of variants and conditions to ensure its performance. Plus, you may be costing your lab money and time:

  • Development delays can allow another lab to launch their assay before yours.
  • Not using robust enough reference materials can lead to your assay not meeting performance claims in production.

While there is clearly a need to evaluate assays with real specimens tested on orthogonal methods, in the development phase multiplexed truth sets such as biosynthetic NGS reference materials are superior to patient specimens.

Here are three reasons not to trust remnant patient samples alone for assessing your clinical NGS assay’s workflow.

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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-generation sequencing, Clinical Implementations

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: allele frequencies, next-generation sequencing, cancer profiling, 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 reference materials, QC Management Software, Rare variants, fusion RNA, next-generation sequencing

 
 

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