Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

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. CNVs are common, affecting a greater fraction of the human genome than single nucleotide polymorphisms (SNPs). CNVs tend to be found in segmental duplications, heterochromatic DNA, replication origins, and palindromic regions2. They can originate in the germline or accumulate as somatic variants, as a result of several proposed mechanisms. Although some genes can be deleted or amplified with no phenotypic consequence, there are examples of CNVs that play important functions in normal biological pathways, such as the amplification of ribosomal genes during early embryogenesis to increase production of ribosomes2. Alternatively, many CNVs are pathogenic and can cause disease, such as diabetes, autism spectrum disorder, Alzheimer’s disease, and cancer.

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

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

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

How am I going to test my assay? Should I use patient samples or biosynthetic materials?

Posted by Dan Brudzewsky on Jan 4, 2018 4:32:00 PM

Assay development and optimization for clinical genetics is increasingly challenging. In an era of clinical genomics, new technologies and clinical utilities constantly call for newer and better performing assays. Having access to an abundant supply of relevant and reliable test material is critical for quick assay development and well-documented assay performance.

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Topics: assay development, biosynthetic reference materials, NGS reference materials

AMP Reference Material Forum: Themes and Highlights

Posted by Catherine Huang on Dec 22, 2017 12:30:00 PM

On November 14, 2017, AMP hosted a forum to discuss genetic testing reference material availability and needs. The forum attracted attendees including EQA providers, developers in industry and government, as well as scientists from clinical laboratories. Topics for discussion included reference material use and needs for assay validation, quality control, and proficiency testing. Throughout the talks, a few themes emerged and were discussed by multiple speakers.

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Topics: Clinical Genetic Testing, AMP2017, reference materials

Higher Quality for Better QC

Posted by Heather Buckley on Dec 15, 2017 4:03:00 PM

For over 30 years, we have dedicated ourselves to helping IVD developers and clinical laboratories ensure the quality of their assays. So when the opportunity arose to enhance our own quality standards, we jumped on it. 

Heather M. Buckley, VP, Quality & Regulatory Affairs

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Topics: QMS, Quality Management Systems, customer requirements, ISO 13485

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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