Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

Russell Garlick

Recent Posts

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.

Read More

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

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
Read More

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.

Read More

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.

Read More

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

What lessons for liquid biopsy have been learned from fetal aneuploidy testing?

Posted by Russell Garlick on Sep 30, 2016 1:06:00 PM

Non-invasive prenatal screening (NIPS) is currently offered in over 80 countries, covering over 80 million annual births, with an estimated volume of over one million screening tests performed annually. First offered in 2011, there has been rapid adoption of these genomic tests in the marketplace.

Read More

Topics: NIPS, ctDNA, biomimetic technology, liquid biopsy, circulating DNA, cell-free, testing

IVD Guidance for NGS Manufacturers

Posted by Russell Garlick on Jul 14, 2016 3:30:00 PM

After 17 months of deliberations since its first open meeting February 20, 2015 on NGS IVD assay oversight, the U.S. Food and Drug Administration (FDA) issued DRAFT guidance for Stakeholders and FDA staff. The document “Use of Standards in FDA Regulatory Oversight of Next Generation Sequencing (NGS)-Based In Vitro Diagnostics (IVDs) Used for Diagnosing Germline Diseases” was published online on July 6, 2016. This document (PDF located here) is for analytical validity and not for clinical validation.

Read More

Topics: LDT, Molecular Diagnostics, Clinical Testing, NGS, FDA, Reference Material

LDT Oversight Counterpoint: Tempering FDA Arguments

Counterpoint to the FDA arguments for laboratory-developed test oversight

Posted by Russell Garlick on Jan 7, 2016 2:56:00 PM

As pointed out by my colleague Trevor Brown in his blog post “LDT Oversight: Why the FDA makes a point” (their case for increased oversight of the new wave of Laboratory Developed Tests [LDTs]), the LDT horse “left the barn”  years ago so why is the FDA calling for a ‘round up’ today? 

Read More

Genetic Profiling of Pediatric Oncology Patients

Recent publication highlights potential of personalized medicine for young cancer patients

Posted by Russell Garlick on Oct 21, 2015 10:38:00 AM

 

There are many challenges for pediatric patients struggling with recurrent or refractory cancer but a recent report and accompanying editorial published in the Journal of American Medical Association brings new hope for patients and their families.1 2This three year study also demonstrates how the principles of precision medicine can be successfully applied with existing DNA and RNA sequencing technologies for many patients.

Read More

Topics: Cancer, Cancer Test, Whole Exome, NGS, RNA-seq, Oncology, Pediatric, Patient Outcome

 
 

Subscribe for Updates

Recent Posts

Categories

see all