Genomic Precision

 A SeraCare blog focused on precision medicine and advanced clinical diagnostics

Yves Konigshofer

Recent Posts

Extracting Formalin-fixed, paraffin-embedded (FFPE) nucleic acids for NGS

Answering frequently asked questions (FAQs)

Posted by Yves Konigshofer on Mar 14, 2017 11:20:00 AM

In the course of patient care, formalin-fixation and paraffin-embedding (FFPE) of biopsy tissue samples are routinely performed, where these samples can be analyzed by histology and archived to link the sample with clinical long-term follow-up. With the development of advanced NGS-based oncology gene panels, it is becoming increasingly important to consider pre-analytic variables when extracting nucleic acids from FFPE-treated samples. This post covers frequently asked questions (FAQs) around the extraction of nucleic acids from FFPE samples for downstream NGS analysis.


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Topics: NGS, next gen sequencing, FFPE Tissue Kit, biopsy tissues, Deparaffinization Solution, Formalin-fixed, paraffin-embedded, nucleic acid, ethanol, molten paraffin

FDA-AACR Liquid Biopsies in Oncology Drug and Device Workshop

Important information for assay development and review by the FDA

Posted by Yves Konigshofer on Aug 8, 2016 9:09:00 AM

The presentations during the FDA-AACR Liquid Biopsies in Oncology Drug and Device Development Workshop on July 19, 2016 included several important pieces of information that will likely guide the development of assays and their review by the FDA.

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Topics: Diagnostics, LDT, Cancer Test, Circulating Tumor DNA, Clinical Testing, NGS, Precision Medicine, Mutation, ctDNA, FDA, Test Development, Reference Material, Oncology

The FDA NGS-based Oncology Panels Workshop

Impressions from the first FDA workshop focusing on NGS-based oncology diagnostic tests

Posted by Yves Konigshofer on Apr 1, 2016 11:08:00 AM

The U.S. Food and Drug Administration on February 25, 2016 held an all-day public workshop entitled “Next Generation Sequencing-based Oncology Panels” at their White Oak campus in Silver Spring, Maryland. Companion diagnostics were a recurring theme of the initial FDA presentations at this Next Generation Sequencing-Based Oncology Panels Workshop and these important tests will be our focus here. The slides that were presented at the workshop are available (PDF) and are referenced below, and those presented by SeraCare’s CSO Russell Garlick start on page 196.

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Does synthetic DNA sequence behave the same as cell-line DNA?

Performance analysis of SeraCare’s Seraseq Solid Tumor Mutation Mix-I AF10 and AF20

Posted by Yves Konigshofer on Feb 5, 2016 11:42:00 AM

A recurring question SeraCare has been asked is whether synthetic DNA sequences perform similarly to cell line-derived sequences. For example, it could be hypothesized that secondary structure and/or the GC content of the DNA around a particular amplicon might lead to a detection bias when only 400 bases on either side of the amplicon are present compared to when many kilobases are present.

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The current state of non-invasive prenatal testing

A personal story of an expectant father intersects with the complex problem of testing specificity and sensitivity

Posted by Yves Konigshofer on Dec 9, 2015 10:51:00 AM

Sometimes a single remark can effectively summarize a very complex problem. While the November 12, 2015 FDA Public Workshop on “Standard Based Approach to Analytical Performance Evaluation of Next Generation Sequencing In Vitro Diagnostic Tests” focused primarily on tests that look for germline and somatic variants, a comment made by Jared Maguire – Counsyl’s ‎Director of Computational Biology – about 1 hour 14 minutes into the workshop explained a lot about the current state of non-invasive prenatal testing (NIPT) and what patients, physicians and insurers are experiencing; more on that later.

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Topics: NIPS, Nipt, Prenatal Test

 
 

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