Diagnostic Precision

A SeraCare blog focused on precision medicine and advanced clinical diagnostics

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Advancing Immuno-Oncology Biomarker Validation with Industry’s First NGS-based TMB Reference Materials

Category: NGS, Immuno-Oncology

Posted by Omo Clement, PhD on Sep 2, 2020
Overview Tumor mutational burden (TMB) is a measurement of the number of mutations carried by a tumor cell genome. By comparing DNA sequences from a patient’s healthy tissue and tumor cells, and using a number of complex algorithms, scientists can determine the number of acquired somatic mutations present in tumors but not in normal tissues.1 NGS is the primary method employed to measure TMB, either through targeted panels or whole exome sequencing (WES);2 the latter is considered the gold-standard measurement today.
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Highlights from the ESHG and ESHRE 2020 Virtual Conferences

Category: NGS, NIPT, Women's health, Reproductive Health, Non-invasive Prenatal Testing, PGT, Preimplantation genetic testing

Posted by Agnes Caruso on Aug 20, 2020
The plans for this year’s NIPT and PGT conferences, like many others, were quickly derailed by the COVID-19 pandemic. The ESHG and ESHRE Annual Meetings were moved to virtual space and even though the format was a new experience, the science did not disappoint. Here we will share some of the highlights from the sessions.
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Design and Development of Compromised FFPE Reference Materials

Category: NGS

Posted by Dana Ruminski Lowe, Ph.D. on Aug 11, 2020
    Tumor profiling assay workflows start from a tissue biopsy sample that is formalin fixed and paraffin embedded (FFPE), a process that introduces various kinds of damage in the nucleic acids in the tissue specimen. Reference materials that closely mimic the damage profile of patient FFPE samples are lacking. Depurination, depyrimidination, deamination, oxidation, nicks, and double strand breaks may be found in DNA extracted from FFPE tissue, despite the use of extraction kits that attempt to repair some of this damage. We have developed a formalin-damaged, multiplexed biosynthetic reference material, Seraseq® Compromised FFPE Tumor DNA, as well as a companion wild-type (WT) material, Seraseq Compromised FFPE WT, to mimic the damage found in patient samples that can be used to assess the entire tumor profiling workflow. We compared the performance of these reference materials in downstream assays to that of FFPE material with minimal DNA damage such as the Seraseq FFPE WT (DNA/RNA) RM product.
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Do COVID-19 infections affect NIPT?

Category: NGS, NIPT, Non-invasive Prenatal Testing, SARS-CoV-2, COVID-19

Posted by Prof. Joris Vermeesch, PhD on Mar 26, 2020
We would like to present a guest blog from Prof. Joris Vermeesch, Ph.D. This blog originally posted on the Noninvasive Prenatal Testing Online Resource Page on the 17th March summarizes our current understanding of any possible interference of SARS-CoV-2 infection on the outcomes of NIPT testing.
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Assessing RNA Extraction with FFPE Fusion RNA Reference Materials

Category: NGS, reference materials, RNA fusion

Posted by Dan Brudzewsky on Mar 11, 2020
This is a third blog in a series on RNA fusions, this time focusing on how the FFPE Fusion RNA materials are used as RNA extraction controls.
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Diagnostic Testing Schemes for NTRK Cancers: All Roads Lead to NGS

Category: NGS, SeraSeq, NTRK, RNA fusion

Posted by Russell Garlick, PhD on Feb 12, 2020
New treatment options for cancer patients with neurotrophic tyrosine kinase (NTRK) rearrangements are a tremendous success, demonstrating first-hand the importance of precision diagnostics. The FDA granted accelerated approval of Bayer's VITRAKVI (larotrectinib) for adult and pediatric solid tumors containing NTRK fusions1. The approval was one of the first tissue agnostic approvals based on genotyping results, and included patients with unresectable or metastatic cancer. For 12 cancer types, the overall response rate was 75% with 22% complete response and 53% partial response. In addition to VITRAKVI, Genentech's entrectinib has a "breakthrough" status and is being evaluated for the potential treatment of advanced or metastatic tumors that harbor NTRK or ROS1 gene rearrangements.
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Evolution of non-invasive prenatal testing (NIPT) testing

Category: NGS, NIPT, #Quality, New Reference Material, reference materials, trisomy, Reproductive Health, Non-invasive Prenatal Testing

Posted by Agnes Caruso on Feb 5, 2020
Prenatal screening for aneuploidy has changed dramatically since the 1970s. Non-invasive methods developed in the 1980s and 1990s, combined measurements of maternal serum analytes and ultrasonography. The problem with those methods was not just a high false-negative rate of 12% to 23%, a high positive rate of 5% and a poor sensitivity, ranging from 50% to 95% 1. Uncertain results frequently led to invasive procedures such as amniocentesis or chorionic villi sampling to perform karyotyping on fetal samples. Both of those procedures carry a risk of miscarriage.
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Multi-Lab Study of Fusion RNA Reference Standards for Targeted NGS

Category: NGS, reference materials, AACR, NTRK, RNA fusion

Posted by Andrew Anfora, PhD on Jan 28, 2020
Sourcing assay validation samples as positive run controls or workflow controls in targeted NGS RNA fusion assays remains a challenge today. This is further exacerbated with clinical labs looking to provide validated NGS assays for patient stratification in a host of new drugs in clinical trials or newly approved targeting fusion genes, such as NTRK genes (Larotrectinib, Loxo/Bayer) and Entrectinib (Genentech/Roche) for rare cancers in adult and pediatric patients, and RET (Loxo/Lilly) for lung cancer. SeraCare produces several RNA fusion reference materials. This article describes the development and multi-laboratory evaluation of a pan-cancer multiplexed Fusion RNA reference standard for analysis of clinically relevant fusion genes in solid tumors. The evaluation was conducted at 5 different laboratories on different NGS platforms (amplicon- and hybridization capture-based) as well as at different RNA inputs within a platform. Results highlight the utility of this Fusion RNA reference material to support clinical NGS assays as positive controls in solid tumor cancer patient stratification for many of these fusion-based targeted therapies.
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Making the Shift from Technological Innovation to Operational Excellence: Delivering on the Promise Of Next-Generation Sequencing for Personalized Medicine

Category: NGS, clinical genomics

Posted by Peter Duncan on Apr 22, 2019
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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AACR 2019 Day One Highlights: Next-Generation Car T Cells

Category: NGS, AACR

Posted by Catherine Huang, PhD on Apr 2, 2019
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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