Diagnostic Precision

A SeraCare blog focused on precision medicine and advanced clinical diagnostics

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How to resolve the challenges of MRD?

Category: NGS, ctDNA, cfDNA, reference materials, MRD

Posted by Yves Konigshofer, PhD on Oct 7, 2020
  This is part 2 of 2 of the MRD blog post. (Click here for part 1). In this section, we will discuss how to overcome some of the most common challenges of MRD testing. Overcoming the Challenges In order to mitigate sequencing errors, methods using Molecular Barcodes (MBCs), Unique Molecular Identifiers (UMIs), etc. (which are essentially all the same) may be used, where each starting molecule is sequenced many times. The MBCs are then used to generate consensus sequences from sequences that were likely obtained from the same starting molecule. The assumption is that errors appear due to somewhat stochastic processes and that the consensus sequences will likely be correct. This requires many observations of the same starting molecule, so it will be recommended to generate 10-fold more sequences than there are molecules. Therefore, with 8,000 genomic equivalents, we might want to target a sequencing depth of 80,000. This is a reason why using 10-fold more input ccfDNA may not necessarily be a good thing (in addition to having to obtain a 10-fold larger liquid biopsy) since we may have to increase sequencing depth accordingly to 800,000, which could increase the cost of sequencing 10-fold, which could reduce the likelihood for payment and running the assay profitably.
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So, you want to monitor Measurable Residual Disease? What are the challenges?

Category: NGS, ctDNA, cfDNA, reference materials, MRD, Minimal Residual Disease

Posted by Yves Konigshofer, PhD on Oct 1, 2020
Part 1 of 2   Background Measurable Residual Disease (MRD) monitoring – for purposes of this blog – will be the act of looking for somatic variants in a liquid biopsy sample by analyzing circulating cell-free DNA (ccfDNA). This is done to monitor the disappearance of a metastatic solid tumor during treatment and to follow any future reemergence of that cancer. Analyzing ccfDNA assumes that circulating tumor DNA (ctDNA) will be present, and the median ctDNA frequency in patient samples across cancers seems to be around 0.5 to 1 %. Thus, the median variant allele frequencies (VAFs) of the somatic variants will start around this range, and the goal of MRD monitoring is to be able to detect them at much lower VAFs. This can be challenging and if we are going to design an assay for MRD monitoring, then we need to be aware of them and overcome them.
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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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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,PhD 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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What is Non-Invasive Prenatal Testing (NIPT)?

Category: NIPT, #Quality, New Reference Material, reference materials, trisomy, Reproductive Health

Posted by SeraCare Team on Jan 20, 2020
Fetal aneuploidy affects about 9 in 1,000 live births. The definition of aneuploidy is an abnormal number of chromosomes ; with 23 pairs of chromosomes in humans, 46 is the normal number, while aneuploidy individuals will have 45 or 47.  In trisomy, there is one additional chromosome, typically chr21, 18 or 13 (it is not a coincidence that these are the smallest chromosomes in humans).  Historically, the invasive methods amniocentesis and chorionic villus sampling (CVS) were used with risk to the pregnancy, with about a 1% chance of miscarriage due to the procedure. Non-invasive methods based upon ultrasound and serum biomarkers are useful screening tests, but were of limited reliability as they were indirect measures of chromosomal abnormalities1.   Photograph courtesy of Flickr user Can H.
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Building and Implementing Liquid Biopsy Assays with the Industry’s Most Patient-Like Reference Materials

Category: NGS, SeraSeq, liquid biopsy, reference materials

Posted by Omo Clement, PhD on Oct 24, 2018
SeraCare’s clinical genomics technologies are developed to address challenges faced across the spectrum of NGS assays. From early development of assays – either IVD assay manufacturers or clinical labs building their own LDTs - there is a scarcity of characterized, complex, difficult variants to ensure the assay can robustly detect all the critical genomic variants in a patient sample. Using our highly characterized, reproducible, and GMP-grade NGS standards, laboratories have a wide range of analytical and clinical validation tools to deeply characterize assay performance such as LOD, linearity, specificity, sensitivity, and reproducibility.   
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Ebola Outbreak 2018: Diagnostics Again are Essential to Minimize Spread and to Control Disease

Category: Accuplex, reference materials

Posted by Catherine Huang, PhD on Jun 25, 2018
On April 4th, 2018, a new outbreak of Ebola Virus Disease (EVD) occurred in Equateur Province in the Democratic Republic of the Congo. As of June 10th, there have been a total of 55 EVD cases and 28 deaths with a case fatality rate of 50.9%. Although the outbreak remains active, public health authorities have expressed cautious optimism because there have been no new cases in two of the three affected areas (Bikoro and Wangata zones) since May 17th, 2018 and the rate of new cases in the third affected zone (Iboko) has slowed.1
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Developing a Rock-Solid Lung Cancer Assay

Category: cancer, NGS, reference materials, Lung Cancer

Posted by Yves Konigshofer, PhD on Mar 15, 2018
Next-generation sequencing (NGS) allows deeper insights than ever before into the human genome and a host of diseases and conditions. So it makes sense that there is a worldwide movement to employ NGS in a growing number of applications. But as the saying goes, with great power comes great responsibility.
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CNVs and Tumor Profiling: New CNV Materials for Breast, Lung, and Brain Cancer

Category: cancer, NGS, reference materials

Posted by Dana Ruminski Lowe, Ph.D. on Feb 14, 2018
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.
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