Although most TMB measurements are made from genomic DNA that has been extracted from formalin-fixed paraffin embedded tissue sections, some diagnostic tests attempt to measure TMB in circulating tumor DNA (ctDNA) extracted from blood samples; an approach referred to as blood TMB (bTMB).
The analytical validation of liquid biopsy-based assays that attempt to monitor for the disappearance and reemergence of cancer can be challenging due to the need for reference materials...
The large range of genetic aberrations and genes involved in Myelogenous malignancies and clonal diseases of hematopoietic progenitor cells which can lead to accumulation of immature blast cells...
Development of SNP Matched NIPT Reference Materials for Validation, Proficiency Testing and Quality Control
Plasma based non invasive prenatal testing (NIPT) by Next Generation Sequencing (NGS) is being adopted into clinical laboratories. However, obtaining sufficient amounts of patient derived reference materials for...
Determining and using the most effective and safest treatment is of great importance in cancer disease management. Recently, a potential biomarker has been identified in immunotherapy: tumor mutational burden (TMB), an assessment of the number of relevant mutations in a tumor.
Genomic cancer testing is a powerful tool for identifying the individual and often complex genomic alterations underlying carcinogenesis and cancer progression. SeraCare has developed reference material that contains 15 clinically-relevant NTRK fusions in a single reference sample.
Validation of a Novel One-Step Digital PCR Platform with Precision Circulating Cell-Free DNA Standards
EGFR (epidermal growth factor receptor) mutation testing is an important drug target for the treatment of non-small cell lung carcinoma (NSCLC). Read about the validation of a novel, fully integrated dPCR platform for the detection and absolute quantification of EGFR T790M.
Measurements of circulating tumor DNA (ctDNA) hold great potential to detect residual disease and monitor therapeutic response and tumor evolution. However, there are many technical challenges including trace levels of circulating cell free DNA, short DNA fragment sizes, low variant allelic fractions, and the need to detect all variant types.
About 10-50% of NSCLCs have one of several activating EGFR driver mutations which have been clinically validated as therapeutic biomarkers for anti-EGFR drugs. Identifying these driver mutations through liquid biopsies is a promising alternative to traditional biopsies; however, the precision of mutation analysis for some of these targets remains a challenge.
Consistent Performance of Highly Multiplexed RNA Fusion Reference Materials Across Different NGS Assays in a Multi-Lab Study
Fusion detection is an important part of cancer disease management, and there is an increasing need for highly multiplexed reference materials to cover mutations which may be rare or difficult to obtain.
In this study, an international group of collaborating laboratories explored the creation of a synthetic reference sample (SRS) in which multiple technically challenging variants are introduced into a known human genomic background. This single SRS with 23 variants was evaluated using 10 NGS workflows.
Enabling Standardised Testing of Liquid Biopsy Assays Detecting EGFR Mutations Using Bespoke Reference Materials
Frequently, patients with non-small cell lung cancer (NSCLC) have limited (if any) tissue available to perform EGFR mutation testing. This can be overcome by testing plasma samples for the presence of mutations in circulating tumor DNA (ctDNA).
Use of Molecular Identifiers and Targeted NGS to Enable Variant Detection Below 1% Allele Frequencies in Circulating Cell-Free DNA
Watch the video to see how Swift BioSciences' analysis accurately and reproducibly identified known variants as low as 0.25%.
CleanPlex UMI Lung Cancer Panel for Detecting Low-Frequency Variants Using Targeted Amplicon Sequencing Approach & Molecular Barcodes
Watch the video and download this free poster to see how the recovered number of UMIs is one of the keys for accurate detection of rare mutations with fewer false positives.
A Comprehensive, Targeted NGS Method that Rapidly and Accurately Detects ctDNA Variants at 0.1% Frequency in Plasma Samples
See how this targeted NGS method is able to distinguish a low-frequency ctDNA signal from background noise in plasma cell-free DNA using a streamlined PCR-based workflow.
MolecularMD performed analytical validation studies for the detection of hotspot mutations and copy number variation using commercially available cfDNA controls, full-length and fragmented cell line DNA dilutions, plasma-derived cfDNA samples and FFPE DNA samples.
Optimization Studies for the Development of Highly Multiplexed Reference Materials in FFPE Format for Solid Tumor Profiling
Sourcing individual FFPE samples (remnant patient specimens or cell line derived) for each of the somatic mutations of interest can be expensive and time-consuming.
The detection of somatic mutations in circulating cell-free DNA(ccfDNA) from plasma samples using next-generation sequencing (NGS) panels is one of the most exciting developments in oncology diagnostics. However...
The need for commutable and comprehensive ctDNA reference materials is evident from the increasing number of liquid biopsy diagnostics and comprehensive panels on the market that are accompanied by reports of discordant results.
Highly Stable and Commutable NIPT Reference Materials for Validation, Proficiency Testing and Quality Control
Plasma-based DNA next-generation sequencing (NGS) diagnostics for non-invasive prenatal testing (NIPT) has exploded in popularity in recent years. However...
Technology to Produce Non-Infectious Recombinant Virus as Reference Materials for Unculturable or Highly Dangerous Viral Pathogens
Diagnostic laboratories and test developers need to design, manufacture, and validate assays for pathogenic viruses and this requires stable, reproducibly manufactured positive reference materials.
Development and Testing of Reference Materials for NGS based Somatic Variant Detection and Fusion Detection in Myeloid Cancers
See how the development of these reference materials aid the development, optimization, and verification of NGS-based myeloid disease testing, providing laboratories greater assurance in their ability to correctly detect these genomic events in myeloid patient samples.
UNC evaluated a test system that preferentially amplifies fragmented DNA to reduce impact of ex vivo release of cellular DNA, and that capitalizes on “unique molecular identifiers” and variable amplicon lengths to improve assay performance.
The utility of circulating cell-free DNA (ccfDNA) has led to the development of an ever-increasing number of ctDNA assays that also make use of fundamentally different analytic methods.
Application of the Highly Sensitive SiMSen-Seq Assay and Seraseq®-Designed Reference Materials to Minimal Residual Disease Detection
The reliable detection of minimal residual disease (MRD) becomes possible as ctDNA assays become more sensitive. Sensitive assays require matched reference materials.
A Novel Circulating Tumor DNA Reference Material Compared on Next-Generation Sequencing to Digital PCR Assays
Watch the video and download this free poster to see how SeraCare has developed a size-selection and DNA processing method to mimic the size profile of native ctDNA.
Flexible Tools For The Development And Performance Verification Of Customized Target Enrichment Panels
Implementation of next-generation sequencing for variant identification and discovery presents difficulties both in the selection of genomic loci for inclusion in a panel, as well as the ability
Multi-Laboratory Assessment of a New Reference Material for Quality Assurance of Circulating Tumor DNA Measurements
The accurate diagnosis and monitoring of cancer, using circulating tumor DNA, is a major challenge, given the low concentration and complexity of the target molecules.
The limited quantities of ccfDNA in plasma and the limited amount of ccfDNA that can therefore be obtained from a single donor can make it difficult to assess the sensitivities and specificities of
Use of Highly Multiplexed Reference Materials to Facilitate Validation of a Clinical NGS Tumor Fusion RNA Assay
NGS Tumor Fusion RNA Assay Next-generation sequencing (NGS) assays for detection of tumor RNA fusions must undergo rigorous validation before clinical implementation.
Custom VariantFlex Technology Allows Rapid Design and Testing of Reference Materials for Tumor Genotyping Assays
Development and validation of tumor genotyping assays requires highly characterized reference materials for effective assessment of accuracy, precision,
Development of Well Characterized Breast, Lung, and Brain Cancer Copy Number Variation Reference Materials
Copy number variation (CNV) can be a key driver of oncogenesis. Pathogenic CNVs are often associated with unfavorable prognosis and drug resistance.
This video shows how Directed Genomics and New England Biolabs use highly multiplexed reference materials during optimization and validation to fine-tune assay performance.
Asuragen’s Associate Director of Bioinformatics explains how SeraCare’s ctDNA allows confident quantification of trace levels of ctDNA in their NGS-based assay.
Assessing Sensitivity of NGS RNA Fusion Assays Using a Multiplexed and Well-Characterized Linearity Panel
Many targeted NGS-based panels have been introduced to detect RNA fusions useful for prognosis and therapy selection in cancer.
Circulating Cell Free DNA Isolated and Amplified from the Plasma of Pancreatic Cancer Patients as Reference Material for ctDNA Assays
The validation and evaluation of circulating tumor DNA (ctDNA) assays poses analytical challenges because the amount of circulating cell-free DNA (ccfDNA) that can be obtained
Patient-Like Circulating Tumor DNA Reference Materials for Evaluation of Next-Generation Sequencing Tests
Clinical oncologists are relying on analysis of circulating tumor DNA (ctDNA) across an increasing number of applications.
AccuSpan™ Zika Linearity Panel Spans the Dynamic Range of Assays and Allows Evaluation of Analytical Sensitivity
In response to the Zika virus outbreak, several PCR-based assays have been developed and approved under the Emergency Use Authorization (EUA).
Next-generation sequencing (NGS) has rapidly advanced the genetic testing for inherited disorders.
Commutability is an important aspect of reference materials and relates to how well the materials can mimic the natural analyte.
Next Generation sequencing (NGS) has improved the diagonistic yield of genetic testing, but has presented new challenges for test development, validation and quality control management.