TMB
Reference Materials for Tumor Mutational Burden Transcriptome Profiling
Tumor Mutational Burden (TMB) has shown the ability to predict the response of some tumor types to immune checkpoint inhibitor therapy. However, TMB is an imperfect biomarker. We have previously measured TMB by whole exome sequencing (WES) in cell lines to establish TMB reference materials. We have now evaluated the same cell lines for expression of the TMB mutations previously identified by WES.
RNA
Optimizing Performance of Whole Transcriptome RNA-Seq Reference Materials
Whole transcriptome RNA-sequencing (RNA-Seq) has emerged as one of the most effective methods for detection of genomic rearrangements in cancer. Enrichment for poly(A) + RNA as part of library preparation is a standard method to select for mRNAs, but ribosomal RNA depletion and exon capture methods are also used. Seraseq® Fusion RNA Mix v4 was developed for targeted NGS panels and performed sub-optimally on RNA-Seq.
NIPT
Development of Matched Maternal-Fetal NIPT Reference Materials
How to assure quality of NIPT tests and concordance of test results between various platforms limited availability of clinical samples which can be used for proficiency testing, assay validations, and run controls?
DNA
Development of Quality Control Reference Materials for MSI Testing
Microsatellite Instability (MSI) occurs in cancer cells when there is deficient DNA mismatch repair.
TMB
Development and performance of formalin-damaged FFPE reference materials
FFPE reference materials that closely mimic the damage profile of cancer patient samples are difficult to design, manufacture and/or source. We have developed an FFPE manufacturing process for reference materials...
TMB
Reference Materials for Measurable Residual Disease (MRD) Monitoring in Circulating Cell-Free DNA
Presented at AMP 2020, this poster describes RMs for the development, validation, and control of MRD assays. We designed our RMs for...
bTMB
Development and validation of blood tumor mutational burden reference standards
We announced the availability of a range of human diseased cell line based Seraseq® Blood TMB (bTMB) reference controls to support the validation and precise measurements of plasma-derived blood tumor mutational burden...
TMB
Development and performance of a formalin-damaged multiplexed DNA tumor mutation FFPE reference material
FFPE reference materials that closely mimic the damage profile of cancer patient samples are difficult to design, manufacture and/or source. We have developed an FFPE manufacturing process for reference materials...
TMB
Development of reference material for blood tumor mutational burden measurement
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).
TMB
Reference Materials for Measurable Residual Disease (MRD) Monitoring
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...
NGS
NGS-based Reference Materials for Fusion and Somatic Variant Detection in Myeloid Cancers
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...
NIPT
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...
TMB
Improving and Standardizing TMB Assay Performance
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.
NTRK
Development of NTRK Reference Materials for Global Assay Standardization
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.
cfDNA
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.
ctDNA
Multi-Center Evaluation of Circulating Tumor DNA Assays
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.
NSCLC
A Non-Small Cell Lung Cancer Reference Material
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.
RNA Fusion
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.
SRS
Interlaboratory Assessment of Complex Variant Detection
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.
EGFR
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).
ccfDNA
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%.
cfDNA
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.
ctDNA
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.
cfDNA
Analytical Validation of Oncomine Breast cfDNA Assay v2
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.
FFPE
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.
ctDNA
Use of Amplified and Synthetic ctDNA to Assess Variant Calls from Targeted NGS Panels
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...
ctDNA
New Technology to Generate Commutable and Comprehensive ctDNA Reference Materials for NGS
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.
NIPT
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...
HCV RNA
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.
NGS
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.
Cancer
Plasma Mutation Spectrum Matches Known Tumor Mutations in Active Cancer Patients
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.
ctDNA
Evaluation of Customizable Circulating Tumor DNA (ctDNA) Reference Materials with Multiple Assays
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.
ctDNA
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.
ctDNA
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.
NGS
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
ctDNA
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.
ccfDNA
Donor-Derived Circulating Cell-Free DNA (ccfDNA) Reference Materials for Concordance Studies
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
RNA Fusion
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.
VariantFlex
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,
CNVs
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.
NGS Validation
Reliable Interpretation of NGS Data Using Highly-Multiplexed Reference Material
This video shows how Directed Genomics and New England Biolabs use highly multiplexed reference materials during optimization and validation to fine-tune assay performance.
Liquid Biopsy
An Efficient and Ultrasensitive NGS Solution for Profiling ctDNA
Asuragen’s Associate Director of Bioinformatics explains how SeraCare’s ctDNA allows confident quantification of trace levels of ctDNA in their NGS-based assay.
RNA Fusion
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.
ccfDNA
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
ctDNA
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.
Zika
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).
NGS
Multiplexed Next-Generation Sequencing Reference Materials for Testing of Inherited Disorders
Next-generation sequencing (NGS) has rapidly advanced the genetic testing for inherited disorders.
ctDNA
A Commutable Circulating Tumor DNA (ctDNA) Reference Material
Commutability is an important aspect of reference materials and relates to how well the materials can mimic the natural analyte.
NGS
Development of Highly Multiplexed Reference Materials for Inherited Cancer Testing
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.