How can specific NGS assay content, chemistry, and analysis make a difference for heme malignancy answers?

In this on-demand webinar from IDT, experts from Duke University Health System present their experience implementing Archer FusionPlex and VariantPlex custom NGS assays for profiling heme malignancies, discussing case studies, why they chose these panels, how they were implemented in the lab, and their experience with the chemistry, workflows, and analysis software.

For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

Archer’s VariantPlex panels are a collection of pan-cancer solid tumor research assays that use next-generation sequencing powered by anchored multiplex PCR (AMP) to identify microsatellite instability status accurately without a matched normal sample.

This white paper from IDT describes an evaluation of the VariantPlex MSI Module, available for research use with VariantPlex panels to assess microsatellite instability status via instability of 114 curated microsatellite loci in solid tumor samples, in comparison with orthogonal methods and reproducibility studies.

Tumor mutational burden (TMB) is rapidly gaining acceptance in oncology research as a key biomarker and indicator of tumor response to immune checkpoint inhibitors. Whole-exome sequencing (WES) of tumor-normal pairs is the reference standard for the calculation of TMB; however, given the cost and other workflow implications of WES, TMB is frequently derived from targeted next-generation sequencing panels.

This scientific poster from IDT describes the measurement of TMB using VariantPlex Pan Solid Tumor and VariantPlex Complete Solid Tumor panels utilizing anchored multiplex PCR chemistry for error correction and bias mitigation.

For Research Use Only. Not for use in diagnostic procedures.

This 20-minute, on-demand presentation sheds light on crucial aspects of bringing a genetic test to market. It covers:

• Advantages of FDA-Cleared Devices: Explore the benefits of utilizing US FDA-cleared Oragene Dx and ORAcollect Dx saliva collection devices in genetic tests and molecular diagnostics.

• Navigating Regulatory Considerations: Gain insights into the regulatory landscape for IVDs and LDTs and the strategic path for bringing genetic tests to market while complying with evolving regulations.

• Ease of Use and Customization: Understand the evidence supporting the ease of use of saliva collection devices with U.S. FDA general clearance. Learn how test kits can be customized to meet specific requirements, with streamlined offerings for test providers, and enabling a convenient experience for patients.

Speakers:

• Austin Udocor, Director, Regulatory Affairs, DNA Genotek Inc

• Tara Crawford Parks, Ph.D., Senior R&D Manager, DNA Genotek Inc

Please click here for the companion eCase study video.

Antibody development, scale-up, and mass manufacturing remain complex processes with many pitfalls and restarts. Part of the challenge is that the skill sets needed for each of the three main steps — development, scale-up, and manufacturing — are considerably different, requiring the commercialization team to master diverse technologies and techniques. Further, the team is faced with decisions on outsourcing parts of the process or investing in in-house expertise and capital expenditures. Often, when a project has narrow performance specifications or tight launch deadlines, seeking out an experienced partner like MilliporeSigma is prudent. This talk covers the key steps in the modern antibody development process for diagnostic assays using advanced technology and discusses case studies in which MilliporeSigma's R&D and manufacturing teams solved some of the toughest challenges in antibody commercialization.  

Please click here for the companion eCase study video.

The immune system plays an important role in shaping cancer progression, and some of the most successful treatments direct the patient’s own immune cells to target cancer cells. This new and rapidly expanding field of immuno-oncology requires high-resolution, quantitative analytical tools at both the population and single-cell level to parse the complex interplay between cancer, immune, and stromal cells.

This scientific review from Bio-Techne discusses how researchers have used Simple Western, and automated Western blot platform, instead of traditional Western blot in developing next-generation CAR T-cell therapies, studying the tumor microenvironment, developing bispecific antibodies, and investigating other aspects of immuno-oncology.

This application note from Bio-Techne introduces Simple Western, an advanced immunoassay platform that overcomes the limitations of traditional ELISA, employing capillary electrophoresis and adding the dimension of molecular weight to protein analysis, providing sensitive, accurate, and reproducible quantitative immunoassay read-outs. While ELISA offers a two-dimensional measurement of antibody binding, Simple Western adds a third dimension by simultaneously measuring antibody binding activity and providing molecular weight size information. This approach enhances the depth and accuracy of protein analysis under varying experimental conditions.

This 20-minute, on-demand presentation sheds light on crucial aspects of bringing a genetic test to market. It covers:

• Advantages of FDA-Cleared Devices: Explore the benefits of utilizing US FDA-cleared Oragene Dx and ORAcollect Dx saliva collection devices in genetic tests and molecular diagnostics.

• Navigating Regulatory Considerations: Gain insights into the regulatory landscape for IVDs and LDTs and the strategic path for bringing genetic tests to market while complying with evolving regulations.

• Ease of Use and Customization: Understand the evidence supporting the ease of use of saliva collection devices with U.S. FDA general clearance. Learn how test kits can be customized to meet specific requirements, with streamlined offerings for test providers, and enabling a convenient experience for patients.

Speakers:

• Austin Udocor, Director, Regulatory Affairs, DNA Genotek Inc

• Tara Crawford Parks, Ph.D., Senior R&D Manager, DNA Genotek Inc

Please click here for the eCase study transcript. 

There is an increasing demand for next-generation sequencing (NGS) library preparation protocols that do not include PCR to avoid the introduction of PCR bias into the pool of DNA for sequencing. The Illumina DNA PCR-Free Prep kit follows a PCR-free workflow and is being increasingly used in sensitive applications such as whole-genome sequencing (WGS) because it is both flexible and easy to automate. Its on-bead tagmentation step is especially important for reducing library preparation time and sample input requirements. These features are of great interest for clinical applications such as tumor evaluations and newborn diagnostics and are also important for research uses.

Miro Canvas is a digital microfluidics (DMF) platform that allows custom low-throughput workflow automation for complex protocols such as NGS library preparation. The system is compatible with a wide range of reagents. This application note describes the results that can be expected when using the Illumina DNA PCR-Free Prep kit in a protocol developed for Miro Canvas. The resulting research-use-only libraries can then be sequenced using Illumina platforms.

Antibody development, scale-up, and mass manufacturing remain complex processes with many pitfalls and restarts. Part of the challenge is that the skill sets needed for each of the three main steps — development, scale-up, and manufacturing — are considerably different, requiring the commercialization team to master diverse technologies and techniques. Further, the team is faced with decisions on outsourcing parts of the process or investing in in-house expertise and capital expenditures. Often, when a project has narrow performance specifications or tight launch deadlines, seeking out an experienced partner like MilliporeSigma is prudent. This talk covers the key steps in the modern antibody development process for diagnostic assays using advanced technology and discusses case studies in which MilliporeSigma's R&D and manufacturing teams solved some of the toughest challenges in antibody commercialization.

Please click here for the eCase study transcript.  

Biofidelity is a pioneer in the genomic technology space, and the UK-based company’s mission is to unlock the benefits of precision medicine for cancer patients. Its technologies can be used for early detection, precise diagnosis, and routine monitoring applications in oncology.

This white paper from LGC SeraCare explains how working closely with LGC Clinical Diagnostics ensures that Biofidelity is provided with the high-quality, bespoke next-generation sequencing reference materials that the company needs to validate its technology for translation into clinical practice.

Proficiency testing allows a laboratory to evaluate if its test performance is satisfactory for the intended clinical purpose. It enables inter-laboratory comparisons by providing the same material to participants. This is important for non-invasive prenatal tests (NIPS or NIPT) since they are not FDA-approved diagnostic tests and are only intended for screening.

This white paper from LGC SeraCare describes a study examining the 2022 College of American Pathologists NIPT participant summary report regarding a case that showed a disparity in fetal sex chromosome status between the participants, with findings supporting the importance of appropriate diagnostic follow-up, genetic counseling, and clinical correlation in prenatal testing.

The BRCA1 and BRCA2 tumor suppressor genes limit DNA damage. Consequently, loss-of-function mutations in these genes lead to increased incidence of breast, ovarian, and prostate cancer. Accurate detection of BRCA variants is paramount for patients with somatic cancer to guide treatment strategies, such as eligibility for PARP inhibitor therapy, and for individuals carrying inherited mutations to consider preventive actions. However, 27 percent and five percent of pathogenic mutations in BRCA1 and BRCA2, respectively, are large genomic rearrangements (LGRs) that are particularly difficult to detect in PCR and targeted NGS-based assays. Therefore, the development of assays that consistently detect BRCA1/2 LGRs will require reliable reference materials for validation, troubleshooting, and routine quality control.

This scientific poster from LGC Seracare describes the development and multi-platform validation of a set of novel multiplexed reference materials containing 20 clinically relevant BRCA1/2 variants, including 11 large genomic rearrangements.

Homologous recombination deficiency (HRD) arises when defects in DNA repair pathways occur, leading to genomic instability. HRD status is an emerging therapeutic biomarker; NGS assays that measure it can be used to stratify ovarian and breast cancer patients and determine eligibility for clinical trials, PARP inhibitors, and platinum-based therapies. Seraseq FFPE HRD reference materials were developed to cover a range of genomic instability scores to help NGS HRD assay validation and development.

This scientific poster from LGC SeraCare discusses a multi-site evaluation across various platforms of high-positive, low-positive, and negative HRD reference materials.

Cancers can be caused by a multitude of distinct genetic abnormalities, and each tumor is unique. Dozens of new targeted therapies have been developed in recent years, but the challenge of providing optimal care to cancer patients lies in the ability to match the genetic profile of the tumor to the most appropriate therapy. Advances in next-generation sequencing (NGS) technologies have enhanced the identification of hundreds of mutations that may contribute to disease progression, and the development of new diagnostic NGS assays is continually evolving. These assays can profile genetic mutations to enable precision diagnostics, personalized treatment selection, stratification of patients for clinical trials, and improved disease monitoring.

This white paper from LGC SeraCare describes the role reference materials play in developing and validating robust precision oncology assays that can perform with the accuracy, sensitivity, and reproducibility required for clinical use, as well as considerations for selecting the most appropriate provider of reference materials.