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White Papers and Videos

Optimization of an Agilent NGS Automated Workflow for the Characterization of NSCLC DNA Samples in a Molecular Diagnostic and Anatomic Pathology Laboratory

White Paper

The Anatomical Pathology laboratory of the SS Annunziata Hospital in Chieti is a reference center for lung cancer. The lab has used next-generation sequencing (NGS) methods to characterize formalin-fixed, paraffin-embedded and plasma samples, searching for alterations in genes that are the target of new drugs.

This whitepaper from Agilent presents a study in which researchers from the Anatomical Pathology laboratory characterized lung cancer samples using a complete Agilent workflow, reliably detecting variants that are not easily detectable with other systems in a single, DNA-based assay, and increasing reproducibility and lab productivity.

Dive Deep Into the Molecular Mechanisms Driving Cancer

White Paper

Qiagen OncoLand is a multiomics oncology database with integrated visualization software that helps cancer researchers explore and integrate high-quality public and private cancer datasets.

This eBook presents four use cases in which researchers employed Qiagen OncoLand for their cancer research publications on the discovery of cancer biomarkers and molecular signatures, and in the development of new targets and therapies.

Analyzing Complex Variants in Clinical NGS Data

White Paper

Molecular profiling and characterization of mutations in cancer tissue have increasingly become a standard of care. Next-generation sequencing technologies facilitate the accurate detection of genetic variants, yet the process of analyzing and classifying more complex alterations remains challenging and time-consuming. Cancer samples are often a mix of different types of cells from the tumor microenvironment; clinical intervention prior to tissue collection may lead to a non-ideal quality sample being used for sequencing. Also, the multitude of clonal populations of cells present in a somatic tumor affects the variant allele frequency of the variant of interest. To identify and interpret complex variants, users often require more insight and in-depth understanding of the processes involved. Sometimes, interpreting these complex variants also requires recognition of the sequencing chemistry and the type of sequencer used.

This whitepaper from PierianDx discusses considerations for interpreting and reporting five different types of complex genetic variants in the context of somatic cancer: co-occurring variants, exon-skipping splice variants, gene fusions, copy number variants, and tumor mutation burden, and microsatellite instability.

The Promise and Progress of Novel Cancer Therapies: Selecting a Laboratory to Support Your Oncology Clinical Trial

White Paper

Clinical trials are integral to the development of novel therapies for cancer patients. Each trial must be carefully designed to include tests to determine the appropriate dosage, side effects, and therapeutic benefit of the investigational drug. Selecting the right laboratory to support both clinical trials and pre-clinical research can improve the success rate of drug development.

This whitepaper from Canopy Biosciences outlines considerations for selecting a laboratory to support oncology clinical trials and describes cases of Canopy’s support for trials investigating a biomarker assay and a therapeutic antibody drug.

Reporting NGS Sequencing Data in Clinical Practice

White Paper

This application note from Qiagen describes generating inherited cancer NGS sequencing reports for clinicians and treating oncologists using the clinical decision support software, QCI Interpret, highlighting variant annotation, report customization, and handling variants of unknown significance.

COSMIC Datasheet

White Paper

The Catalogue of Somatic Mutations in Cancer (COSMIC) is the largest database of somatic mutations in human cancer. COSMIC contains over 37 million coding mutations, phenotypic and genotypic annotations of 1.4 million cancer samples, and descriptions of mechanisms that drive cancers and mutations that drive resistance to precision medications.

This whitepaper from Qiagen provides an overview of COSMIC (Catalog of Somatic Mutations in Cancer), highlighting the database’s curation, transparency, and features for data mining, utilization, and manipulation.

Understanding the Uncommon: How to Confidently Identify Rare Cancer Mutations with QCI Interpret One

White Paper

This application note from Qiagen presents an example workflow for detecting rare cancer mutations from large next-generation sequencing panels using QCI Interpret One clinical decision support software and interpretation service. The software delivers variant- and disease-specific evidence for genes in somatic panels. The classifications are based on the peer-reviewed publications, oncologist-reviewed interpretation, and expert second opinion. The software also offers a variant classification system coupled with the evidence of pathogenicity, clinical actionability, and various filtering options.

Introducing Professional Assay Services - RNAscope ISH Experts in Tissue Expression Analysis

Video

This webinar from ACD presents use cases in immuno-oncology, cell and gene therapy, neuroscience, single-cell RNAseq validation, biomarker validation, and others demonstrating applications for RNAscope in situ hybridization services. Uses include spatial visualization of cellular heterogeneity in tumors, biomarker validation, biodistribution analysis of adeno-associated virus vector and transgene expression, CAR-T cell tumor infiltration assays, and others.

Introducing a Novel Chromogenic ISH Assay for High-Resolution Detection of DNA Copy Number and Structural Variants

Video

Genomic DNA anomalies are important biomarkers and drug targets in many cancer types. DNA in-situ hybridization (ISH) is the standard method to directly visualize these molecular alterations, but currently available fluorescent ISH (FISH) assays provide limited morphological detail due to the use of fluorescent nuclear staining as compared to chromogenic staining. Furthermore, FISH techniques rely on fluorescence microscopes, risk the loss of fluorescent signal over time, and involve imaging at high magnifications. There is thus an unmet need for a sensitive and robust chromogenic DNA ISH assay that can enable high-resolution detection of genomic DNA targets with the ease of bright-field microscopy.

This on-demand webinar from ACD demonstrates how the DNAscope assay can detect DNA copy number and structural variations with high specificity and enables greater morphological detail, higher resolution, and simpler interpretation than traditional DNA ISH assays without the need for specialized equipment. The DNAscope chromogenic duplex (red/blue) staining allows researchers to use a standard bright-field microscope to visualize and quantify gene copy number and structural variations in tissues with spatial and morphological context at single-cell resolution.

Professional Assay Services Dual RNAscope ISH & IHC/IF for Tumor Microenvironment and Immune Cell Analysis

White Paper

This application note from ACD shows how combining RNAscope ISH technology with immunohistochemistry or immunofluorescence assays allows for the spatial analysis of targets, biomarkers, cytokines, and CAR-T cells within the tumor microenvironment. These assays support preclinical immuno-oncology research and target validation, and they address a need for monitoring CAR-T cell infiltration and activation in pre- vs post-treatment clinical biopsies.

A Novel Chromogenic In Situ Hybridization Technology for High-Resolution Detection of DNA Copy Number and Structural Variations

White Paper

Genomic DNA anomalies are important biomarkers and drug targets in many cancer types. DNA in-situ hybridization (ISH) is the standard method to directly visualize these molecular alterations, but currently available fluorescent ISH (FISH) assays provide limited morphological detail due to the use of fluorescent nuclear staining as compared to chromogenic staining. Furthermore, FISH techniques rely on fluorescence microscopes, risk the loss of fluorescent signal over time, and involve imaging at high magnifications. There is thus an unmet need for a sensitive and robust chromogenic DNA ISH assay that can enable high-resolution detection of genomic DNA targets with the ease of bright-field microscopy.

This white paper from ACD compares DNAscope — a novel chromogenic DNA ISH assay — to traditional ISH assays for cancer research applications, finding DNAscope to reliably detect various chromosomal structural aberrations at single-gene resolution with high sensitivity and specificity without requiring specialized lab equipment or personnel.

DNAscope: A Novel Chromogenic In Situ Hybridization Technology for High-Resolution Detection of DNA Copy Number and Structural Variations

White Paper

Genomic DNA anomalies are important biomarkers and drug targets in many cancer types. DNA in-situ hybridization (ISH) is the standard method to directly visualize these molecular alterations, but currently available fluorescent ISH (FISH) assays provide limited morphological detail due to the use of fluorescent nuclear staining as compared to chromogenic staining. Furthermore, FISH techniques rely on fluorescence microscopes, risk the loss of fluorescent signal over time, and involve imaging at high magnifications. There is thus an unmet need for a sensitive and robust chromogenic DNA ISH assay that can enable high-resolution detection of genomic DNA targets with the ease of bright-field microscopy.

This poster from ACD, presented at AACR 2021, demonstrates use of a novel chromogenic ISH assay to detect DNA copy number and structural variations, showing specific and efficient detection of gene rearrangements (ALK), amplifications (ERBB2, EGFR, MET), and deletions (TP53 and CDKN2A) without specialized equipment, providing an alternative to commonly used FISH assays in many cancer research applications.

Diagnostic Challenges in Cancer Immunotherapy: An Expert Panel Discussion

Video

Cancer immunotherapy is an exciting new advance for the successful treatment of many forms of metastatic cancer. However, only a minority of patients with terminal cancer have durable response with approved immuno-oncology treatments.

This on-demand webinar features a panel of experts in the field who provide key insights into the current advances in cancer diagnostics and immunotherapy, as well as challenges facing the discipline.

The panelists bring a wealth of expertise and differing viewpoints in clinical laboratory practice, cancer research, translational sciences, and immuno-oncology diagnostics and therapeutics at the molecular and cellular levels important to the care and management of cancer patients and treatment outcomes. Each speaker will have an opportunity to share their perspectives on this topic, which will be moderated by Dr. Russell Garlick, Chief Scientific Officer at LGC SeraCare. The presentation will be followed by a live Q&A to allow attendees to address the experts directly.

Pan-Cancer Gene Expression Analysis of Tissue Microarray Using EdgeSeq Oncology Biomarker Panel and a Cross-Comparison with ERBB3 Immunohistochemical Analysis

White Paper

ERBB3, a member of the human epidermal growth factor (EGFR/HER) family of receptor tyrosine kinases, is overexpressed in metastatic breast cancer, non–small cell lung cancer, and other tumor types. Overexpression has been associated with worse clinical outcomes. There are currently no approved ERBB3-directed agents.

This poster from HTG investigates the expression levels of ERBB3 in solid tumors and normal tissue using the HTG EdgeSeq Oncology Biomarker Panel, with the results suggesting unique protein-level regulation of ERBB3 in tumor cells.

Immune-Checkpoint Genes as Predictive Biomarkers of Trabectedin in Advanced Soft-Tissue Sarcoma: A Spanish Group for Research on Sarcomas (GEIS) Translational Study

White Paper

Though several second-line options are accessible for the treatment of advanced soft-tissue sarcoma, there is a lack of predictive biomarkers available to support the selection of these drugs. Trabectedin specifically targets mononuclear cell lineages (macrophages and monocytes) and ultimately could inhibit tumor angiogenesis. Moreover, trabectedin seems to induce the expression of immune-checkpoint proteins such as PD-L1. However, the predictive value of these factors remains unknown.

This poster from HTG investigates the expression of immune checkpoint genes and others as potential predictors of response to trabectedin in 139 soft-tissue sarcoma patients.