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White Papers and Videos

Hereditary Cancer NGS Testing: Benefits, Challenges, Methods, and Considerations

White Paper

This compendium of application notes from Qiagen describes the benefits and challenges of next-generation sequencing tests for hereditary cancers, as well as opportunities to improve multi-gene panel testing, variant annotation, risk assessment, and reporting of sequencing data with QCI Interpret clinical decision support software.

ARUP Laboratories Reduces Turnaround Time on Panel Analysis by 30 Percent with GenomOncology

White Paper

The GenomOncology (GO) Precision Oncology API Suite extends the knowledge of GenomOncology’s Precision Oncology Platform by integrating directly with in-house systems and workflows, providing users an extensive database of annotations and treatment options that can be utilized to enhance patient care. The GO Precision Oncology API Suite is utilized at numerous institutions across the United States, including the CAP-, ISO 15189-, and CLIA-certified diagnostic lab, ARUP Laboratories (ARUP).

Interested in learning more about how ARUP utilizes GenomOncology’s precision oncology solutions? Then read our latest case study to gain insight into how:

  • ARUP selected and implemented the GO Precision Oncology API Suite in 2019 due to the depth of annotation sources within the solution, its overall flexibility, and its ability to be easily integrated into ARUP’s current workflows and processes. 
  • ARUP reduced its turnaround time on panel analysis and variant annotation by nearly 30%, enabling its Clinical Variant Scientist team to analyze more cases and spend less time documenting variant classification information. 
  • ARUP has chosen to extend its use of the GO Precision Oncology Suite by integrating the GO Clinical Trial and Therapy Matching APIs into its current workflows to strengthen its patient care offerings.

The Best Spatial Biology Publications From 2020

White Paper

This blog post from NanoString presents selected cancer research publications from 2020 that used spatial analysis to make discoveries about the tumor microenvironment, immune response to tumors, and predicting cancer treatment response.

The Pancreatic Cancer Action Network Increases Biomarker-Driver Clinical Trial Matching Capabilities with GenomOncology

Video

In this on-demand webinar from GenomOncology, speakers from the Pancreatic Cancer Action Network (PanCAN) and GenomOncology discuss how PanCAN utilized GenomOncology’s Clinical Trial Matching solution to streamline the organization’s biomarker-driven clinical trial matching process.

The 30-minute on-demand webinar covers:

  • The challenges associated with utilizing the ever-evolving precision medicine data in patient treatment matching, and how GenomOncology’s clinical trial matching solution navigates through this growing data to streamline the matching of patients to accurate, relevant clinical trials.
  • How GenomOncology enabled PanCAN to increase the number of biomarker-driven searches by 300 percent and reduce the time spent on biomarker-driven clinical trial searches by 50 percent.
  • PanCAN’s upgrade to GenomOncology’s Precision Decision, which enables the PanCAN team to advance their treatment searching capabilities through the addition of the patient's prior intervention history.

The Pancreatic Cancer Action Network Increases Biomarker-Driven Clinical Trial Matching Capabilities by nearly 300% with GenomOncology.

White Paper

Learn how the Pancreatic Cancer Action Network (PanCAN) utilized GenomOncology’s Clinical Trial Matching solution to streamline the organization’s biomarker-driven clinical trial matching process. Read more about:

  • The challenges associated with utilizing the ever-evolving precision medicine data in patient treatment matching, and how GenomOncology’s clinical trial matching solution navigates through this growing data in order to streamline the matching of patients to accurate, relevant clinical trials.
  • How GenomOncology enabled PanCAN to increase the number of biomarker-driven searches by 300% and reduce the time spent on biomarker-driven clinical trial searches by 50%.
  • PanCAN’s upgrade to GenomOncology’s Precision Decision, which enables the PanCAN team to advance their treatment searching capabilities through the addition of the patient's prior intervention history.

Flexible Capabilities to Enable Comprehensive Genomic Profiling

Video

Comprehensive genomic profiling (CGP) is becoming standard of care in oncology. It allows clinicians to maximize clinical information from limited biopsy samples so that patients are matched with approved therapies or enrolled in relevant clinical trials.

In this on-demand webinar from Illumina, a panel describes the implementation of a comprehensive genomic profiling (CGP) assay at their institutions and discusses how flexible automation, sample batching, data analysis and reporting solutions are key to CGP testing.

Learn:

  • The value of a flexible, future-proof DNA+RNA CGP assay.
  • The impact of reflex CGP testing on testing decision trees and workflow consolidation.
  • The value of sample management and genomic literacy for oncologists and molecular tumor boards.

Comprehensive Genomic Profiling: Maximize Identification of Molecularly Matched Therapies

White Paper

Comprehensive genomic profiling (CGP) can detect actionable variants to maximize the ability to match cancer patients with the appropriate molecular treatment regimens. This ebook from Illumina provides an in-depth overview of how CGP can improve patient outcomes.

A single CGP test using minimal sample can assess multiple DNA and RNA variant types across hundreds of genes. Sophisticated analytics interpret these results and produce easy-to-interpret reports that include recommended therapies and clinical trials.

 

Multimodal Analysis of Human Squamous Cell Carcinoma Reveals a Potential Driver of Metastasis

White Paper

What can a detailed map of the tumor microenvironment (TME) reveal about cancer progression and treatment? Researchers at the Stanford University School of Medicine integrated single-cell and spatial transcriptomics to create a high-resolution atlas of cell types and states in cutaneous squamous cell carcinoma and characterize the spatial organization of the tumors and their surrounding tissues.

By coupling single-cell and spatial analysis, the team was able to identify a subpopulation of tumor-specific keratinocytes present at leading edges of the tumor as a key player in communication between tumor cells and cells in the TME. Of particular note is the potential for this novel subtype to act as a target for investigation into cases where patients fail to respond to treatment.

Sample Preparation for Single-Cell Applications in Oncology

White Paper

To understand tumor heterogeneity, tumor microenvironment contexture, and therapeutic response and resistance, researchers need high-resolution views of the cell types and states that drive cancer. Single-cell analysis relies on being able to isolate, dissociate, and suspend living single cells. The sample preparation process is an integral part of the workflow and plays a critical role in data quality.

This whitepaper from 10x Genomics introduces the core concepts and best practices to optimize sample preparation for single-cell research in oncology, providing pertinent protocols, technical notes, video tutorials, and other resources for each step of the sample preparation workflow.

Basic and Intermediate Quality Control Systems: Enhancing the Knowledge and Performance in Your Laboratory

White Paper

This whitepaper from Bio-Rad summarizes systems, practices, and statistics used for quality control (QC) of diagnostic tests in medical laboratories, including information on how often controls should be run, how to calculate basic QC statistics, and optional QC protocols.

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.