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White Papers and Videos

Accelerating TCGA Exploration with Manually Curated Clinical Metadata

White Paper

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing. TCGA covers 33 types of cancer with multi-omics data, such as RNA-seq, DNA-seq, copy number, microRNA-seq, and protein mass spectrometry and array (reverse-phase protein arrays, or RPPA). Subsequent analyses of individual TCGA datasets, as well as pan-cancer meta-analysis, have revealed new cancer subtypes with important implications for the molecular mechanisms of cancer.

This white paper from Qiagen describes how curators processed TCGA datasets for Qiagen OmicSoft Lands databases, which allow access to uniformly processed datasets, in-depth metadata curation, and data exploration tools that enable quick insights from TCGA data as well data from other repositories and consortia.

Understanding Immune Cell Function in Cancer

White Paper

Characterizing how cancer affects immune cell function allows researchers to identify potential therapeutic targets and devise novel avenues of attack. Researchers can gain insights into the cells that orchestrate the immune response, they can create agents to kill cancer cells directly or mark them for lysis, and they can engineer customized receptors to improve immune cell activity and efficacy. Understanding cancer drivers also helps scientists create disease models that better recapitulate the properties and dynamics of cancers in human patients. In addition to primary outcomes, analyzing cellular function during clinical trials gives scientists a way to chart the specific mechanisms activated during a treatment strategy. This information helps identify predictive biomarkers for treatment efficacy, areas for potential adjustments or improvements, and patient profiles for which the treatment is particularly effective or ineffective.

This white paper from IsoPlexis presents four articles discussing immune cell function in cancer, recent high-impact studies in immuno-oncology, the link between polyfunctionality and persistence, how immune cell response relates to cancer prognosis, and how boosting polyfunctionality improves performance.

Advances in Cell and Immunotherapies in Treating Cancer: An Expert Panel Discussion

White Paper

Cellular and immune therapies in cancer treatment have come a long way in the few decades since the first cDNA piece of the human T-cell receptor gene was cloned in 1984. Now, co-stimulatory and co-inhibitory molecules are being routinely used to modulate T-cell function. Autologous and allogeneic cancer therapies have moved from experimental trials to clinical settings. Clues to the immunosuppressive tumor environment are being deciphered and deployed in targeted cell and immune therapies. We now have the tools to transform cold tumors — adept at evading the immune system — into hot tumors that are more easily seen by the immune system and targeted with therapies. Personalized therapeutics are enhancing the safety and efficacy of cellular and immune therapy paradigms by selectively targeting malignant tissue. But there is still much to learn.

This white paper from IsoPlexis summarizes a panel discussion in which four experts in cellular and immunotherapy for cancer treatment shared their thoughts on the growing demands for cell therapies, the safety of novel therapies, cancer vaccines, and other topics in cell and immunotherapy research.

Lessons Learned from a National Program to Improve Access to Cancer Testing and Treatment During COVID-19

White Paper

COVID-19 created a crisis for cancer patients who have faced extraordinary uncertainty since March 2020. Global headlines continue to report on cancer surgery cancellations, as well as patients presenting with more advanced stages of disease because of delayed diagnosis. Cancer patients have an estimated two-fold increased risk of contracting COVID-19 and a three-fold risk of dying compared to the general population.

Some tissue biopsy delays can be offset by a minimally invasive blood draw to enable oncologists to select targeted treatment options and monitor disease progression. Circulating tumor DNA (ctDNA) testing is already widely deployed throughout the United States but is not yet standard of care in many places in the world. In exceptional cases, for example, Canadian patients who can access this testing through an oncologist must wait for blood samples to be shipped over the border, analyzed in US labs, and then for results to arrive weeks later. This current scenario costs thousands of dollars per patient and is not accessible to all patients who would benefit.

This white paper from Canexia Health describes the key findings from a pilot project to bring ctDNA testing to over 2,000 cancer patients with advanced breast, lung, and colorectal cancer in the Canadian health system during the COVID-19 pandemic.

Best Practices for Bringing Liquid Plasma Biopsy In-House

White Paper

Liquid biopsy is a powerful tool for matching cancer patients with targeted therapies and for cancer recurrence monitoring. Currently, most liquid biopsy testing is conducted by sending patient samples to a third party. Test send-out can be more costly and less efficient compared to conducting liquid biopsy in-house within a hospital, health system, or cancer center laboratory.

This white paper from Canexia Health outlines the advantages and limitations of liquid biopsy as compared to tissue biopsy and describes best practices for bringing liquid biopsy in-house, including considerations for blood collection, plasma isolation, assay and sequencing technologies, data analysis, and reporting.

A Guide to Next-Generation Sequencing Methods in Liquid Biopsy

White Paper

Analysis of circulating nucleic acids in bodily fluids, also known as “liquid biopsy”, is a new and revolutionary development in the world of diagnostics and personalized medicine. Liquid biopsies have rapidly gained prominence with their potential to identify specific biomarkers with a non-invasive sample collection process, diminishing the need for expensive, high-risk, and painful tissue biopsies.

This white paper from Zymo Research outlines next-generation sequencing methods and considerations for liquid biopsy, including sample collection, cell-free DNA isolation, the advantages of epigenetic-based biomarkers, and profiling techniques.

PGDx elio tissue complete: A Pan Solid Tumor CGP Test

White Paper

This white paper from PGDx presents data demonstrating the predictive value and specifications of the elio tissue complete comprehensive genomic profiling test across several genomic alterations, cancer biomarkers, and tumor types.

 

Enabling Precision Therapy in Oncology: Liquid biopsy complements tissue testing for comprehensive genomic profiling

White Paper

Comprehensive genomic profiling (CGP) of tumors identifies specific acquired molecular alterations, thereby enabling biomarker-directed therapies for many cancer types. Although historically performed on tumor tissue, recent efforts have focused on alternative methods of obtaining the same information.

This white paper from PGDx presents data that supports the incorporation of circulating tumor DNA (ctDNA) analysis into cancer care to increase biomarker detection and decrease time to treatment, demonstrating the concordance between tissue NGS and the PGDx elio plasma resolve assay.

 

The PGDx elio tissue complete test is a Viable Alternative to Send-Out Testing for Comprehensive Genomic Profiling

White Paper

Next-generation sequencing has emerged as the preferred approach for comprehensive genomic profiling in cancer. Less than 20 percent of late-stage cancer patients receive the molecular tumor testing necessary to help guide treatment strategies. PGDx elio tissue complete, an FDA 510(k) cleared and CE-IVD marked decentralized pan solid tumor CGP test, demonstrated high concordance with the Foundation Medicine FoundationOne test.

This white paper from PGDx presents results from a study comparing the PGDx elio tissue complete test to send-out testing for comprehensive genomic profiling, finding it to be a viable local testing solution for molecular laboratories and may thereby increase patient access to accurate tumor profiling at a faster turnaround time.

Serial Monitoring of Plasma ctDNA in Metastatic Colorectal Cancer Patients Detects Changes in Key Mutations and Disease Progression Using the Follow It Assay from the Exactis Trial

White Paper

Colorectal cancer is the third leading cause of cancer-related deaths. Clinical responses of metastatic colorectal cancer to first-line treatment range from 35 to 60 percent, but even responders inevitably develop therapeutic resistance. Liquid biopsies have become a useful tool in precision medicine for therapy selection and have immense potential as a monitoring tool for the emergence of therapy resistance.

This poster from Canexia Health presents data from a study investigating if longitudinal plasma ctDNA mutation monitoring can aid in predicting clinical progression before standard-of-care CT imaging, with the goal of establishing the Follow It assay as a liquid biopsy tool to assess progression over time in metastatic colorectal cancer patients.

Seraseq Blood TMB Mix Score 7, 13, 20, 26

White Paper

Tumor mutational burden, as measured by exome or panel sequencing of tumor tissue (tTMB) or blood (bTMB), has been identified as a potential predictive biomarker for treatment benefit in patients with various cancer types receiving immunotherapy targeting checkpoint pathways. However, significant variability in TMB measurement has been reported due to differences in preanalytical and laboratory methods, panel size, number of genes covered, and bioinformatics pipelines. Reference standards have been proposed and evaluated for tTMB analysis by the Friends of Cancer Research TMB Harmonization Consortium to enable standardization across different NGS panel providers and to determine the correlation of panel-TMB scores with WES-TMB scores. Reference standards for bTMB may be even more important given the unique challenges and higher sensitivity required for bTMB assays.

This datasheet from LGC SeraCare provides details about the blood TMB assessments for Seraseq Blood TMB Mix Score 7, 13, 20, 26 reference materials as determined using the TruSight Oncology 500 ctDNA panel.

Find the accompanying poster for this data sheet from SeraCare here.

Accredited Cancer Centers Improve Precision Oncology Care with GenomOncology

White Paper

In this on-demand webinar from GenomOncology, Chief Technology Officer Ian Maurer and Director of Product Management James Cole discuss:

  • The impacts, benefits, and technical requirements of a model precision oncology program.
  • How GenomOncology’s precision oncology solutions support precision oncology programs by providing clinicians access to up-to-date precision oncology information, integrating with institution systems, and presenting relevant data that can be utilized to improve patient outcomes.
  • The several ways numerous institutions have utilized GenomOncology to enhance their precision oncology programs to streamline their data enablement, improve their overall decision support, and enhance their insights and analytics to improve their overall patient cancer care.

Using Whole-Exome Sequencing to Guide Clinical Trial Enrollment for Patients with Cancer

White Paper

Advances in precision medicine are not currently available to all patients, especially those being treated in community cancer settings. This growing gap is challenging community health­care systems to provide cost-effective, scalable, and innovative solutions for underserved patients.

This case study from Qiagen discusses how Protean BioDiagnostics partnered with Qiagen Digital Insights to develop a proprietary, multiomic, datacentric diagnostic guidance system to deploy whole-exome sequencing into clinical practice and give oncologists and practitioners access to the latest evidence-based diagnostics, therapeutics, and new clinical trials.

Manual Curation vs. Artificial Intelligence: Can Automated Variant Evidence Retrieval Replace Human Judgment?

White Paper

This white paper from Qiagen examines evidence comparing the quality of Stanford University’s Automatic Variant evidence Database (AVADA) to the manually curated Human Gene Mutation Database (HGMD) for variant annotation in clinical genomics.

Serum Protein Signatures as a Non-Invasive Tool for Monitoring Nonalcoholic Steatohepatitis

White Paper

Nonalcoholic fatty liver disease (NAFLD) is a liver condition that affects up to 25 percent of the global population. Nonalcoholic steatohepatitis (NASH) refers to an aggressive form of NAFLD that is predicted to rise exponentially through the year 2030. Diagnosing the severity of NAFLD and NASH heavily relies on liver biopsy. Non-invasive techniques for NAFLD diagnosis and prognosis include imaging and measuring the enzymes alanine aminotransferase (ALT) and aspartate aminotransferase (AST). However, ALT and AST measurements are not sufficiently sensitive or specific, and non-invasive imaging modalities are not accurate or precise enough to differentiate between stages of steatosis or fibrosis.

This white paper from SomaLogic describes the potential of using proteomic signatures to improve non-invasive diagnosis and monitoring of liver pathology, and the potential of the SomaScan Proteomic Platform to identify such signatures.