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White Papers and Videos

The Role of Chimerism Following Hematopoietic Stem Cell Transplantation

White Paper

This white paper from Devyser details the role of chimerism in patients following hematopoietic stem cell transplantation, the utility of chimerism analysis as a tool for clinical decision making, and considerations for maximizing the potential of chimerism assays in the clinic.

How Co-Occurring Oncogenic Mutations Impact Clinical Outcomes

White Paper

Next-generation sequencing (NGS) has revealed comprehensive genomic tumor profiles and showed that the presence of a single somatic mutation can be insufficient to implicate a gene in the development of cancer. While initial studies of somatic mutations focused on the impact of single mutations, researchers are now investigating the cooperative effects induced by multiple mutations arising simultaneously in one tumor. The event of multiple mutations emerging concurrently is referred to as co-mutation or mutation co-occurrence. Co-mutations have been investigated in many tumor types, and studies have suggested that co-mutations might be a core determinant of oncogene-driven cancers.

This white paper from Qiagen presents use cases in acute myeloid leukemia and glioma demonstrating the importance of adequately annotating and interpreting co-mutations in human cancers, and how the presence of co-occurring mutations can inform diagnosis, prognosis, and therapy options.

Deep Ultra High-Plex Spatial Phenotyping of Human Cancer Tissues

White Paper

Single-cell spatial phenotyping has transformed cancer research and is poised to play formative roles in the development of effective therapeutic strategies.

This poster from Akoya Biosciences presents ultra-high plex single-cell spatial phenotyping of whole slide human FFPE tissues with 100 protein biomarkers encompassing immune cell lineage, activation states, immune checkpoints, tissue structure, apoptosis, DNA damage, and metabolism enabled by the PhenoCycle-Fusion system.

Development of Blood TMB Reference Materials for Validation of cfDNA-Based Targeted NGS Assays That Measure TMB in Patient Blood Samples

White Paper

Tumor mutational burden (TMB) is a promising biomarker for predicting positive patient response to immune checkpoint inhibitors. TMB measurements can be determined using genomic DNA extracted from FFPE-preserved tissue biopsy samples. However, assessment of TMB from a surrogate blood sample (liquid biopsy), referred to as blood TMB (bTMB), is an attractive alternative clinical diagnostic tool that would allow clinicians and patients to avoid the invasive challenge of tissue biopsies.

This poster from LGC SeraCare presents data supporting the use of blood tumor mutational burden (bTMB) reference materials that can aid in the development, validation, and quality control of circulating cell-free DNA assays used to determine TMB scores from blood samples.

Novel Reference Materials for the Analysis of Methylation in Liquid Biopsies

White Paper

Liquid biopsies have begun to incorporate analyses of epigenetic modification for screening purposes to detect cancer-derived DNA in the blood. Additionally, epigenetic modifications are being used to assign a tissue of origin to the cancer to direct confirmatory diagnostic procedures. Obtaining sufficient amounts of ccfDNA for assay development validation, and proficiency testing is difficult. Furthermore, methods of analyzing the epigenetic modifications, such as bisulfite conversion, can damage a significant fraction of the input material; but, failing to carry the methods to completion can result in an over-estimation of methylation.

This poster from LGC SeraCare presents data on three reference materials created to address challenges associated with assessing the methylation of circulating cell-free DNA in order to support the design, optimization, and validation of liquid biopsies for detecting cancer-derived DNA in the blood.

The Challenge of Standardizing the Measurement of an Imprecise Biomarker like HRD

White Paper

How genomic characteristics indicating homologous recombination deficiency (HRD) are measured, integrated, and distilled varies across assays, which can create uncertainty around treatment options and enrollment into clinical trials. This also makes the path of follow-on companion diagnostics challenging because perfect agreement between imprecise measurements is unlikely.

This poster from LGC SeraCare presents data on the characterization and implementation of a set of reference materials, composed of HRD negative, borderline, and positive tumor/normal matched cell lines, for the standardization of HRD assessment.

Reference Materials for ctDNA-Based Measurable Residual Disease (MRD) Assay Development and Validation

White Paper

Monitoring measurable residual disease (MRD) via liquid biopsy is a method for catching early-stage cancer and disease relapse long before traditional diagnostics, which generally require significant disease progression for detection. Assays in development include those that target patient-specific variants and fixed panels for all patients. Regardless, detection of variant allele frequencies at extremely low levels, well below the limit of detection of typical circulating tumor DNA (ctDNA) assays, presents a challenge that can be surmounted with well-designed reference materials that allow for assessment of sensitivity and specificity.

This poster from LGC SeraCare presents data supporting the use of the Seraseq ctDNA MRD Panel kit, composed of four tumor fractions at decreasing levels, to validate both patient-specific and fixed-panel targeted cfDNA NGS MRD assays.

Comprehensive NGS-Based Reference Materials for Variant Detection in Lymphoid Cancer

White Paper

Lymphoma is a cancer of the lymphatic system and represents the second-largest heme disorder. Next-generation sequencing (NGS) is an important technology to identify the genetic changes involved in lymphoid malignancies. Genome-level understanding of these changes can aid in the identification of lymphoma subtypes and aid in diagnosis, prognosis, therapy selection, and patient risk-stratification.

Cancer biopsies are often preserved by formalin-fixed, paraffin-embedding (FFPE) procedures, which provide long-term preservation but introduce damage to nucleic acids that are present in the tissue, including double-stranded breaks, nicks, and oxidation. The gold standard for Lymphoma diagnosis is the surgical removal of the lymph node, making FFPE the preferred sample format for analysis.

This poster from LGC SeraCare presents data illustrating the performance of biosynthetic reference materials that allow analysis of a broad range of somatic mutations and gene fusions and can aid testing laboratories in accurately detecting and quantifying various types of genetic events in lymphoma patient samples.

Quantitative RNAscope Image Analysis Guide

White Paper

This white paper from ACD provides examples of RNAscope in situ hybridization assays, discusses experimental considerations, addresses common challenges, introduces Halo image analysis solutions, and answers common quantitative image analysis questions.

Characterization of Immune Cell Phenotypes Through Quantification of the 12-Plex Spatial RNAscope HiPlex v2 Assay Using the HALO Image Analysis Platform

White Paper

Comprehensive spatial analysis is ideally accomplished by combining multiplexing technologies that allow simultaneous visualization of multiple target genes within the same sample with image analysis tools that can provide quantitative, single-cell level data to accurately interpret gene expression within the context of the tissue.

This application note from ACD demonstrates how the Halo image analysis platform can be employed with the RNAscope HiPlex v2 assay to quantitatively assess differential expression of 12 RNA targets, quantify six distinct cell phenotypes based on gene expression, and analyze spatial relationships between cell phenotypes within the Tumor Microenvironment.

Stroma Liquid Biopsy - Substantiating Correlations for Stromal Conditioning Using Blood Biomarkers and Tumor Tissue Profiles

White Paper

Liquid biopsy has emerged as a novel approach to tumor characterization, offering advantages in sample accessibility and tissue heterogeneity. However, as mutational analysis predominates, the tumor microenvironment has largely remained unacknowledged in liquid biopsy research.

This white paper from Biotech Support Group describes how it may be possible to create a liquid biopsy-based clinical tool to provide relevant information about the state of the tumor microenvironment to accurately quantify intra-tumoral stromal content at numerous time points from a noninvasive blood draw.

What Steps to Follow When Developing Multiplex IHC Assays

White Paper

Immunohistochemistry has long been the gold-standard method for understanding the in situ expression patterns of therapeutically relevant proteins that are prognostic, predictive, or selective for patient management in targeted oncology. However, the detection of one or two proteins no longer provides enough information to draw effective conclusions for patient stratification and therapy guidance. New demands placed on clinical tissue specimens, an emphasis on teasing more information from increasingly small biopsy material, have further spurred the development of multiplex IHC strategies.

This white paper from CellCarta describes the optimization and validation of a brightfield chromogenic triplex CD8/Granzyme B/FOXP3 immunohistochemistry assay and discusses how this assay could be used for future clinical applications to better predict response to therapy.

Quantification of sBCMA in Human Plasma Using a High-Throughput Hybrid IP-MRM Based Mass Spectrometry Workflow

White Paper

B-cell maturation antigen (BMCA) is expressed on the surface of normal and malignant plasma cells and is a rational target for treatment of multiple myeloma. Multiple emerging therapies including CAR T-cells, antibody-drug conjugates (ADC), and bi-specific antibodies are directed at the plasma cell surface BCMA. In addition to surface-bound BCMA, a soluble form of the extracellular domain (sBCMA) is generated and released in the bloodstream, when cleaved by a γ-secretase. sBCMA not only provides information about patient prognosis but can also report on the extent of disease burden following treatment. However, measurement of sBCMA with conventional ligand binding methods can present challenges due to potential interferences from endogenous ligands APRIL and BAFF as well as high concentrations of therapeutic antibodies and ADCs.

This poster from CellCarta presents an overview of a high-throughput hybrid immunoaffinity liquid chromatography-multiple reaction monitoring-based method for the precise and accurate quantification of B-cell maturation antigen.

Decentralizing Precision Oncology Trials: Opportunities and Challenges for Implementing a Patient-Centric Model

White Paper

This report from PGDx is a summary of a GenomeWeb Virtual Roundtable discussion in which panelists discussed how pharmaceutical companies and researchers are rolling out decentralized clinical trial strategies employing telemedicine, mobile apps, wearable monitoring devices, and local labs and imaging centers to facilitate greater patient participation in research.

Development of Blood TMB Reference Materials for Validation Of ccfDNA-Based Targeted NGS Assays That Measure Tumor Mutational Burden in Patient Blood Samples

White Paper

Tumor mutational burden (TMB) is a promising biomarker for predicting positive patient response to immune checkpoint inhibitors. TMB measurements can be determined using genomic DNA extracted from FFPE-preserved tissue biopsy samples. However, assessment of TMB from a surrogate blood sample (liquid biopsy) referred to as Blood TMB (bTMB), is an attractive alternative clinical diagnostic tool that would allow clinicians and patients to avoid the invasive challenge of tissue biopsies. Obtaining concordant bTMB results across assays has been challenging, thus we have developed the new Seraseq Blood TMB reference materials at various mutational burden levels (7, 13, 20 & 26) from high-quality genomic DNA extracted from tumor-derived and their SNP-matched normal cell lines.

This poster from LGC Clinical Diagnostics demonstrates the use of the Seraseq Blood TMB Score reference materials to provide a tumor-normal matched blood TMB control to aid the development, validation, and quality control of cell-free DNA assays to determine blood tumor mutational burden scores of cancer patients.