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White Papers and Videos

Assess HER2 Status in Solid Tumors to Inform Eligibility for Enhertu

White Paper

Historically, HER2 has been identified as a predictive biomarker only in select tumor types — most notably in breast cancer. However, HER2-positive status is a negative prognostic factor in multiple metastatic solid tumors, often associated with more aggressive disease and a poor prognosis. What if there were more options for patients with HER2-positive (IHC 3+) metastatic solid tumors?

HER2-positive actionability has recently expanded beyond breast and gastric cancers to include non-small cell lung, endometrial, ovarian, cervical, colorectal, pancreatic, biliary tract, and bladder cancers, among others. Performing HER2 IHC testing in metastatic solid tumors at diagnosis can further the understanding of a patient’s disease state and biomarker profile.

This core visual aid from AstraZeneca and Daiichi Sankyo describes the relevance and prevalence of HER2 positivity across metastatic solid tumors; provides detail on the nuances of ASCO-CAP scoring criteria guidelines, including sample requirements and staining interpretation; and outlines who, when, and how to test for HER2 positivity using IHC testing.

The Emergence of Multi-Modal Real-World Data: The Power of Clinico-Genomic Data Versus Traditional RWD Sources

White Paper

The shift toward precision medicine in drug discovery and clinical development underscores the importance of multi-modal real-world data (RWD). Traditional RWD sources often lack detailed biomarker data, crucial for developing targeted therapies for complex diseases. Recent FDA guidelines and advancements in data-linking technologies have enabled the integration of clinical and genomic data, providing a more comprehensive view of patients' health and treatment responses. This integration facilitates more precise clinical trial designs and could significantly improve patient outcomes by enabling the development of personalized therapies. Multi-modal data also allow for population-scale studies and deeper insights into disease mechanisms and treatment efficacy.

This white paper from NeoGenomics explores the potential of clinico-genomic data to revolutionize healthcare by guiding drug development and therapeutic interventions, highlighting the superiority of clinico-genomic data over traditional real-world data sources, which mainly consist of electronic medical records and medical claims.

Assessment of a Novel Fluidics Platform for Rapid Sample Processing from Whole Blood to Library

White Paper

This poster from Volta Labs describes an evaluation by Broad Clinical Labs of a walk-away, end-to-end DNA extraction to library construction platform from Volta Labs, which employs digital fluidics technology controlling the sample chemistry, using it to create a clinical grade whole genome starting from whole blood.

The Callisto Sample Prep System Supports Robust and Versatile Sample Prep for High-Quality HiFi Long-Read Sequencing

White Paper

Highly accurate (HiFi) long-read SMRT (single-molecule real-time) DNA sequencing on the PacBio platform is now commonly used, particularly for applications where short-read NGS has been proven to be inadequate. These include de novo assembly of haplotype-resolved reference genomes, detection and characterization of large structural variants, interrogation of challenging genomic regions, direct methylation analysis, and metagenome deconvolution. Recent advances in the accuracy, throughput, and speed of HiFi sequencing — combined with a significant reduction in per-base cost — promise to broaden access and accelerate the adoption of long-read sequencing in life sciences research and the clinic. Proportionate improvements in the scalability, robustness, and cost of sample preparation for HiFi sequencing are needed.

This application note from Volta Labs demonstrates the extraction of high-quality high molecular-weight DNA and the preparation of SMRTbell libraries in different reaction formats, from a range of inputs, and with different workflow parameters, generating high-quality HiFi sequencing data and variant calls with minimal training and a significant reduction in hands-on time.

Digital Fluidics Enables Broad-Based Access to Push-Button NGS Sample Prep

White Paper

Decades and billions of dollars have been dedicated to advancing sequencing technologies and genomic data analysis. This has resulted in a reduction in sequencing cost by six orders of magnitude and an explosion in sequencing-based applications. However, the sample preparation process remains a significant bottleneck. When samples are processed manually, variable sample quality, laborious protocols, and high per-sample cost remain significant obstacles to scalability and consistency. Automated liquid handlers enable higher throughput, and process but significant barriers to implementation persist. These include high capital expenditure, the need for multiple, dedicated instruments, specialized infrastructure and/or skills, lengthy method development, and ongoing maintenance costs.

This poster from Volta Labs describes a benchtop automated sample prep system and presents three case studies demonstrating the system’s ability to produce higher yields of quality DNA, produce libraries from lower inputs, and produce slightly better variant calling than standard manual protocols.

Digital Fluidics Simplifies NGS Library Preparation in a Clinical Setting

White Paper

Process control is essential to ensure high success rates and consistency when preparing samples for NGS-based assays. Automation facilitates process control. Conventional liquid handlers are widely employed in clinical laboratories but require a significant investment in equipment, method development, and validation — as well as skilled personnel to operate and maintain. Volta Labs is introducing a reimagined digital fluidics technology that utilizes electrical, thermal, and magnetic fields to enable programmable, precise, and plastic-free liquid manipulation. This enables high-performance, walk-away NGS sample preparation, and opportunities to improve operational efficiency. Pre-optimized methods enable rapid implementation with minimal training.

This poster from Volta Labs describes how authors from Volta and Helix investigated the feasibility and potential benefits of the Volta Labs automated sample prep platform in a clinical setting by automating an established commercial library prep method for PCR-free WGS, finding it to deliver comparable or superior library quality compared to traditional protocols.

Automated Hybridization Enrichment of Hartwig OncoAct Panel Using the Volta Labs Digital Fluidics Platform

White Paper

The Hartwig Medical Foundation is a not-for-profit organization dedicated to providing cancer patients with the best treatment options. As part of this mission, they have developed a WGS-based molecular diagnostic test, OncoAct WGS, which generates a tumor-normal comparison from fresh tumor and normal material and returns a molecular diagnostic report supported by information from knowledge bases and the Hartwig database. Not all samples (e.g., FFPE tissue, fresh biopsies with a tumor cell content of 10-20 percent) are suited for OncoAct WGS. They therefore developed a targeted sequencing assay, OncoAct Panel, to inform treatment options for more patients. The OncoAct WGS workflow is fully automated, and the foundation is working toward a fully automated hybridization capture workflow with the highest possible quality and robustness for standard diagnostic use. The foundation entered into a collaboration with Volta Labs to explore the benefits and feasibility of automating the OncoAct Panel workflow on the innovative digital fluidics platform developed by Volta Labs.

This poster from Volta Labs presents results from a Hartwig Medical Foundation study exploring the automation of the OncoAct WGS-based molecular diagnostic panel using Volta Labs' digital fluidics platform, demonstrating that automated post-hybridization capture and wash steps can achieve or surpass the performance of established manual methods.

Two Industry Leaders on Dealing With the Growing Complexity of Genomic Cancer Data

White Paper

The Clinical Knowledgebase (CKB) powered by The Jackson Laboratory (JAX) is a dynamic, digital resource for interpreting complex cancer genomic profiles in the context of gene variant knowledge and protein impact, therapies, and clinical trials. Illumina has teamed up with JAX in the newly released Connected Insights software, which integrates CKB as a knowledge source.

In this podcast, Mendelspod’s Theral Timpson speaks to Cara Statz from JAX and Erica Schnettler from Illumina about how their combined technologies are helping researchers and oncologists deal with the increasing complexity of cancer genomic data. They discuss oncologists' experience dealing with an overwhelming amount of new scientific data, and both guests give their advice for new labs setting up cancer testing and oncology clinical research.

Powering Diagnostics at Scale: Large Custom Projects

White Paper

This e-book from Cytiva describes customer success stories in which Cytiva collaborated with diagnostics developers on large custom projects to provide lyophilized reagents for a point-of-care device, design and build a multiplex lateral-flow assay, provide magnetic beads for a blood screening test, create kits for a cell analysis device, and create a new facility to lyophilize and package reagents for a sequencing platform.

Powering Diagnostics at Scale: Small- to Mid-Size Custom Projects

White Paper

This e-book from Cytiva describes customer success stories in which Cytiva collaborated with diagnostics developers on small- to mid-sized custom projects to scale up a rapid COVID-19 test, customize an early cancer test, improve a food-and-beverage test, assemble a kit for an immunodiagnostic test, and provide quality control for a diagnostic test.

Join the Pharmacogenomics Revolution

White Paper

This infographic from Thermo Fisher Scientific shows how pharmacogenomic testing can improve care, lower costs, and reduce health disparities across medical fields.

Integrating Pharmacogenomics Into the Standard of Care

White Paper

Pharmacogenomics (PGx) is used to understand how variations in key areas of an individual’s DNA may impact the efficacy of a medication, dosage considerations, and adverse drug reactions (ADRs). Ideally, testing is performed in advance of prescribing medication so that the physician or the pharmacist can streamline medication selection, reduce trial-and-error, and minimize ADRs. Alternatively, it can help explain why a medication is not working or causing an ADR to get the individual back on the best therapeutic path.

This white paper from Thermo Fisher Scientific discusses hurdles to the wider adoption of PGx and how PGx can improve care and reduce wasted time and costs for the healthcare system, patients, insurers, and patients’ employers — highlighting applications in oncology, pain management, and mental health.

Pharmacogenomics Laboratory Spotlight: Introduction to the PGx Program at the Arkansas Children’s Hospital

White Paper

In this white paper from Thermo Fisher Scientific, the pathologist-in-chief and the pharmacogenomics (PGx) pharmacy clinical coordinator at Arkansas Children's Hospital discuss how they utilize PGx testing, their considerations when selecting panels, the impact of PCR technology, the future of PGx testing at the hospital, and advice for other labs.

Copy Number Variant Detection Without a Panel of Normals Using Anchored Multiplex PCR and Next-Generation Sequencing

White Paper

Copy number variations (CNVs) are genomic aberrations in which the number of copies of a region of the genome differs from the expected number. Errors in DNA replication, repair, recombination, and other processes can cause CNVs. CNVs may be a cause of disease, a symptom, or both. Copy gains or losses affecting oncogenes or tumor suppressor genes are one mechanism by which cancers may arise, proliferate, or persist. CNVs may be targetable by, or grant resistance to, certain therapies. CNV signatures may indicate chromosomal instability resulting from homologous recombination deficiency.

This scientific poster from IDT introduces a new CNV method designed to work with NGS panels that relies only on data from the sample of interest to determine copy number and breakpoints instead of using matched normal tissue or a panel of normal samples.

McArthur Lab Fights Global Threats to Human Health

White Paper

This case study from Pure Storage describes how Andrew McArthur, genomics professor and researcher at McMaster University, uses Pure Storage FlashBlade to reduce the time to diagnosis, keep up with the demands of COVID-19 surveillance, and develop new ways to combat antimicrobial resistance.