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White Papers and Videos

Improvement of Formalin-Fixed Paraffin-Embedded Reference Materials for Molecular Analyses

White Paper

Although some forms of precision medicine have existed for decades, next-generation sequencing (NGS) of tumors has yielded a plethora of mutations that inform clinical care. It is not uncommon for commercial NGS-based cancer gene panels to target more than 500 genes with several of those serving as biomarkers for therapeutic decisions. Beyond some of the common driver mutations, the acquisition of reference materials that contain even some of the mutations desired for assay optimization, validation, and monitoring is difficult.

This scientific poster from LGC SeraCare presents a new approach to FFPE reference materials, designed to ensure more accurate and reproducible results in NGS-based assays.

Multisite Evaluation of a Reference Material for Analysis of Genetic Variants of DPYD to Support Pharmacogenetic Testing Associated with Fluoropyrimidine-induced Toxicity

White Paper

Fluoropyrimidine-based drugs (FP), such as 5-fluorouracil and capecitabine, are widely prescribed chemotherapy treatments for various cancers, with approximately two million patients treated globally each year. However, severe FP toxicity occurs in 10 to 30 percent of patients, often due to a deficiency in the dihydropyrimidine dehydrogenase (DPD) enzyme, which is encoded by the DPYD gene. DPYD genotyping identifies variants that cause DPD deficiency, helping to identify patients at risk of severe or fatal toxicity and allowing for preemptive treatment modifications. ​With the rising global cancer incidence, the availability of multiplexed pharmacogenomics reference material specific to DPYD will be crucial to enable labs to validate and QC their assays more effectively and accurately. ​

This scientific poster explores how Seraseq DPYD DNA Mutation Mix can enhance the accuracy and consistency of genetic testing associated with fluoropyrimidine-induced toxicity for better patient outcomes.

The Next Generation of Reference Materials for Analytical Validation of Liquid Biopsy Assays

White Paper

Liquid biopsy testing supports early disease diagnosis, therapy selection, and surveillance. Recent advances in next-generation sequencing (NGS) have enabled larger panel sizes, pan-cancer target sets, and increased sensitivities. FDA guidelines for liquid biopsy assay validation state that regions of the genome containing actionable variants must be tested with high confidence. As circulating tumor DNA (ctDNA) panels become larger and more capable, inclusive and highly multiplexed analytical validation materials are needed to assess assay sensitivity and limit of detection of many variant types.

This poster from LGC SeraCare, presented at AMP 2024, highlights advancements in Seraseq ctDNA Mutation Mix v4 that help improve analytical validation, ensuring more accurate results.

Renowned GI Oncologist Discusses MRD Testing and the Future of Cancer Detection

White Paper

Mark Lewis is a well-known GI oncologist at Intermountain Health in Salt Lake City, Utah. Gifted with a passionate communication style, he has over 93,000 followers on X. Next month, he will live-tweet his upcoming colonoscopy.  

In this episode, Lewis joins Theral Timpson in an ongoing series on minimal residual disease (MRD) testing, a revolutionary blood test that is helping detect residual cancer, causing a paradigm shift in patient management. He says MRD testing has transformed his own practice and describes how this “liquid biopsy” approach, previously common in hematology, is also advancing the detection of solid tumors.

“News flash,” he says in today’s show, “we were trained a certain way. My training ended 12 years ago, and I had fantastic training. I did my fellowship at the Mayo Clinic. But if I practiced now the way I was trained then, my patients would be so underserved, almost to the point of malpractice.”  

Lewis considers MRD testing a key part of his own standard of care and anticipates its broader adoption among GI oncologists. He also highlights the recent findings from the GALAXY study, which show improved survival rates for patients utilizing MRD testing, underscoring its potential to reshape GI oncology practices in the near future.

Featured Guest:

Mark Lewis, MD

Director of Gastrointestinal Oncology

Intermountain Healthcare

Aperio GT 450 Scanner Improves Throughput By 64 Percent and Reduces QC Tech Time by 94 Percent in Workflow Study

White Paper

NeoGenomics is a large research and reference laboratory located in California and has experienced significant increases in annual slide volumes. The NeoGenomics senior management team was tasked with evaluating ways to scale up digital pathology operations to keep up with increasing demand.

This white paper from Leica Biosystems reports on a study in which NeoGenomics Laboratories compared the performance of the Aperio GT 450 and Aperio AT2 digital pathology slide scanners, measuring throughput, QC tech time, and other performance metrics.

Comprehensive NGS Profiling to Enable Detection ALK Gene Rearrangements and MET Amplifications in Non-Small Cell Lung Cancer

White Paper

Targeted therapies have expanded treatment options for diseases like non-small cell lung cancer. While NGS-based tumor profiling can detect multiple targetable alterations from limited tissue, many settings employ only single-variant and single-gene analysis. Improved detection of amplifications and gene rearrangements can provide more complete tumor characterization to identify all possible therapies.

This white paper from Labcorp presents data showing that comprehensive genomic profiling with PGDx elio tissue complete demonstrates high concordance with conventional diagnostic approaches for ALK gene rearrangements and provides greater insight into the underlying genomic events and genomic co-alterations that may impact clinical outcomes.

MicroRNA: A New Era in Biomarker Discovery with Tim Williams and Paola Ulivi

White Paper

In this episode, we delve into the groundbreaking role of microRNA as a cancer biomarker with Tim Williams, professor of clinical pathology at the University of Cambridge Veterinary School, and Paola Ulivi, a leading researcher at the Instituto Romagnolo Per Lo Studio Dei Tumori Dino Amadori (IRST) in Italy. MicroRNA, which recently garnered its discoverers a Nobel Prize, has emerged as a powerful tool for detecting and tracking cancer progression.

Williams and Ulivi share their latest research, highlighting how microRNA’s rise in cancer diagnostics parallels the evolution of fragmentomics, which analyzes cell-free and circulating tumor DNA. We explore the key differences between using RNA and DNA in biomarker development, the advancements in tools driving these discoveries, and the timeline for microRNA-based diagnostic tests to reach clinical practice.

“There’s a lot of potential,” says Ulivi, “but the challenge in translating this into clinical practice will be the standardization and normalization of the process."

Join us as we discuss the promise, obstacles, and future of microRNA in transforming how we diagnose and treat cancer.

 

Featured Guests:

Tim Williams

Professor of Clinical Pathology

University of Cambridge Veterinary School

 

Paola Ulivi

Researcher

Instituto Romagnolo Per Lo Studio Dei Tumori Dino Amadori (IRST), Italy

Unlocking Precision: InoKey, A Disease-Agnostic Custom Discovery-to-Targeted-Proteomics Solution for Drug Development

White Paper

Despite the profound impact of genomics and transcriptomics in revolutionizing healthcare and research, these technologies might not always provide robust predictions about which individuals will respond effectively to a given therapy. Proteomics, the ultimate assessor of cell and tissue health, offers a clear picture of a patient's phenotype and provides substantial predictive potential. One critical gap remains: bridging unbiased discovery proteomics findings and targeted proteomics assays to monitor dysregulated protein biomarkers with high precision and accuracy in the form of a clinically validated assay.

This case study from Inoviv demonstrates how InoKey, an end-to-end discovery-to-targeted-proteomics solution, formulated a high-throughput LC-MS/MS workflow to stratify patients' plasma proteomes in response to SARS-CoV-2 infection, informing an assay that outperformed other severity score models and robustly predicted patient outcomes for a streamlined clinical treatment escalation strategy.

Simplifying Genomic Analysis with Microfluidics Technology

White Paper

Microfluidics is the manipulation of small volumes of fluids (nanoliters or less) within networks of channels that are tens to hundreds of microns in diameter. Microfluidic instruments have low sample and reagent volume requirements and short analysis times and can facilitate the type of miniaturization that has led to the rise of lab-on-a-chip technologies. Microfluidic platforms are used across a broad range of application areas including pharmacogenomics, sample identification, and agricultural genomics, and are revolutionizing the way research in these areas is carried out.

This ebook from Standard BioTools includes five articles discussing the benefits of microfluidics-based PCR in enabling precision medicine, automating lab activities, singleplexing versus multiplexing, considerations for cost-effective analysis in genomics-driven fields, and challenges and perspectives in evaluating immune function and mechanisms of cell differentiation.

With Exosome Analysis, Highly Sensitive Monitoring of ESR1 Mutations is Possible

White Paper

With the rise of precision oncology therapies — particularly those that target specific variants or remain effective despite specific mutations — there is more need than ever for routine, highly sensitive monitoring of the cancer mutations that arise during a patient’s treatment journey. In some cases, mutations are indicative of the onset of resistance to treatment; detecting them early enables a shift to a different therapy to stay ahead of the cancer.

Unfortunately, most available tests lack the sensitivity required to detect these critical mutations. Consider the challenges in picking up that tiny signal: it may be just one new mutation, potentially coming from one of many tumors or just one part of a tumor. Ideally, routine testing should be noninvasive, meaning this weak signal has to be identified from a simple blood sample amid overwhelming amounts of genetic material from sources other than the tumor. Standard liquid biopsy tests that use cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) are not sensitive enough to detect these important mutations reliably.

This white paper from Asuragen details evidence that querying exosomal RNA in addition to cfDNA can boost sensitivity for routine monitoring of cancer mutations, offering physicians and their patients a more effective strategy for early detection of key variants, empowering them to make more informed treatment decisions along the way.

NGS: Changing the Game in CFTR Analysis

White Paper

Cystic fibrosis is a multisystem disorder of exocrine function and typically affects the lungs, pancreas, intestines, and sweat glands. Cystic fibrosis (CF) is one of the most common, recessively inherited Mendelian conditions. Incidence varies widely between different geographical and ethnic populations, in part reflecting ethnicity-specific mutational distribution. The CF transmembrane conductance regulator (CFTR) gene has been identified as the causal gene for cystic fibrosis and CFTR mutation analysis remains one of the most frequently requested genetic tests in the clinical setting worldwide.

In this expert review from Devyser, Stewart Payne, a consultant clinical scientist for the UK National Health Service and head of molecular genetics at the North West Thames Regional Genetics Service, discusses genetic testing for CF, CFTR mutations, the improvements in testing enabled by NGS, targeted therapies, and future prospects.

cfDNA Whole-Genome Methylation Sequencing with NESSI-seq

White Paper

Although cell-free DNA (cfDNA) has potential as a powerful genetic and epigenetic biomarker of disease, cfDNA methylation-based liquid biopsies have yet to meaningfully enter clinical testing due to limitations in cfDNA biology and available methods to detect and analyze methylation. cfDNA is highly fragmented and nicked, and it occurs in low concentrations in circulation. Available methods to detect and analyze DNA methylation introduce significant DNA damage, errors, and biases.

This white paper from Wasatch Biolabs presents a whole-genome cfDNA application of NESSI-Seq, a novel library preparation technology that enhances specificity, sensitivity, and data quality leveraging Oxford Nanopore Technologies to capture the advantages of native sequencing and long reads.

NESSI-Seq preserves DNA in its native state, eliminating the need for bisulfite conversion and PCR amplification and enabling accurate methylation and hydroxymethylation analysis. NESSI-Seq technology improves the specificity, sensitivity, and clinical viability of cfDNA methylation assays to facilitate clinical applications of cfDNA assays across diverse therapeutic areas. This approach holds promise for advancing personalized medicine and cfDNA-based liquid biopsies by providing more reliable and comprehensive genomic and epigenomic data. The potential for tissue-of-origin and copy number variation analyses using wgNESSI-Seq are demonstrated in this white paper, showcasing its broad applicability and impact.

ctDNA Testing Could Lead to New Ways of Staging Cancer Patients Says Ben Weinberg, MedStar Georgetown

White Paper

Today, we go to the frontlines of cancer treatment for a case study on the use of ctDNA testing in the clinic. 

ctDNA, or circulating tumor DNA, is now used as a biomarker in new testing to detect cancer — or its absence — in a patient’s blood. Oncologists, such as Ben Weinberg, are increasingly using ctDNA testing to guide treatment. Weinberg is an associate professor of medicine and an attending physician specializing in colorectal cancer at MedStar Georgetown University Hospital.

“Even though I give chemotherapy for a living, I would love to give less chemotherapy,” he said, speaking about the primary use for ctDNA testing. “We have to break apart some of the older paradigms of how we stage patients."

Weinberg says that if a patient is ctDNA undetectable, it may not matter if they are stage II or stage III. Staging has been part of the guidelines suggesting that the doctor must give chemotherapy because there’s a survival benefit. 

“That was true in large randomized studies, but that may not be true for the patient sitting in front of us,” says Weinberg.

Where are we at in the treatment of colorectal cancer today, and how is this new testing impacting oncology are the questions of today’s program? Weinberg ends with the hope that this could also be a new biomarker for drug development.

 

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Speaker:

Benjamin Weinberg, MD

MedStar Georgetown University Hospital

The Importance of Optimizing DNA Extraction Conditions for Formalin Fixed Paraffin Embedded Tissues (FFPET)

White Paper

The pre-analytic extraction of formalin-fixed paraffin-embedded tissues (FFPETs) appears to have a profound effect on the ability to obtain meaningful data from the DNA therein. As part of preparing FFPETs, the formalin fixation step preserves the structure of tissues through covalent modifications but can also damage nucleic acids through that same process. Over the last decade, the emergence of molecular pathology, which benefits from gentler fixation compared to histopathology and, especially, immunohistopathology, has led to changes in how FFPETs are prepared. The remnant FFPETs from over a decade ago may be far from representative of what is now prepared for molecular pathology by many laboratories.

This poster from LGC Clinical Diagnostics discusses the optimization of FFPET extraction for gently fixed samples.

Next-Generation Liquid Biopsy Reference Material Performance Across NGS Assays and Platforms

White Paper

Liquid biopsy testing has grown to support early disease diagnosis, therapy selection, and disease and treatment surveillance in cancer survivors. Recent advances in next-generation sequencing (NGS) have enabled larger panel sizes, allowing the detection of a wider range of pan-cancer genomic alterations. The FDA states assay validation requires testing regions of the genome containing actionable variants with high confidence, but multiplexing at this level across all types of variants is not possible using cancer cell lines or engineered cells.

This poster from LGC Clinical Diagnostics describes the development and multi-site evaluation of the expanded Seraseq ctDNA Mutation Mix v4 reference materials for measuring assay sensitivity and the limit of detection of a range of variant types in cancer liquid biopsy testing.