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 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.

Bio-Techne offers a suite of precision medicine services spanning translational biomarker discovery through clinical trial assay and downstream development, as well as commercialization of companion diagnostic products. As part of these services, Asuragen, a Bio-Techne brand, has developed a multiplex, RT-qPCR assay system QuantideX for ultrasensitive RNA quantification, for which clinical and analytical performance has been demonstrated in multiple disease indications. The ultra-sensitivity of the QuantideX technology is extensible to multiple genetic targets and is portable between qPCR platforms. The QuantideX platform has a simple workflow that facilitates implementation across molecular laboratories and demonstrates excellent reproducibility to enable widespread decentralization of testing.

This white paper from Asuragen reviews case studies showcasing the effectiveness of the QuantideX RT-qPCR assay system in expediting patient stratification and enhancing clinical trial enrollment, emphasizing the importance of selecting appropriate molecular targets and developing high-performance clinical trial assays and companion diagnostics that are easy to deploy.

The AmplideX PCR/CE SMN 1/2 Plus and AmplideX SMA Plus kits are in vitro nucleic acid amplification kits for the determination of SMN1 and SMN2 exon 7 copy number. Both kits are PCR assays that amplify distinctive SMN1 and SMN2 gene regions and an endogenous control (EC) gene from purified genomic DNA in a single reaction for up to 94 samples per run. Fluorescently labeled SMN1- and SMN2-specific amplicons are resolved by capillary electrophoresis (CE) and referenced to co-amplified EC gene products to determine copy numbers. The kits resolve SMN1 and SMN2 exon 7 copy numbers and identify hybrid peaks associated with chimeric genes resulting from gene conversion. Additionally, they determine the status of three important polymorphism variants, including two associated with SMN1 gene duplication and one associated with reduced disease severity due to improved SMN2 splicing.

This technical note from Asuragen discusses the latest clinical research on the SMN1 and SMN2 variants detected by the AmplideX SMN 1/2 Plus and SMA Plus Kits, including how they relate to the underlying genetics and outcomes for spinal muscular atrophy disease prognosis and carrier risk.

Many genetic diseases are associated with DNA mutations that are highly difficult to robustly detect using conventional methods. While progress has been made in characterizing these dark genomic regions in a research setting, the testing approaches employed for amplification and sequencing are often complex and inefficient. These limitations impose serious barriers to using these tests in clinical trials or as companion diagnostics. This white paper from Asuragen describes how AmplideX products can serve as clinical trial assays and/or companion diagnostics to therapies developed for genetic diseases and highlights how this technology can be expanded for other challenging genetic disorders with unmet testing needs.

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.

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.

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.

Implementing a comprehensive molecular profiling solution that addresses all of the relevant biomarkers — including those of emerging importance such as tumor mutational burden (TMB) — delivers accurate and actionable findings. This, in turn, empowers laboratories to gain the confidence of the treating oncologists, equipping them with the necessary insights to bring optimal care and the most effective treatments to patients.

This case study from Labcorp reports on how a hospital network adopted the PGDx Elio Tissue Complete solution to accommodate the growing number of actionable biomarkers and genomic signatures and support the oncologists’ needs.

Rapid biomarker identification necessitates the exploration of comprehensive solutions for biomarker-guided solid tumor testing solutions. Adopting an FDA-cleared solution with a PLA code can reduce onboarding and implementation time and effort and facilitate reimbursement.

This case study from Labcorp describes how a large health network adopted the FDA-cleared PGDx Elio Tissue Complete assay to accommodate the growing number of actionable biomarkers while reducing validation time and effort and improving reimbursement rates.

The quantity and quality of tumor specimens are central to successful comprehensive genomic profiling (CGP) using the OmniSeq Insight test. Control of preanalytic variables and optimal tissue stewardship are critical to achieving accurate and reproducible laboratory testing. Published guidelines for molecular testing of tumor tissue, in particular next-generation sequencing procedures, have lagged because of the newness and dynamic nature of the technology, limited published empirical data, and assay-specific dependence due to heterogeneity of methods and performance characteristics of individual tests.

This white paper from Labcorp provides best practices in tissue handling and stewardship to maximize the likelihood of successful OmniSeq Insight CGP testing and minimize issues with DNA/RNA quality and quantity that can lead to partial or complete test failures.

In many countries, lung cancer incidence is increasing, and approximately 240,000 patients are projected to be diagnosed with lung cancer in 2023 in the United States. The majority of cases will be non-small cell Lung Cancer (NSCLC), which constitutes about 85 percent of all lung cancers. With the emergence of immunotherapy and targeted therapy for specific biomarkers, significant advances have been made in survival rates and quality of life for these patients.

This review from Labcorp discusses the rationale behind molecular testing of patients with advanced NSCLC, highlights the benefits of comprehensive genomic profiling (CGP) at diagnosis, and presents four cases that demonstrate the need for tissue stewardship in the context of biomarker testing.

Precision oncology promises to revolutionize cancer treatment through targeted therapies based on a tumor's unique molecular profile. However, realizing this vision requires comprehensive genomic testing capabilities.

This case study from Labcorp describes how a university research center sought to consolidate fragmented genomic testing and implement comprehensive profiling to match patients to targeted therapies and clinical trials, partnering with Labcorp to implement the PGDx Elio Tissue Complete IVD assay as an in-house alternative solution.

Guidelines recommend patients with advanced non-small cell lung cancer (NSCLC) undergo broad molecular testing for EGFR, ALK, ROS1, BRAF, NTRK 1/2/3, MET, KRAS RET, ERBB2 and PD-L1 prior to selecting first-line systemic therapy.

This graphical abstract from Labcorp summarizes a study published in Oncology and Therapy that evaluated the impact of prior single-gene testing on comprehensive genomic profiling (CGP) results, finding it to increase subsequent CGP test cancellations, turnaround time, and the likelihood of incomplete molecular profiling due to tissue insufficiency.

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.