This infographic from Biofortuna describes how custom lyophilized reagent beads — spheres of customizable freeze-dried material, such as enzymes or other reagents, containing a specific volume of material per reaction — are created, from optimizing the formulation through to quality control.
This infographic from Agena Bioscience describes the challenges that tumor profiling and precision medicine pose to molecular pathologists and patients, such as test turnaround time, test failure, and the complexity of analysis, and it discusses strategies to manage these challenges and improve outcomes.
As more targeted therapies become available, labs are required to test an expanding set of clinically actionable genomic targets. Next-generation sequencing (NGS) has enabled broad genetic testing, but its long turnaround times, high costs, and failure rates present new obstacles for labs to overcome.
This white paper from Agena Bioscience identifies three opportunities for labs to lead improvements in cancer treatment: expediting treatment by reducing testing times, lowering failure rates for better outcomes, and reducing testing costs to increase patient accessibility. By addressing these challenges, laboratories can significantly contribute to improving the overall quality of patient care, ensuring timely and successful treatment, and expanding access to molecular tumor profiling.
The rapid growth in molecular genetics, the development of new targeted treatments, and the decreasing costs of next-generation sequencing (NGS) have fueled the expansion of large sequencing panels. However, the adoption of comprehensive genomic tests in the clinic is not yet widespread, with challenges such as tumor heterogeneity, drug combination implementation, and complex bioinformatics impeding its wide adoption. The white paper from Qiagen highlights the use of the Human Somatic Mutation Database and the Human Genomic Mutation Database to optimize productivity, interpret complex genetics reports, and discriminate between actionable variants and variants of uncertain significance (VUS). These databases help clinicians to evaluate secondary findings, establish their role in the disease, and evaluate their therapeutic, prognostic, and predictive potential. Additionally, the paper emphasizes the need for periodic re-evaluation of detected variants, as their clinical impact may change over time and the importance of seeking novel information and off-label therapies for patients.
Whole genome sequencing (WGS) and whole exome sequencing (WES) have become essential tools in clinical genomics. However, data analysis tasks remain a bottleneck due to the need for bioinformatics expertise, execution speed, and operational costs. To address these challenges, Qiagen has developed the CLC Genomics Workbench Premium, a user-friendly platform for next-generation sequencing (NGS) secondary analysis with a wide range of applications and visualization options. This white paper introduces the Qiagen CLC LightSpeed Module, which enables clinical labs to perform hereditary secondary analysis with high accuracy at unprecedented runtimes. The authors present benchmark results on the performance of LightSpeed Clinical concerning speed, costs using Amazon Web Services (AWS), and accuracy on WGS and WES datasets. They demonstrate that LightSpeed Clinical offers the fastest germline calling FASTQ-to-VCF pipeline currently available, with flexible deployment options for both on-premise and cloud use, making it the most cost-effective and energy-efficient solution for hereditary WGS and WES secondary data analysis.
Comprehensive Genomic Profiling (CGP) is a method of cancer diagnosis and prognosis that uses genomic information to determine treatment plans. CGP is an important tool in cancer care, given that cancer is the second leading cause of death in the US and is understood to be a disease of the genome. Assessing the clinical utility of CGP is complex given the increasing number of genomic markers it identifies, resulting in challenges for US healthcare payers who have to navigate these complexities in their coverage policies.
Evaluating CGP on a gene-by-gene basis is not sustainable, and coverage policies are gradually shifting to consider CGP as a holistic process, despite the challenges posed by the expanding number of genes included and a dynamic evidence base. There is also a need for alternative evidence models to demonstrate the value of CGP, including real-world data and value-based models of evidence. This may foster better collaboration between payors, health systems, biopharma, patient advocates, and other stakeholders throughout the healthcare system.
This white paper explores the evolving dialogue around CGP between payers, health systems, biopharma, patient advocates, and other stakeholders, including the complexities of assessing the clinical utility of large cancer panels and new models to demonstrate the value of comprehensive testing.
In the post-pandemic world, cold-chain shipment of diagnostic products is frequently disrupted, and it is often that lab users receive items that might be compromised during transportation. Lyophilization is a simple way to extend the benefits of molecular diagnostic assays while also reducing shipping and storage costs. It is an especially valuable feature for point-of-care test kits where storage and shipping limitations may exist. It’s also beneficial for testing in remote locations where shipping delays or logistics restraints could compromise test efficacy.
This talk features Singapore-based biotech BioAcumen Global, which has developed the first ISO 13485 lyophilization manufacturing facility in the region dedicated to PCR assays that can be transported at room temperature. Applications include but are not limited to human infectious diseases and animal diagnostic detection which are used in a wide variety of settings throughout the world.
The talk showcases a recent study done by LGC Biosearch Technologies and BioAcumen Global which demonstrates the strong performance of lyophilized reagents compared to freshly mixed reagents in a 1-step real-time PCR assay. Technical considerations when developing a lyophilized assay will also be shared as the optimization could be different compared to a conventional wet version of the same assay.
Learning Points:
Whole-exome sequencing (WES) is a cost-effective method for translational cancer research, as it enables the detection of rare gene variations and the discovery of new cancer biomarkers. Despite the significant contributions of genome-wide association studies, linkage analysis, and candidate gene mutation screening approaches to understanding hereditary cancers, over 50 percent of hereditary cancer risk remains unexplained, implying the need for further investigation into rarer genetic susceptibility alleles. WES provides a comprehensive approach to uncovering missing heritability in hereditary cancers, helping to determine if the majority of missing heritability is due to rare genetic variants. WES analysis poses challenges in variant interpretation, which may lead to missing important variants if not done properly. QIAGEN Digital Insights offers QCI Interpret Translational, a comprehensive tool that translates raw sequencing data into meaningful, interpretable results. This application note from Qiagen explains how this next-generation sequencing (NGS) variant assessment software solution enables rapid, evidence-powered variant annotation, filtering, and triage for human exome, genome, and large cohort sequencing data. By addressing the challenges of WES analysis, this tool empowers researchers to decipher which detected variants have functional significance and which are irrelevant to the phenotype in question.
Formulated with diagnostic kit developers in mind, RapiDxFire qPCR 5X Master Mix GF (GF denotes glycerol-free) from LGC Biosearch Technologies can be combined with gene‑specific primers and hydrolysis probes for immediate use in high-throughput laboratory‑developed test workflows or further processed for lyophilization for use in point-of-care point-of-care devices. Provided at a 5X concentration without passive reference dye, this flexible master mix allows more reaction volume for sample and can detect up to 5 targets simultaneously. The RapiDxFire qPCR 5X Master Mix GF, manufactured in an ISO 13485-certified facility, is available in a range of pack sizes, from small sizes for developmental work to large-scale production batches, ideal for diagnostic test development workflows.
This application note from LGC Biosearch Technologies demonstrates the performance of RapiDxFire qPCR 5X Master Mix GF pre- and post‑lyophilization using an African Swine Fever Virus ASFV detection assay designed by BioAcumen Global.
With the cost to sequence genomes declining dramatically, scientists and researchers are applying next-generation sequencing (NGS) technology to new discoveries and clinical research applications at a rapidly expanding rate. These applications are driving the need for sample preparation workflows that prepare the DNA/RNA libraries prior to sequencing. The increasing appetite for new kits plus the demand for higher-throughput solutions often mean that start-up to sequencing can take months. The development of vendor-qualified, automated library protocols offers a solution to this growing problem.
With over 35-years' experience in automated liquid handing, including the Sciclone and Zephyr next-generation sequencing (NGS) workstations, and a pioneer in NGS automation, Revvity has a proven portfolio of automated NGS library preparation solutions.
This scientific brief from Revvity examines how vendor-qualified automated library protocols are shrinking the time laboratories spend to start sequencing from months to days. It also reviews the three steps of library readiness and describes how each one can impact start-up times.
Case studies are also presented that demonstrate the impact of these solutions on NGS application installation and start-up. With at least one vendor offering over 130 of these vendor-qualified automated library protocols, laboratories can now make considerable progress in reducing times to sequencing and data generation.
Long-read sequencing technology has enabled the detection and characterization of structural variations (SVs) at a higher resolution than ever before, including deletions, insertions, duplications, inversions, and translocations, with significant impacts on gene expression and disease development. The technology generates tens of thousands of base pair-long reads, allowing for the detection of larger SVs that may be missed by short-read sequencing. Although challenges such as the high error rate remain, the benefits of haplotype-resolved assemblies and accurate detection of SVs have already led to new insights into the genomic basis of diseases such as cancer, autism, and schizophrenia. Long-read sequencing has the potential to greatly improve our understanding of health and disease.
This white paper from Geneyx introduces the use of long-read sequencing for the detection of structural variants, the technologies behind long-read sequencing, the performance characteristics of long-read sequencing for structural variant detection, and the advantages of long reads for understanding genomic diversity and disease.
Pharmacogenomics (PGx) is a field of medicine that studies the association between genetic variations and drug metabolism. PGx provides valuable insights into how individuals metabolize drugs, which can impact the effectiveness of medications and increase the risk of side effects. The adoption of PGx in clinical and diagnostic environments is gaining traction as knowledgebases and novel genetic insights continue to improve.
This white paper from Geneyx describes pharmacogenomics, gives examples of genes that impact drug metabolism, discusses the accuracy of PGx tests and the value of testing, gives examples of PGx applications in clinical practice, and discusses PGx in drug discovery and development.
This white paper from Geneyx describes the importance of genetic screening, types of inherited genetic disorders, genetic testing methods used for carrier screening, ethical issues surrounding carrier screening, and future directions.
The natural complexity of microbial communities and technical biases in metagenomics workflows present challenges for microbiome researchers seeking to make meaningful, comparable measurements across different laboratories. To promote assay standardization and validation, ATCC has developed internal controls prepared as whole-cell and nucleic-acid mixtures composed of three genetically engineered bacterial strains. ATCC's spike-in standards serve as a tool for quantitative metagenomic analysis, enabling the precise identification and quantification of spike-in reads and allowing for the normalization of data generated during 16S rRNA and shotgun metagenomic sequencing assays.
This white paper from ATCC discusses the development and application of the spike-in standards for microbiome research to promote assay standardization and validation in metagenomic analysis.
Mycoplasma contamination affects approximately 15-35 percent of continuous cell cultures, causing various detrimental effects such as chromosomal abnormalities and inhibition of cell metabolism. Traditional culture-based techniques and DNA staining with fluorochromes have been used for mycoplasma testing in research laboratories; however, these methods are laborious, costly, and have undefined limits of detection. As a result, there is a need for alternative molecular-based detection systems with improved sensitivity and efficiency. ATCC has designed quantitative mycoplasma DNA controls for use in evaluating the sensitivity of molecular-based detection systems. This white paper from ATCC demonstrates the use of these controls in assessing two different molecular-based detection systems: Bio-Rad QX100 Droplet Digital PCR and CFX96 Touch Real-Time PCR platforms. Both systems were found to sensitively detect and quantify mycoplasma DNA, with the CFX96 Touch platform exhibiting higher accuracy at lower concentrations of genomic material.
