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White Papers and Videos

A Modular Approach for Determining Microsatellite Instability Status in Solid Tumor Samples

White Paper

Archer’s VariantPlex panels are a collection of pan-cancer solid tumor research assays that use next-generation sequencing powered by anchored multiplex PCR (AMP) to identify microsatellite instability status accurately without a matched normal sample.

This white paper from IDT describes an evaluation of the VariantPlex MSI Module, available for research use with VariantPlex panels to assess microsatellite instability status via instability of 114 curated microsatellite loci in solid tumor samples, in comparison with orthogonal methods and reproducibility studies.

Tumor Mutational Burden Quantification Using Small- and Moderate-Sized Targeted Anchored Multiplex PCR Panels and Next-Generation Sequencing

White Paper

Tumor mutational burden (TMB) is rapidly gaining acceptance in oncology research as a key biomarker and indicator of tumor response to immune checkpoint inhibitors. Whole-exome sequencing (WES) of tumor-normal pairs is the reference standard for the calculation of TMB; however, given the cost and other workflow implications of WES, TMB is frequently derived from targeted next-generation sequencing panels.

This scientific poster from IDT describes the measurement of TMB using VariantPlex Pan Solid Tumor and VariantPlex Complete Solid Tumor panels utilizing anchored multiplex PCR chemistry for error correction and bias mitigation.


For Research Use Only. Not for use in diagnostic procedures.

Custom Antibodies – Capabilities and Case Studies: An eCase Study Transcript

White Paper

Antibody development, scale-up, and mass manufacturing remain complex processes with many pitfalls and restarts. Part of the challenge is that the skill sets needed for each of the three main steps — development, scale-up, and manufacturing — are considerably different, requiring the commercialization team to master diverse technologies and techniques. Further, the team is faced with decisions on outsourcing parts of the process or investing in in-house expertise and capital expenditures. Often, when a project has narrow performance specifications or tight launch deadlines, seeking out an experienced partner like MilliporeSigma is prudent. This talk covers the key steps in the modern antibody development process for diagnostic assays using advanced technology and discusses case studies in which MilliporeSigma's R&D and manufacturing teams solved some of the toughest challenges in antibody commercialization.  

Please click here for the companion eCase study video.

On the Cutting Edge of Immuno-Oncology with Simple Western and Single-Cell Western

White Paper

The immune system plays an important role in shaping cancer progression, and some of the most successful treatments direct the patient’s own immune cells to target cancer cells. This new and rapidly expanding field of immuno-oncology requires high-resolution, quantitative analytical tools at both the population and single-cell level to parse the complex interplay between cancer, immune, and stromal cells.

This scientific review from Bio-Techne discusses how researchers have used Simple Western, and automated Western blot platform, instead of traditional Western blot in developing next-generation CAR T-cell therapies, studying the tumor microenvironment, developing bispecific antibodies, and investigating other aspects of immuno-oncology.

Signals Notebook Delivers Unexpected Dividends for a Growing Swedish Pharmaceutical Company

White Paper

This case study from Revvity Signals describes how Camurus, a biopharmaceutical company in Lund, Sweden, came to select the cloud-based Signals Notebook for their electronic lab notebook needs, as well as the positive changes the system made for the company.

Signals Notebook Data Sheet

White Paper

Used by more than one million scientists and powered by ChemDraw, Signals Notebook is a collaborative, cloud-native electronic lab notebook (ELN) serving chemists, biologists, formulators, and others in pharmaceutical, biotechnology, chemical, agrochemical, flavor and fragrance, and oil and gas research and development.

This data sheet from Revvity Signals provides use cases for the Signals Notebook, an electronic lab notebook delivered as software as a service designed to cater to the multifaceted needs of R&D scientists.

Biofidelity – Customer Spotlight

White Paper

Biofidelity is a pioneer in the genomic technology space, and the UK-based company’s mission is to unlock the benefits of precision medicine for cancer patients. Its technologies can be used for early detection, precise diagnosis, and routine monitoring applications in oncology.

This white paper from LGC SeraCare explains how working closely with LGC Clinical Diagnostics ensures that Biofidelity is provided with the high-quality, bespoke next-generation sequencing reference materials that the company needs to validate its technology for translation into clinical practice.

Multi-Site Evaluation of Novel BRCA1/2 Reference Materials Including Large Genomic Rearrangements

White Paper

The BRCA1 and BRCA2 tumor suppressor genes limit DNA damage. Consequently, loss-of-function mutations in these genes lead to increased incidence of breast, ovarian, and prostate cancer. Accurate detection of BRCA variants is paramount for patients with somatic cancer to guide treatment strategies, such as eligibility for PARP inhibitor therapy, and for individuals carrying inherited mutations to consider preventive actions. However, 27 percent and five percent of pathogenic mutations in BRCA1 and BRCA2, respectively, are large genomic rearrangements (LGRs) that are particularly difficult to detect in PCR and targeted NGS-based assays. Therefore, the development of assays that consistently detect BRCA1/2 LGRs will require reliable reference materials for validation, troubleshooting, and routine quality control.

This scientific poster from LGC Seracare describes the development and multi-platform validation of a set of novel multiplexed reference materials containing 20 clinically relevant BRCA1/2 variants, including 11 large genomic rearrangements.

Multi-Site Evaluation of FFPE Homologous Recombination Deficiency Reference Materials

White Paper

Homologous recombination deficiency (HRD) arises when defects in DNA repair pathways occur, leading to genomic instability. HRD status is an emerging therapeutic biomarker; NGS assays that measure it can be used to stratify ovarian and breast cancer patients and determine eligibility for clinical trials, PARP inhibitors, and platinum-based therapies. Seraseq FFPE HRD reference materials were developed to cover a range of genomic instability scores to help NGS HRD assay validation and development.

This scientific poster from LGC SeraCare discusses a multi-site evaluation across various platforms of high-positive, low-positive, and negative HRD reference materials.

The Critical Role of NGS Reference Materials in Precision Oncology Applications

White Paper

Cancers can be caused by a multitude of distinct genetic abnormalities, and each tumor is unique. Dozens of new targeted therapies have been developed in recent years, but the challenge of providing optimal care to cancer patients lies in the ability to match the genetic profile of the tumor to the most appropriate therapy. Advances in next-generation sequencing (NGS) technologies have enhanced the identification of hundreds of mutations that may contribute to disease progression, and the development of new diagnostic NGS assays is continually evolving. These assays can profile genetic mutations to enable precision diagnostics, personalized treatment selection, stratification of patients for clinical trials, and improved disease monitoring.

This white paper from LGC SeraCare describes the role reference materials play in developing and validating robust precision oncology assays that can perform with the accuracy, sensitivity, and reproducibility required for clinical use, as well as considerations for selecting the most appropriate provider of reference materials.

Reference Materials for the Development of Assays for the Detection of Measurable Residual Disease in Acute Myeloid Leukemia

White Paper

The detection of minimal residual disease (MRD) in acute myeloid leukemia (AML) can present a challenge because it can require detecting just a few malignant cells within thousands — if not millions — of normal cells. One of the major challenges associated with the development and validation of assays for MRD in AML is the absence of cell-based reference materials that feature diverse mutations that may be encountered clinically. To begin to address the need for standards, LGC SeraCare developed full-process cell-based reference materials that contain several mutations and formulated them at concentrations down to one in 100,000 in a background of normal leukocytes.

This scientific poster from LGC SeraCare describes the generation and validation of cell-based and ccfDNA-based reference materials for the development and validation of assays for the detection of MRD in AML.

Enabling Remote scRNA-seq Pharma Studies

White Paper

Biopharma looks to single-cell RNA-seq for biomarker discovery, to identify targets that can personalize therapy and increase efficacy. Most scRNA-seq technologies require complex equipment that is too expensive for sample collection sites, forcing biopharma to rely on cryopreservation to ship samples to advanced research labs across the globe. Cryopreservation damages fragile and sparse cells, biasing samples — what you freeze is not what you thaw.

This application note from Revvity discusses how the Hive scRNA-seq Solution can enable scRNA-seq studies with global sample collection and centralized lab processing for use in biomarker and target discovery.

Noteworthy Single-Cell RNA-seq Datasets on Inflammatory Diseases

White Paper

Inflammatory diseases encompass a wide range of conditions characterized by chronic inflammation, such as rheumatoid arthritis, inflammatory bowel disease, and asthma. Understanding the intricate mechanisms underlying these diseases is crucial for developing targeted therapies. This is where single-cell RNA sequencing (scRNA-seq) data is a game-changer for researchers. By analyzing gene expression profiles at the individual cell level, scRNA-seq unveils the remarkable heterogeneity of cell types involved in inflammation. With scRNA-seq, researchers can decipher the intricate orchestration of the inflammatory response, identifying key genes, pathways, and potential therapeutic targets.

This white paper from Elucidata features single-cell RNA datasets that capture the comprehensive molecular landscape of inflammatory diseases, curated versions of which can be found and analyzed on Elucidata’s cloud platform Polly.

Notable Datasets Using GWAS in Advancing Disease Understanding

White Paper

Genome-wide association studies (GWAS) are crucial for understanding how genetic variations relate to diseases and traits. When integrated into a platform like Polly, the datasets offer valuable insights into diverse conditions, guide therapeutic discoveries, and promote multi-omics research. GWAS has significantly advanced disease research by identifying specific genetic variants associated with conditions such as ulcerative colitis and age-related macular degeneration (AMD). These findings enable more precise diagnostics and personalized treatments. GWAS also sheds light on conditions like aneurysmal human aortic tissue, offering insights for prevention and therapy.

This white paper from Elucidata presents datasets enhancing the understanding of genetic variations identified through GWAS and giving deeper insights into the genetic underpinnings of various traits and conditions to advance the possibilities in personalized medicine and scientific discovery.

Achieving 100 Percent Automation and Seamless Scalability with a Cost Saving of ~$1.34M in Single-Cell Data Compute and Processing

White Paper

This case study from Elucidata details how a US-based cancer diagnostics company partnered with Elucidata to streamline their data management workflow — from ingestion, preprocessing, and curation to insight generation — for raw single-cell multiome data to identify diagnostic markers for AML.

Their research team utilized the Google Cloud Platform (GCP) to store and use/reuse the raw data. However, the process of uploading large files from the sequencer to GCP, processing them, and subsequently downloading them for additional analysis proved to be laborious and error-prone, requiring redundant effort. Moreover, the absence of standardized naming conventions or classifiers for data storage made it challenging to meet the company's evolving data requirements. They were in dire need of a reliable and efficient data management system.