Clinical metagenomic next-generation sequencing (mNGS), the comprehensive analysis of microbial and host DNA and RNA in samples from patients, is rapidly moving from research to clinical laboratories. This emerging approach is changing the diagnosis and treatment of diseases, with applications in a range of areas, including oncology, human host gene expression (transcriptomics), and antimicrobial infections and resistance.
In this webinar, Elif Dagdan, the director of the Center for Medical Genetics at Augusta Hospital Bochum in Bochum, Germany, will discuss real-world applications of using clinical mNGS to improve diagnostics of cancer and infectious diseases. The talk will also feature challenges and opportunities of using mNGS in disease diagnostics and how Dagdan’s lab uses clinical variant interpretation and reporting software from Qiagen to detect and characterize pathogenic somatic variants.
Dagdan will discuss:
How mNGS can be used to assess homologous recombination deficiency (HRD) status in patients with ovarian cancer.
How mNGS can be used to assess cell-free microbial DNA via liquid biopsy to aid in early-stage lung cancer diagnosis.
How mNGS can improve the accuracy and speed of infectious disease diagnostics, with a use-case on cardiovascular infections in intensive care units.
We are pleased to announce the availability of a new release for COSMIC, the Catalogue of Somatic Mutations in Cancer. COSMIC Actionability v9 adds new actionability data to the world’s largest, expert-curated somatic mutation database. The release includes 5 new fully curated somatic genes, 948 new clinical trials, and 100 new oncology drugs.
In this article, we provide a summary of the COSMIC Actionability v9 release highlights.
COSMIC, the Catalogue of Somatic Mutations in Cancer, is an expert-curated database encompassing the wide variety of somatic mutation mechanisms causing human cancer. Owned and maintained by the Wellcome Sanger Institute, COSMIC is exclusively licensed through QIAGEN.
COSMIC’s team of variant scientists manually curates key cancer genes to provide in-depth information on mutation distributions and effects. The team relies on a semi-automated curation process of cancer genomes to provide broad somatic annotations toward target discovery and identification of patterns and signatures. To date, COSMIC contains nearly 24 million somatic mutations associated with human cancers.
COSMIC Actionability is a standalone product within the COSMIC database that focuses on providing information on the availability and development of drugs targeting somatic mutations in cancer. COSMIC’s certified curation team integrates data from case studies, clinical trials, and regulatory bodies to represent a full picture of the current precision oncology pipeline (from drug development, through safety and clinical phases, to market and repurposing).
Actionability contains information on three core units: mutations, diseases and drugs. By capturing relations between these units, COSMIC’s team identifies existing and upcoming drugs that target specific genetic variants in different cancer types. COSMIC Actionability is a cutting-edge, ‘living-tool’ that provides the most up-to-date data for precision oncology applications.
→ View the full Actionability v9 release notes here.
Learn more about COSMIC and how the industry-leading database can help you identify biomarkers, annotate variants, and explore the etiology of human cancers here.
See first-hand how COSMIC can be used in your lab by downloading sample data here.
Skin cancer is one of the most common forms of cancer, with nearly 3 million people globally affected each year.* Of every 3 diagnosed cancers, 1 is a skin cancer.** While basal cell carcinoma, squamous cell carcinoma, and melanoma are the most common types, there are several rare skin cancers that are often underrepresented in scientific literature.
The latest Catalogue of Somatic Mutations in Cancer (COSMIC) release, v98, focuses on rarer skin cancers like adnexal tumors, Merkel cell carcinoma, Kaposi sarcoma, dermatofibrosarcoma protuberans, and extramammary Paget's disease—providing deeper insight into the somatic mutations behind them and their clinical implications.
The inclusion of these rare skin tumors in COSMIC will allow clinicians to better understand the molecular mechanisms behind these cancers, which in turn aids in more accurate diagnosis and personalized treatment planning. Now, researchers and drug developers have more resources to help identify potential drug targets and develop new precision therapies for rare skin cancers.
In COSMIC v98, 776 new samples were curated from publications and 25,236 new variants were found in the rare skin tumors newly included. 17 new skin tumor types or subtypes were added to the histology classification system. Users can explore all of the variant data and sample metadata using the COSMIC Cancer Browser on the website. All the tumor types in COSMIC derive from samples that have been found to have somatic mutations in them.
The COSMIC v98 release marks a significant step forward in addressing the underrepresentation of rare skin cancers in scientific literature and databases.
→ Learn more about COSMIC here. (more…)
We are pleased to announce the release of the latest version of the Human Somatic Mutation Database, a new somatic database developed by QIAGEN that contains extensive genomic content relevant to solid tumors and hematological malignancies. HSMD 2.1.1 enhances the database with the latest cutting-edge cancer content, including new clinical trials, new drugs, and new variants that have been clinically observed or curated from scientific literature to help users better understand and define precise function and actionability.
HSMD 2.1.1 release highlights
View the full list of new content updates here.
About HSMD
Combining over 2 decades of expert curation and data from real-world clinical oncology cases, HSMD is a new somatic database from QIAGEN that serves as a single, trusted data source for clinical labs to validate, assess, and better understand the clinical significance of detected variants.
HSMD aggregates manually curated content from the QIAGEN Knowledge Base, the industry’s largest collection of biological and clinical findings, with data from over 500,000 real-world clinical oncology cases that have been analyzed and interpreted by QIAGEN’s professional clinical interpretation service, to eliminate the need to manually collect information across knowledge bases and provide deep genomic insight into the molecular characterizations of your patient’s tumor.
Easy to search with new content added weekly, HSMD enables users to explore key genes or mutations with driving properties or clinical relevance, and lets users search for associated treatment options, off-label therapies, resistance markers, and regional and/or disease-specific clinical trials.
Learn more about HSMD here.
[NEW!] HSMD Software Developer Now Available: Integrate HSMD into your in-house analytical tool for increased efficiency. You’ll be able to link out to the full HSMD online content via endpoints (API keys). HSMD Software Developer access provides integration keys for +1.5 million cancer-associated variants.
In oncology research, identifying potentially actionable gene alterations and exploiting cancer’s molecular vulnerabilities is becoming increasingly difficult. Due to the sporadic nature of somatic cancers, the number of variants detected is rapidly rising.
Clinical research labs are tasked with confidently identifying meaningful mutations that could influence or improve decisions at the point of care. To do this, they need ready-access to trusted data to validate biomarkers and better assess their biological and clinical relevance. And this is precisely what the Human Somatic Mutation Database (HSMD) provides.
HSMD can be used to:
HSMD 2.0 comes with over 140,000 new alterations, improved data visualization and new structural variants. The dataset now contains over 419,000 clinical oncology cases and over 1.5 million mutations associated with over 4.2 million relationships from PubMed, drug labels, clinical trials, clinical guidelines and public databases such as gnomAD and HGMD.
Read the statistics sheet.
Check out these recent articles citing Biomedical Genomics Workbench, a comprehensive, highly accurate NGS data analysis platform, providing researchers with a user-friendly, customizable human hereditary disease and cancer analysis solution for biomarker discovery and validation. Below are a few examples of how researchers from Pennsylvania to Japan are using Biomedical Genomics Workbench to accelerate their research.
Relaxin Reverses Inflammatory and Immune Signals in Aged Hearts
First author: Brian Martin
A team based out of the University of Pennsylvania studied the cardiovascular benefits of relaxin—a pregnancy hormone—on both young and old rats to determine its effects on the heart’s aging process. They extracted RNA and analyzed genomic changes, importing raw transcript data into Biomedical Genomics Workbench and mapping reads to the rat reference genome. The study, which ran in PLOS ONE, concluded that relaxin both alters gene transcription and suppresses inflammatory pathways and genes associated with heart failure and aging. This has therapeutic potential for cardiovascular and inflammation-related diseases, such as heart failure, diabetes and atrial fibrillation.
Comparison of Genetic Profiling of Primary Central Nervous System (CNS) Lymphoma Before and After Extra-CNS Relapse
First author: Kosuke Toyoda
In 2017, a team of Japanese scientists studied the mechanism of chemotherapy resistance in lymphomas of the CNS (central nervous system), which were previously identified as promising targets for immune checkpoint blockade therapy. They performed comprehensive genomic analysis in the hope of better understanding tumor oncogenic evolution and overcoming the immune privilege. The team compared the impact of extra-CNS relapse, using Biomedical Genomics Workbench to call variants. Their report, which ran in Blood Journal, suggested that the evolution of mutations enabled systemic disease progression with a breakthrough of immune privilege, characterized by immunological overpowering and the dysregulation of B-cell proliferation signaling.
Assessing the GeneRead SNP for Analysis of Low-Template and PCR-Inhibitory Samples
First author: Maja Sidstedt
When forensic DNA laboratories use massive parallel sequencing for human identification purposes, chances are good that the DNA samples are heterogeneous and of varying quality. SNP assays must therefore be able to handle impurities and low amounts of DNA. Using Biomedical Genomics Workbench to analyze sequencing data, a Swedish team evaluated the GeneRead Individual Identity SNP panel, which handled multiple extraction methods and withstood inhibitor solutions and was concluded to be satisfactory for casework-like samples. Read about the study, which ran in PLOS ONE in January this year.
To request your no-obligation trial of Biomedical Genomics Workbench, just click here.
There are few meetings as important to the bioinformatics community as Intelligent Systems for Molecular Biology (ISMB), which is celebrating its 25th year at the upcoming event in Prague to be held July 21-25. Organized by the International Society for Computational Biology, ISMB is known for its wide range of presentations, from big-picture keynotes to its targeted “birds of a feather” discussions and much more. We love attending this conference as a way to connect with other bioinformatics geeks and hash out (bad pun fully intended) best practices for computational biology.
This year’s ISMB will be held in conjunction with the European Conference on Computational Biology. Organizers announced 14 communities of special interest (COSIs) that will be running themes throughout the event; examples include structural bioinformatics, visualization of biological data, and bioinformatics education.
Another COSI focuses on methods for understanding the impacts of genetic variation. In the VARI-COSI workshop taking place all day July 24, experts will offer a number of presentations and discussions on relevant topics. Our own Anika Joecker, Director of Clinical Partnering Bioinformatics, will give a talk entitled “The importance of using a most comprehensive knowledgebase for the identification of pathogenic variants in cancer and inherited diseases.” She’ll speak about HGMD as well as the QIAGEN Knowledge Base, which contains hundreds of thousands of manually curated pathogenic variants associated with oncology and inherited disease. The session will include real-world examples showing how scientists have used QIAGEN Clinical Insight Interpret and Ingenuity Variant Analysis to improve diagnosis and treatment for patients.
If you’re attending ISMB this year, enjoy!
Next month we'll meet in Copenhagen for the ESMO 2016 Congress. It's October 7-11, and we're looking forward to see you there and show you our solutions.
We are proud to be part of the collaborative effort to improve cancer care. Our new NGS solutions for cancer research include NGS data analysis and interpretation using QIAGEN Clinical Insight (QCI)* and other bioinformatics tools.
Visit us at booth #206 for a chat and a demonstration of our oncology solutions.
Read more about QIAGEN Clinical Insight
More information about ESMO 2016
The European Association for Cancer Research is hosting EACR24 in Manchester, UK on July 9-12, 2016.
We're looking forward to attend the congress and present our solutions. Please visit us at booth D450 and join our session on July 10:
QIAGEN’s new NGS solutions for cancer research – a sample to insight approach
When: Sunday, July 10 at 7 p.m. - 8:30 p.m.
Location: Room Exchange 9
The session will feature data generated with the GeneReader NGS System, new targeted DNA sequencing solutions and a clinical ctDNA study with Biomedical Genomics Workbench. Invited speakers are:
Finger food and refreshments will be provided
We're looking forward to seeing you at EACR!
Learn more about Biomedical Genomics Workbench
Get more details about EACR24
Part four of our webinar series on liquid biopsies:
Circulating cell-free DNA purification, sequencing and data interpretation
Identification and monitoring of cancer mutations of circulating cell-free DNA (cfDNA) is a key application in liquid biopsy. In the webinar series, we discuss various new technologies and present a complete sample to insight workflow for cfDNA mutation analysis. In this webinar, we show how mutations can be best identified from this type of data and how they can be interpreted. Anika Joecker, Global Solution Product Manager Bioinformatics, Clinical Program, present our solutions for analysis and interpretation of cell free DNA.
https://clcbio.23video.com/v.ihtml/player.html?token=1d44ef16da780f0a29b214aad388d7cd&source=embed&photo%5fid=13428465
