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 that the Winter 2023 Release of QCI Interpret, QIAGEN’s decision support software platform for the annotation, classification, and reporting of somatic and germline variants, is now available.
Expanding on the software’s current capabilities, the QCI Interpret Winter 2023 Release brings new variant classification and assessment tools, functionality improvements, and even more variant content for prevalent hereditary diseases for faster, more informed variant analysis.
QCI Interpret now offers a new optional Triage Mode inline assessment tool to accelerate variant review workflows. The Triage Mode can be toggled on and off (Figure 1).
For novel unassessed variants, the Assessment, Actionability (somatic workflow only), and the Reportability values match the Computed Classification. Users can then add assessment notes (Figure 2). This new feature is intended to help high volume laboratories quickly assess and triage variants.
QCI Interpret’s literature coverage of genes, involved and associated with disease(s), strongly differentiates QCI Interpret from other decision support software by providing a fully certified and manually curated bibliography of approximately 1,000 genes with continuous expansion.
In the QCI Interpret Winter 2023 Release, the bibliography coverage is enhanced and expanded with a focus on genes that are routinely tested and proposed for carrier screening by the latest ACMG practice resource (Genetics in Medicine (2021) 23:1793–1806; https://doi.org/10.1038/s41436-021-01203-z).
Specifically, the bibliography coverage was fully certified and manually curated for Tier 3 genes with continued curation of Tier 4 genes, to provide a comprehensive and complete carrier screening interpretation workflow based on the latest ACMG recommendations summarized below:
In QCI Interpret, a new ClinVar column displays the assessment (P, LP, VUS, LB, B) and number of ClinVar submitters as pulled from the QIAGEN Knowledge Base. A hyperlink takes the user to the respective ClinVar VCV page (phenotype agnostic) (Figure 3).
Pathogenic (P), Likely Pathogenic (LP), VUS, Likely Benign (LB), and Benign (B) interpretations sent to ClinVar are tallied. The hyperlink takes the user to the NCBI variant specific page for additional detail.
For the complete QCI Interpret Winter 2023 Release Notes, please contact your QIAGEN Digital Insights account representative or email our support team at ts-bioinformatics@qiagen.com.
QCI Interpret is a clinical decision support software platform for the annotation, classification, and reporting of actionable alterations from NGS data for oncology and hereditary disease applications. Using augmented molecular intelligence and expertly curated content from the QIAGEN Knowledge Base, QCI Interpret applies a rules-based approach to automatically compute pathogenicity classifications (Pathogenic to Benign) and actionability classifications (Tier 1 to 4) for each alteration according to professional guidelines from ACMG/AMP and AMP/ASCO/CAP, respectively.
Pathogenicity and actionability classifications in QCI Interpret are accompanied by clear visibility into the criteria and evidence supporting the classifications. This workflow starts with a variant call format (VCF) file, so it is compatible with the output from any NGS platform. The final report includes the alterations, interpretations, and references specified throughout the assessment process, which has customizable automation capabilities allowing for streamlined clinical decision support workflows.
The latest release of COSMIC, the Catalogue of Somatic Mutations in Cancer, is now available. In the new update, referred to as v97, there is also a new release of COSMIC Actionability (v7). With the two releases, the world’s largest expert-curated somatic mutation database focuses on blood cancer curation and adds new content, clinical trials, and categories for assessing patient responses in clinical trials.
Here, we provide a summary of the release highlights.
Every four months, COSMIC content and features are updated by the Wellcome Sanger Institute to ensure the database contains the latest findings and evidence. Over the last 5 releases (15 months), COSMIC has increased the number of genomic mutations by over 15%. Here is what’s new in the COSMIC v97 release.
Total genomic variants
Total patient samples
*Of this, 41,161 are whole genome samples
Curated papers
→ View the full COSMIC v97 release notes here.
COSMIC Actionability delivers the latest data on the availability and development of drugs targeting specific somatic mutations in cancer. Actionability covers clinically relevant mutations and alteration types in relevant genes for some of the most frequently sequenced cancer types such as lung, breast, melanoma, ovarian, and colon cancer. Here is what’s new in the Actionability v7 release.
Fully curated genes
*In total, there are 311 genes included
Total variants included
Total clinical trials
*Of this, 3,756 clinical trials have results
→ View the full Actionability v7 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 and the quality of the database’s content by downloading sample data here.
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.
Many labs struggle with prioritizing clinically- and biologically-relevant variants among the millions of variants detected using NGS. Labs are starting to consolidate smaller panels into one large comprehensive cancer panel to test all cancer types. This presents fresh challenges: interpretation of the data and meeting turnaround times.
Fortunately, with COSMIC’s Cancer Mutation Census and Actionability, labs have the trusted data they need for accurate prioritization at their fingertips.
Here's how.
CMC delivers a score for each variant based on manually-curated information regarding cancer genes and genetic variants. It also provides data on variant frequencies in cancer and non-cancer populations. It utilizes data from many reliable sources, including ClinVar, gnomAD, DNA conservation as reported by GERP, and COSMIC Mutations per AA.
CMC’s algorithmic evaluation of variant significance across the whole set of coding mutations in COSMIC lets you identify variants with the highest potential of biological relevance. The latest version of CMC—v96—describes over 4.9 million somatic variants. It segregates them into four tiers (see Figure 1, below) in order of highest confidence and evidence of driving cancer (Tier 1) to the lowest (Tier 4).
The benefit?
During your NGS data analysis, you can easily match the CMC score to the identified mutations in your NGS test using genomic coordinates, cDNA, or protein change. This lets you rank the mutations in your NGS data according to the CMC score—prioritizing potential biological cancer-driving mutations.
Figure 1. CMC tiers allow you to rapidly classify somatic variants by their potential to drive cancer.
COSMIC Actionability delivers the latest data on the availability and development of drugs targeting specific somatic mutations in cancer. Actionability covers clinically-relevant mutations and alteration types in relevant genes for some of the most frequently sequenced cancer types such as lung, breast, melanoma, ovarian, and colon cancer. This data is updated quarterly; for more information on the latest Actionability release, see below.
With Actionability, you can prioritize clinically-actionable mutations related to your patient’s specific cancer type. This lets you know which of those potentially biologically-relevant mutations are also therapeutically actionable.
Like CMC, Actionability also classifies alterations into four tiers:
Actionability currently covers 62 tier 1, 21 tier 2, 527 tier 3, and 91 tier 4 alterations and alteration types, including those associated with the most common tumor profiling biomarkers and cancer types (see Table 1, below).
Table 1. Genes and cancer types currently included in Actionability data. List of genes adapted from Illumina's TSO500 tumor profiling biomarkers for multiple cancer types [1]. Note: some genes are not yet fully curated, but have been prioritized for curation in Actionability V7 (tentatively launching October 2022).
CMC and Actionability help you rank biologically and clinically relevant mutations easily and efficiently. With the complete set of COSMIC downloadable files, you can further refine the priorities of relevant mutations with the mutational frequency in your patient’s cancer type, as well as resistance mutations.
COSMIC Actionability is updated with new content every quarter. The latest release, V6, contains the following:
See the complete release statistics in Figure 2, below.
Figure 2. COSMIC Actionability V6 release statistics.
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 and the quality of the database's content by downloading sample data here.
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