When it comes to NGS variant interpretation, content is king. But when your lab’s genomics software platform relies largely on data-sharing and crowdsourced information, how reliable are your reports?
Commercial genomics software platforms support molecular diagnostic workflows by providing unified interfaces connected to selected knowledge bases. These variant interpretation tools take a list of variants and return aggregated information retrieved from individual knowledge bases. This content is then used to filter and prioritize variants and ultimately derive a diagnosis and/or treatment recommendation. Therefore, a lab’s ability to accurately interpret a variant’s biological and clinical significance lies in the strength of its genomics software platform's knowledge base.
In recent years, crowdsourcing has become increasingly prominent as a means of supplementing the data obtained from more traditional sources, such as academic papers and drug labels. Around the world, initiatives and working groups, such as ClinVar, have developed centralized resources where users can submit variants reported in patient samples and assess their significance. Even commercial software companies, such as Sophia Genetics, have created “global data-sharing networks,” enabling their users to upload and share data with other users in the network.
While crowdsourcing is beneficial when it comes to solving challenging cases, there is one inherent issue: crowdsourced data lacks standardization. Clinical laboratories and medical institutions generate patients’ genetic variants through different sequencing protocols and NGS pipelines. This leads to genetic variants that are not interoperable. As a result, data contained in crowdsourced resources is not as reliable as data contained in a standardized, exert-curated knowledge base.
But there is an inherent dilemma: For many molecular diagnostic labs, purchasing a new variant interpretation platform is not option. The question then becomes, how can molecular diagnostic labs fill in the gaps of their crowdsourced data to ensure their variant interpretation is accurate and timely.
QIAGEN Digital Insights offers two proprietary databases that can supplement your lab’s current variant interpretation platform with trusted, expert-curated content.
HGMD Professional remains the largest, manually curated resource for finding disease-causing mutations. Founded and maintained by the Institute of Medical Genetics at Cardiff University, the database attempts to collate all known (published) gene lesions responsible for human inherited disease, giving you the best possible chance of reaching a diagnosis.
Unlike other competitors who offer little to no data curation or overload users with unhelpful literature and volumes of conflicting data, HGMD Professional combines electronic and human search procedures during data curation in order to provide high-quality information. For more than 30 years, a team of expert curators has consistently screened peer-reviewed biomedical literature in over 250 journals to update HGMD Professional.
A research team at Cardiff University updates HGMD Professional quarterly. As of November 2022, HGMD Professional contains over 377,510 detailed mutation reports and more than 11,500 expert-crafted variant summaries of disease-associated/functional polymorphisms. HGMD Professional adds over 45,000 mutation reports per year.
How can HGMD Professional boost your content?
→ Using the public version of HGMD? Your lab does not have access to over 3 years of expert-curated data contained in HGMD Professional. See what else you’re missing here.
The “somatic version” of HGMD Professional, the Human Somatic Mutation Database (HSMD) is a new somatic database developed by QIAGEN that contains extensive genomic content relevant to solid tumors and hematological malignancies. Available as a web-based application, HSMD contains content from over 4.2 million mutations from two sources. Content is curated from over 420,000 real-world clinical oncology cases and the QIAGEN Knowledge Base.
HSMD provides gene-level, alteration-level, and disease-level information, including clinically observed gene and variant frequencies across diseases. Clinically relevant content in HSMD is placed into the perspective of clinical treatments, providing the links between biomarkers and targeted therapies, and is backed up with relevant scientific and clinical evidence. Users can easily search and explore mutational characteristics across genes, synthesize key findings from drug labels, clinical trials, and professional guidelines, and receive detailed annotations for each observed variant. In addition, users can interrogate a bibliography of over 150,000 variant-specific PubMed articles. HSMD also provides access to individual summaries of alteration-type specific information written by PhD scientists.
As QIAGEN Clinical Insights, QIAGEN’s clinical decision support platform for variant analysis, interpretation, and reporting, continues to be adopted by a growing number of molecular diagnostic labs around the world (The platform recently surpassed interpreting over 3 million NGS patient cases worldwide), the data contained in HSMD is increasing at a compounding rate. HSMD adds a minimum of 70,000 new clinical oncology cases each year.
How can HSMD boost your content?
→ Learn how a national cancer research center in Serbia is using HSMD to confidently identify meaningful mutations in somatic tumor testing here.
Explore, search, and test HGMD Professional and HSMD for free. To demonstrate the quality, flexibility, and simplicity of HSMD, QIAGEN Digital Insights offers complimentary, 5-day trials of both expert-curated database. Start your free trial today.
→ Request your free trial of HGMD Professional here.
→ Request your free trial of HSMD here.
You need biomedical relationships knowledge for innovative data- and analytics-driven drug discovery. Yet this knowledge is locked in thousands of publications and dozens of databases. Collecting, structuring and integrating this knowledge is a challenging task that is time- and resource-consuming.
What if you could break knowledge silos and confidently power your drug discovery with data science using a high-quality and industry-validated source of structured and integrated biomedical relationships?
We are excited to introduce QIAGEN Biomedical Knowledge Base, the leading knowledge about biomedical relationships, manually structured and integrated from thousands of sources by experts. It is a vast collection of diverse causal relationships between genes, diseases, drugs, targets, functions, toxicological processes and more, all of which are enriched with full context. QIAGEN Biomedical Knowledge Base delivers high-quality data ideally suited for major data science-driven drug discovery applications. These include knowledge graph construction and analysis, analytics- and artificial intelligence (AI)-driven target identification and drug repositioning, development of target, disease and drug intelligence portals, disease subtype and biomarker identification and many more.
QIAGEN Biomedical Knowledge Base fuels QIAGEN Ingenuity Pathway Analysis (IPA), our premier ‘omics data analysis and interpretation software. This is data you know well, and now you can access it directly.
"For over 20 years, we have been assembling the world's leading source of molecular knowledge and data used to inform decisions from bench to bedside. This knowledge and data power market-leading products such as QIAGEN IPA, QIAGEN OmicSoft, QCI Interpret and online databases like HGMD and HSMD," said Dr. Jonathan Sheldon, Senior VP of QIAGEN Digital Insights. "Previously, our focus was to make our knowledge and data solely accessible through our industry-leading applications. Now, in addition, we are unlocking and giving the keys to our knowledge and data to fuel drug discovery with data science. The data is in a format and structure that makes it easy to integrate our reliable molecular data into data science projects within pharma and biotech."
Using QIAGEN Biomedical Knowledge Base, you’ll make biomedical discoveries that are:
See how QIAGEN Biomedical Knowledge Base empowers you to leverage biomedical knowledge graph analysis, fuel your data- and analytics-driven drug discovery and transform your research. Learn more and request your trial today.
