What to do when your genomics software platform needs a content boost
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.
Supplement your genomics software platform with expert-curated databases
QIAGEN Digital Insights offers two proprietary databases that can supplement your lab’s current variant interpretation platform with trusted, expert-curated content.
Human Gene Mutation Database (HGMD) Professional
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?
- Easily verify whether an observed mutation has been previously described to be responsible for causing human inherited disease
- Obtain an overview of the pathogenic mutational spectrum of a particular gene or disease
- Quickly access detailed reports for disease-associated human inherited mutations
→ 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.
Human Somatic Mutation Database (HSMD)
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?
- Analyze complex NGS reports. You can use HSMD to extract only the most relevant, actionable information that will directly impact clinical decision-making.
- Find off-label therapies. In addition to listing approved therapies and open clinical trials, HSMD identifies off-label and investigational drugs available in your specific geographic region.
- Use HSMD to avoid over-interpretation of variants of unknown significance (VUS) by identifying only the relevant mutations across a gene.
→ Learn how a national cancer research center in Serbia is using HSMD to confidently identify meaningful mutations in somatic tumor testing here.
Does your lab’s genomics software platform need a content boost?
Try HGMD Professional and HSMD for free
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.