QIAGEN launches QCI Secondary Analysis, a new cloud-based secondary analysis solution for oncology and inherited disease applications that enables high-throughput data analysis with limited resource and infrastructure investment.
Next-generation sequencing (NGS) has rapidly gained popularity as a diagnostic testing approach due to its unparalleled ability to comprehensively analyze genetic information with high throughput and precision. However, small and decentralized labs face significant hurdles when it comes to adopting NGS testing. From high upfront costs associated with acquiring the necessary equipment, to the complexity of bioinformatics tools and compliance management that require specialized expertise in data analysis and data security, adopting NGS poses challenges for labs with limited staff and infrastructure.
To empower small and decentralized labs to easily adopt NGS testing, QIAGEN has launched a new secondary analysis solution for oncology and inherited disease applications that enables high-throughput secondary analysis for use with any clinical NGS data. QCI Secondary Analysis is an agnostic, cloud-based software-as-a-service (SaaS) solution that supports all QIAGEN QIAseq panels and seamlessly integrates with QCI Interpret, QIAGEN’s clinical variant interpretation and reporting software, to deliver highly scalable and customizable Sample to Insight workflows for oncology and inherited disease applications.
“Our goal is to empower molecular testing labs, regardless of size, budget, and experience, to leverage the power of comprehensive genomic information to advance precision medicine in every setting. Due to NGS adoption barriers, including complexity and cost, a vast majority of small- to mid-size molecular laboratories rely on limited single-gene tests or choose to outsource sample testing for more comprehensive NGS analysis. However, with the launch of our new NGS secondary analysis software, we are making NGS testing more accessible to decentralized labs.”
Jonathan Sheldon, Senior Vice President of QIAGEN Digital Insights. “
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“QCI Secondary Analysis is particularly valuable for labs looking to start running NGS-based tests because it’s a turnkey solution with easy-to-use features for the everyday lab technician. With the availability of this new solution, QIAGEN has simplified the whole bioinformatics pipeline, providing an integrated workflow that minimizes resource investment and maximizes productivity.”
Can Koşukcu, Senior Bioinformatics Application Scientist of DiagnoSeq, an early-access customer of QCI Secondary Analysis.
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Expanding on the QIAGEN Clinical Insights (QCI) portfolio, QCI Secondary Analysis is designed to streamline analysis from a range of assay types, enabling labs to process more sequencing data without extensive time and resource investment. The turnkey solution is deployed on the QIAGEN Clinical Cloud, a secure cloud environment ensuring the highest degree of isolation and data protection, including compliance with ISO 27001, General Data Protect Regulation (GDPR), and the Health Insurance Portability and Accountability Act (HIPPA) requirements.
While QCI Secondary Analysis is a plug-in-play solution that can support any panel, NGS instrument or software, the true value of this new offering is how it complements QIAGEN’s Sample to Insight portfolio. QCI Secondary Analysis is validated for use for all QIAseq panels, can be used with LightSpeed Clinical, a new software module within QIAGEN CLC Genomics Workbench Premium that enables ultra-fast NGS analysis, and directly integrates with QCI Interpret, QIAGEN’s variant interpretation and reporting platform that has been trusted to analyze and interpret more than 3.5 million NGS patient test cases worldwide.
Learn more about QCI Secondary Analysis here.
Every clinical NGS lab is unique. That’s why QIAGEN offers a comprehensive portfolio of secondary analysis solutions designed to meet the needs of each lab. Take our quiz to find out which secondary analysis solution is right for you based on your lab’s computing resources, personnel expertise, and annual sample volume.
HGMD Professional 2024.1 is now available, expanding the world’s largest collection of human inherited disease mutations to 510,804 entries—that’s 6,796 more than the previous release.
For over 30 years, HGMD Professional has been used worldwide by researchers, clinicians, diagnostic laboratories and genetic counselors as an essential tool for the annotation of next-generation sequencing (NGS) data in routine clinical and translational research. Founded and maintained by the Institute of Medical Genetics at Cardiff University, HGMD Professional provides users with a unique resource containing expert-curated mutations all backed by peer-reviewed publications where there is evidence of clinical impact.
HGMD Professional is powered by a team of expert curators at Cardiff University. Data are collected weekly by a combination of manual and computerized search procedures. In excess of 250 journals are scanned for articles describing germline mutations causing human genetic disease. The required data are extracted from the original articles and augmented with the necessary supporting data.
The number of disease-associated germline mutations published per year has more than doubled in the past decade (Figure 1). As rare and novel genetic mutations continue to be uncovered, having access to the latest scientific evidence is critical for timely interpretations of NGS data.
Figure 1. Mutation entries in HGMD Professional 2024.1. The number of inherited disease-associated germline mutations published per year has more than doubled since 2015.
View the complete HGMD Professional 2024.1 statistics, below.
Unlike new machine learning or artificial intelligence platforms that rapidly index millions of journal articles for mutations, HGMD Professional leverages human judgement and expertise—every catalogued mutation has been “touched” by a trained scientist to ensure accuracy, relevance, and context.
Learn more about the industry-leading database here, where you can explore features, watch videos, and request a complimentary 5-day trial.
As the cost of an individual genome becomes more attainable, laboratories in North America and Europe are experimenting with offering clinical exome and genome sequencing for oncology.
In the second installment of our Advancing Clinical NGS series, Dr. Sheryl Elkin, Chief Scientific Officer at QIAGEN Digital Insights, discusses the clinical utility, cost-effectiveness, and patient impact of implementing genome sequencing as a routine part of precision oncology care
The first human genome, sequenced through the Human Genome Project, took 13 years and cost 3 billion dollars, and its completion was announced in 2003 (1). This version of the human genome was not even complete: a draft version of the human genome was published in 2000, and the genome was filled in to 92% “completion” in April 2003. The true completion of the genome, from “telomere to telomere” was not achieved until nearly twenty years later, in 2022.
The sequencing of the human genome represents an enormous step in the understanding of human biology, both in terms of normal function and disease. However, at the time that the human genome project concluded, the idea that individuals could have their genomes sequenced for routine diagnostics, in a therapeutic timeframe, was nearly inconceivable.
In 2007, the cost to sequence a single human genome was still hovering around $10,000,000, with the cost decreasing on a slope comparable to Moore’s law. However, the commercial transition from Sanger (dideoxy chain termination) DNA sequencing to next generation sequencing (NGS) technology led to a substantial reduction in the cost of DNA sequencing, and by 2015, the first “$1000 genome” was achieved. In effect, though, the true and complete cost of genome sequencing was not reflected in the $1000, which does not include any of the costs of downstream analysis. The amount of data generated by the sequencing of a genome created enormous and costly analytic challenges.
"The value of the genome sequencing in oncology depends on the ability to translate generated data into clinical applicability."
Sheryl Elkin, Ph.D.CSO, QIAGEN Digital Insights
Currently, genome sequencing as a diagnotistic tool in oncology is out of reach for the vast majority of patients. Yet, as the economics of genome sequencing continues to evolve, the technology further develops, for both the sequencing chemistry and the data analytics required to make sense of the information. As a result, laboratories in North America and Europe are starting to experiment with offering clinical exome and genome sequencing for oncology.
In a new white paper, Dr. Sheryl Elkin, CSO of QIAGEN Digital Insights, examines the opportunities and challenges of implementing exome and genome sequencing for oncology. Click the button below to read the full paper.
The latest release of COSMIC Actionability v11 adds 21 new curated genes and over 840 clinical trials
The latest release of COSMIC Actionability v11 is now available. This release updates all previously recorded clinical trials with new or additional results, as well as enriches the world's largest expert-curated somatic mutation database with 21 new fully curated somatic genes, 88 new somatic variants, and 163 additional oncology drugs.
See what else is new in the release highlights below.
*no relevant clinical data was identified
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.
Learn more about COSMIC and how the industry-leading database can help you identify biomarkers, annotate variants, and explore the etiology of human cancers.
COSMIC and HSMD are two expert-curated databases that enable biopharma labs to improve the cancer drug discovery and development process.
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COSMIC and HSMD are two expert-curated databases that provide clinical testing labs with trusted data to identify and annotate biomarkers and support clinical trial matching.
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Genome and exome sequencing is transforming cancer diagnostics and care. In the first installment of our Advancing Clinical NGS series, learn how molecular diagnostic labs can overcome the complexity of implementing bioinformatics workflows for cancer genome and exome sequencing.
How can whole-genome sequencing (WGS) and whole-exome sequencing (WES) be integrated into health care systems to replace the standard of care for oncology? These next-generation comprehensive precision diagnostic tests have the potential to become the best practice for oncology molecular testing in health care systems around the world.
Compared to panel sequencing, WGS and WES offer the ability to comprehensively cover the coding sequence so that either the entire genome, exome or virtual gene panels can be investigated for present and future diagnostic needs; they enable comparability and standardization across different laboratories; and they accurately measure (instead of estimate) complex biomarkers, including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). However, despite clear advantages, the implementation and wide-scale adoption of cancer genome and exome sequencing in clinical settings is lacking.
In this blog, we discuss how clinical diagnostic labs can overcome challenges of implementing WGS and WES for cancer and show how QCI Interpret for Oncology, the industry’s most advanced clinical decision support solution for precision oncology NGS testing, can be used to analyze and interpret WGS and WES panels for cancer with speed and precision.
QCI Interpret for Oncology is clinical decision support software that combines the unmatched accuracy and consistency of QIAGEN’s proprietary expert (MD/PhD) curation with the superior efficiency of machine curation (AI-powered curation) to enable high-confidence variant interpretation and reporting. The software dynamically computes pathogenicity and actionability based on the AMP/ASCO/CAP or ACMG/AMP guidelines for every variant in over 31,000 cancer types with full transparency. To simplify and accelerate interpretation, users have access to over 490,000 preformulated, oncologist-reviewed variant impact summaries and the in-software option to submit rare or novel variants to QIAGEN's professional variant interpretation service. Panel- and sequencer-agnostic, QCI Interpret for Oncology can be fully customized to accommodate targered panels, comprehensive genomic profiling, exomes, and genomes.
Below we highlight key features of QCI Interpret for Oncology that help labs overcome the complexity of implementing cancer genome and exome panels for precision oncology applications.
Use QCI Interpret for Oncology as a variant analysis, interpretation, and decision support software to evaluate somatic genetic variants in the context of professional association guidelines, published clinical cases, clinical trials, and publicly available databases. Quickly retrieve curated variant lists obtained from comprehensive tumor genomic profiling.
Use QCI Interpret for Oncology to group, filter, and prioritize genetic variants from the variant lists. Find actionable mutations in driver genes and match driver alterations with specific drugs allowing personalized therapeutic management. Sort your variants by interpretation type, alteration type, and clinical actionability in search for those that could be used as prognostic and therapeutic biomarkers.
QCI Interpret for Oncology also provides evidence-based variant classification based on AMP/ASCO/CAP guidelines. Clinical cases are deeply curated to gather specific evidence for automated computation of an AMP-recommended classification into 4 categories: Tier 1- variants of strong clinical significance (Level of evidence A and B), Tier 2- Variants of potential clinical significance (Level of evidence C and D), Tier 3 –Variants of unknown clinical significance, and Tier 4- Benign or Likely benign variants. For each computed classification the criteria engaged are displayed along with the supporting evidence.
QCI Interpret for Oncology goes beyond genomic descriptive information to include data on clinical impact (diagnostic, prognostic, predictive), matched drugs available, and therapeutic effect. When searching for appropriate therapeutic options, the actual diagnosis is usually used to match treatments and clinical trials. QCI Interpret for Oncology offers the opportunity to search for treatment and clinical trials even in the case of an unknown diagnosis.
QCI Interpret for Oncology enables you to simultaneously search for both single nucleotide variants (SNVs) and copy number variants (CNVs) in each sample. The software provides an integrative view of the small variations together with large exonic indels. To narrow down the list of variants, you can filter and prioritize them according to actionability.
QCI Interpret for Oncology lists the co-occurring variants in each sample. If the mutations occur in the same gene, the software’s “protein view” shows the presence of the mutations, their positions, and their effect on the protein.
In addition, the software identifies and lists co-occurring variants in each clinical sample, providing evidence on the clinical effect with reference to relevant guidelines. The software allows you to filter variants according to genes in which actionable mutations are detected and to visualize the co-mutations that exist in the sample. Users also receive an expert explanation on the clinical effect of the co-occurring mutations with reference to clinical guidelines.
QCI Interpret for Oncology is an end-to-end solution for NGS data analysis, interpretation, and reporting that helps clinical diagnostic labs scale the process of FASTQ to final report. Comprised of two integrated software applications with an additional in-software option to send rare or novel variants to QIAGEN’s on-demand variant interpretation service, QCI Interpret for Oncology alleviates the complexities of regulating in-house bioinformatics pipelines to reduce turnaround time, simplify variant interpretation, and support confident decisions.
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The winter 2023 release of HGMD Professional (HGMD Pro) is now live, boasting a remarkable expansion of 47,306 new entries in a short 3-month span. With this release, the world's largest collection of human inherited disease mutations reaches a significant milestone, now housing over 500,000 entries. In total, HGMD Pro 2023.4 now contains 504,008 entries.
For over 30 years, HGMD Professional has been used worldwide by researchers, clinicians, diagnostic laboratories and genetic counselors as an essential tool for the annotation of next-generation sequencing (NGS) data in routine clinical and translational research. Founded and maintained by the Institute of Medical Genetics at Cardiff University, HGMD Professional provides users with a unique resource containing expert-curated mutations all backed by peer-reviewed publications where there is evidence of clinical impact.
HGMD Professional is powered by a team of expert curators at Cardiff University. Data are collected weekly by a combination of manual and computerized search procedures. In excess of 250 journals are scanned for articles describing germline mutations causing human genetic disease. The required data are extracted from the original articles and augmented with the necessary supporting data.
The number of disease-associated germline mutations published per year has more than doubled in the past decade (Figure 1). As rare and novel genetic mutations continue to be uncovered, having access to the latest scientific evidence is critical for timely interpretations of NGS data.
Figure 1. Mutation entries in HGMD Professional 2023.4. The number of inherited disease-associated germline mutations published per year has more than doubled since 2015.
View the complete HGMD Professional 2023.4 statistics, below.
Unlike new machine learning or artificial intelligence platforms that rapidly index millions of journal articles for mutations, HGMD Professional leverages human judgement and expertise—every catalogued mutation has been “touched” by a trained scientist to ensure accuracy, relevance, and context.
Learn more about the industry-leading database here, where you can explore features, watch videos, and request a complimentary 5-day trial.
As you may remember, six months ago COSMIC launched new, improved beta download files. These new files contain the same gold standard data found in COSMIC's current files, but presented in a more accessible and interoperable manner. COSMIC aims to to lead by example in encouraging data to be FAIR (Findable, Accessible, Interoperable and Reusable) compliant, and as part of this goal, COSMIC will be phasing out its current files for COSMIC v100. We want to help make this transition as smooth as possible, so keep reading to find out what changes have been made, why they've been made, and how these changes will benefit you.
These new files have been named "Beta" to help you distinguish them from the files you are used to, but they represent the final version and the content and layout are stable.
We will be phasing out current file formats in May 2024 in line with release v100, meaning that, we will be retiring our current download files and only the new style files will be available to download.
With this in mind, here’s how the COSMIC team is helping to ease this transition:
→ Get the details on COSMIC's latest release here.
The Cancer Gene Census (CGC) catalogues genes with mutations causally implicated in cancer and explains how dysfunction of these genes drives cancer.
With COSMIC v99, new high-quality genes have been added to the CGC ─ three to Tier 1 and three to Tier 2. The genes are HGF, RAD50, RRAS2, GSK3B, MUC6 and RAP1B.
More, cancer hallmark annotations have been added to each of the 8 existing CGC Tier 1 genes (SRC, SRSF2, STAT3, STAT5B, STK11, SUFU, TBX3, TNFRSF14). Cancer hallmark annotations summarize the effect of Tier 1 genes on the phenotypic traits shared by cancers.
The CGC has been compiled over 19 years and is periodically reviewed. This ensures that gene assignment to the Census reflects the latest evidence indicative of the strength of a causal association between a gene and one, or more, cancer types, and consistency in the application of the COSMIC inclusion criteria for CGC Tier 1 and Tier 2 assignment. Based on this, and following a recent review, TSHR has been re-assigned from Tier 1 of the Census to Tier 2, and its previous designation as an oncogene rescinded.
→ Want more details? Read the full COSMIC v99 release notes here.
v99 is the second release available through COSMIC's new, improved download files. These new files contain the same gold standard COSMIC data found in its current files, but presented in a more accessible and interoperable manner.
The COSMIC team wants to lead by example in encouraging data to be FAIR (Findable, Accessible, Interoperable and Reusable) compliant, and as part of this goal, they will be phasing out their current files for COSMIC v100 in May 2024. This means that the current download files will be retired and only the new style files will be available to download.
→ Learn more about COSMIC's new files and transition support here.
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.
Interpretation of genomic variants in tumor samples still presents a challenge in clinical settings. Variant interpretation is fragmented across disparate databases, and aggregation of information from these requires building extensive infrastructure. The Human Somatic Mutation Database (HSMD) is an easy-to-use, somatic database from QIAGEN that contains extensive genomic content relevant to solid tumors and hematological malignancies. Pulling content from over 500,000 real-world clinical oncology cases and 40+ databases contained in the QIAGEN Knowledge Base, HSMD gives genetic counselors access to over 1.7 million somatic variants characterized in over 1,400 cancer-related genes. To demonstrate the efficiency and clinical utility of HSMD, we present a use-case for using the database to assess the biological and clinical relevance of anaplastic lymphoma kinase (ALK) gene.
About 3-7% of patients with non-small cell lung cancer (NSCLC) have rearrangements in the ALK gene. These genetic alterations are relatively rare compared with epidermal growth factor receptor (EGFR) or KRAS mutations (1). ALK rearrangements are often seen in people who don’t smoke and who are younger. These oncogenic mutations lead to the constitutive activation of the ALK tyrosine kinase domain, a protein that causes cancer cells to grow and spread. To date, several therapies have been developed to target ALK gene changes, known as ALK inhibitors. These include, Crizotinib (Xalkori), Ceritinib (Zykadia), Alectinib (Alecensa), Brigatinib (Alunbrig), and Lorlatinib (Lorbrena).
Therefore, clinical diagnostic labs that perform somatic genomic testing need to be able to define the precise biological function and clinical actionability of ALK mutations. However, given their relatively rarity, ALK mutations require thorough assessment and curation to accurately interpret their clinical significance and recommend effective treatment strategies.
HSMD is a web-based database that provides deep insight into small variants, such as SNVs, indels, frameshifts, fusions and copy number variants that have been clinically observed or curated from scientific literature to help users better understand and define precise function and actionability. Unlike other somatic databases, such as ClinVar and Genomenon that use crowdsourcing or human-absent machine learning, HSMD uses augmented molecular intelligence—the combination of machine learning and human curation—to curate each somatic variant. The result is higher quality data that is up-to-date, consistent, comprehensive, and accurate. This focus on human effort, review and certification is critical. It means clinical diagnostic labs can trust the data in HSMD and proceed with confidence to interpret and report somatic tests.
Here, we present a step-by-step use-case of how your clinical diagnostic lab can use HSMD to search and explore mutational characteristics across the ALK gene, synthesize key findings from drug labels, clinical trials, and professional guidelines, and receive detailed annotations for each observed variant.
HSMD is a web-based application. When you open the interface, the homepage provides five search options. Users can search by Gene, Alteration, Disease, Drug, or Clinical Trial (Figure 1).
Search by gene: When you search by gene in HSMD, you access the total number of genes listed in the database. You can then further narrow your search by viewing data from the QIAGEN Knowledge Base or focusing exclusively on clinically observed variants.
When you search for ALK p.F1174L in HSMD, you receive a description of the alteration with links to relevant literature, external links to the alteration in ClinVar, dbSNP, and OncoKB, and a summary of alteration details, including chromosome position, alteration type, functional impact, and population frequency (Figure 2).
Once you narrow your focus to searching for only clinically observed variants, you receive a table and distribution graph that shows the number of observed clinical cases for a particular gene across all cancer types.
Continuing the example using ALK p.F1174L, you can clearly see the alteration’s distribution by disease through a table and graph. As you scroll down, you receive information on it's biological impact, as well as the gene’s frequency in different populations (Figure 3). You can also view the biological impact and allele frequency (Figure 4).
Click to enlarge the images.
HSMD enables you to view relevant drugs and clinical trials for a ALK p.F1174L. You receive a list of drugs approved for use with ALK p.F1174L (Figure 5a), as well as recruiting clinical trials for that alteration (Figure 5b). In addition, HSMD provides an extensive bibliography for ALK p.F1174L, with clickable links to each article (Figure 6).
Click to enlarge the images.
As demonstrated by the use-case, incorporating HSMD into your somatic variant interpretation workflow enables you to 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. With HSMD, you can efficiently ask and answer the following key questions:
HSMD is a one-stop shop for all the content a clinical diagnostic lab needs to assess the biological relevance and clinical actionable of somatic variants. QIAGEN Digital Insights offers free, no-obligation trials of HSMD. You can see what kind of content the database offers, explore the search functionality, and determine if this database can save you time and money.
Take the first step. Request a free trial of HSMD here.
Want to learn more?
Explore HSMD resources, videos, and use-cases here.
Need a FASTQ to final report solution for oncology NGS testing?
QCI Interpret for Oncology is an end-to-end solution for NGS data analysis, interpretation, and reporting that helps clinical diagnostic labs scale the process of FASTQ to final report.
QCI Interpret provides a comprehensive and flexible reporting system that automatically incorporates significant variants, key findings, annotation sources, and interpretation summaries. Reports can be fully customized to meet your lab’s brand and formatting requirements. This sample report is for a pan-cancer multimodal panel and shows results with TMB and MSI biomarkers and a KRAS alteration detected.
