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.
Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast amount of genetic variations in a cost-effective manner. However, there are still inconsistencies and debates about how to process and analyze this "big data". To accurately extract relevant information from genomics data, choosing appropriate tools, knowing how best to use them, and interpreting the results correctly is crucial.
In this article, we discuss an important step in the NGS data analysis workflow–variant filtering and prioritization–including how to overcome challenges, best practices, and how to determine which NGS variant analysis solution is right for you.
Variant filtering is a secondary NGS analysis step that consists of identifying highly confident variants and removing the ones that are falsely called. The variant filtering step used to be mostly left out from deeper testing, even though it can has been shown to significantly improve precision of variant calls.
Variant prioritization is a vital step in discovering causal variants in order to identify disease-causing mutations. This is because the results of NGS technologies and applications, such as whole-exome sequencing (WES) or whole-genome sequencing (WGS), will often consist of a list of several thousands of variants of unknown significance, many of which are proved to benign (even though any rare variant has the potential to be pathogenic).
On average, WES of human samples detects approximately 20,000–30,000 SNVs and indel calls (1).
Therefore, variant prioritization accelerates and simplifies variant interpretation because the results enable the interpretation of variants of unknown significance. It is a process that with filtering identifies which variants found via NGS testing are likely to affect the function of a gene.
1. Content and curation - During the variant filtering and prioritization processes, narrowing down tens of thousands of variants to a manageable list often entails a laborious process of seeking gene-phenotype relationships by consulting numerous separate databases. In addition, when testing for rare genetic diseases, public databases are widely used for the initial elimination of common variants [minor allele frequency (MAF) > 0.01]. However, some public databases may not have variants that are present within private databases, such as the Human Gene Mutation Database (HGMD) Professional.
If causative variants can be identified earlier due to a high rank from prioritization, it’s possible that the full filtered variant list can be short-circuited, reducing the total number of variants reviewed and therefore the time to analyze a case. Additionally, accurate prioritization is a step towards the ultimate goal of fully automating the analysis of the sequencing data for NGS testing.
3. Standardization - Variant filtering and prioritization must be consistent, reproducible, and standardized. However, many clinical research and translational labs use multiple software tools to perform different steps in the NGS secondary analysis workflow, including annotation, variant filtering, and prioritization. Using multiple software tools can introduce workflow complexities and inconsistencies. Now, the gold standard is for NGS labs to use one solution that automates and standardizes variant annotation, filtering and prioritization through a single, user-controlled workflow.
1. Automated curation - To help accelerate the variant filtering and prioritization process, select a NGS assessment software solution that eliminates manual curation by providing users accesses to multiple sources of pre-curated content to rapidly and comprehensively prioritize variants [including Single Nucleotide Variants (SNVs), indels, structural, and Copy Number Variants (CNVs)].
2. Powerful algorithms - With the exponential growth of biomedical data sets in NGS testing, it is increasingly important to combine large data sets with machine learning and powerful algorithms in order to quickly identify potential causal variants within minutes.
3. Transparency and full-user control - To enable consistent, reproducible, and standardized variant filtering and prioritization, select a software solution that dynamically computes assessments with full transparency and gives users total control over parameters, policies, and output.
QCI Interpret Translational is a NGS variant assessment software solution that enables rapid, evidence-powered variant annotation, filtering, and triage for human exome, genome, and large cohort sequencing data.
Leveraging the QIAGEN Knowledge Base, the industry’s largest collection of biological and clinical findings, QCI Interpret Translational improves research efficiency and accuracy by automating manual curation processes, dynamically and transparently assessing variants according to society guidelines with full user-control, and optimizing resource allocation, allowing users to focus on what matters most: transforming genomic data into publishable insights.
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