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Variant Interpretation with QCI Interpret

Skip the diagnostic odyssey and get answers now

With the world’s largest source of globally trusted molecular knowledge, QCI Interpret gives you the best possible chance of delivering a diagnosis for every patient, every time.

Analyze with Precision. Interpret with Confidence.

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Finding answers starts with
the right knowledge base

For genetic testing labs, missing even one article among millions can mean the difference between a diagnosis or an inconclusive result. With the world’s largest knowledge base, QCI Interpret for Hereditary Diseases gives you the best possible chance of solving any case in the shortest amount of time.

>3 million patient cases interpreted by QCI Interpret
99% solve rate, while reducing variants for follow-up by 94% to 100%

The power of augmented
molecular intelligence

QCI Interpret is a clinical decision support software powered by augmented molecular intelligence that helps clinical labs not only make faster decisions—but the right decisions. 

Connected to the exclusive QIAGEN Knowledge Base, the industry’s most comprehensive, manually curated resource that is updated weekly, QCI Interpret for Hereditary delivers variant-specific, scientific evidence in context of phenotype or diagnosis. Interactive filters prioritize variants and proprietary algorithms dynamically and transparently compute ACMG/AMP variant classifications, enabling users to generate evidence-based reports with efficiency, confidence, and reproducibility.

The content core of QCI Interpret for Hereditary, the QIAGEN Knowledge Base is the world’s largest source of globally trusted molecular knowledge. Built manually over 30 years by hundreds of MD- and PhD-level expert curators and augmented by artificial intelligence to rapidly identify, extract, and enhance evidence, the QIAGEN Knowledge Base is unrivalled in breadth, depth, and accuracy. To date, the QIAGEN Knowledge Base has been trusted to analyze and interpret NGS data from over 3 million clinical cases worldwide.

The QCI Interpret difference

World's Largest Knowledge Base

Built over 2 decades, the QIAGEN Knowledge Base is the world’s largest collection of biological and clinical findings certified by expert curation.
Encompassing over 40 databases and maintained by hundreds of certified MD- and PhD-level expert curators who enter more than 46,000 new findings each week, the QIAGEN Knowledge Base is continuously updated to contain the latest evidence from peer-reviewed papers, clinical and functional studies, on- and off-label drugs, and professional guidelines.

Powered by Augmented Molecular Intelligence, the QIAGEN Knowledge Base is built on our own comprehensive ontology that uniformly models relationships between different entities, such as the relationship between a variant, the gene that it resides in, and the observed phenotype.

Phenotype Network Analysis

The Phenotype Network allows users to input symptoms relevant to a case and receive relationships to candidate diseases and mutated genes.
The Phenotype Network feature provides a diagram of inferred, content-driven, relationships between a mutated gene, symptoms observed, and a candidate disease.

This feature uses the disease models from the QIAGEN Knowledge Base to expand from the symptoms provided that are relevant for the case to a disease which may be diagnosed based on any of the symptoms in the context of the mutated gene implicated in the disease.

CNV Interpretation Support

Quickly evaluate copy number variants (CNVs) to determine if the same/similar CNVs have been observed in clinical cases or as common genetic variants.
Better assess the physical structure, functional impact, and clinical relevance of CNVs and gene fusions detected in NGS secondary analysis pipelines.

The software provides bibliographic coverage of over 60,000 CNV case reports with filters to match by overlap, auto-classification of CNV pathogenicity using the new ACMG/ClinGen CNV guidelines for hereditary workflows, population allele frequency data for CNVs, and improved handling of CNVs and splice variants at the exon- and breakpoint-levels.

HGMD Professional

Unique to QCI Interpret is access to HGMD Professional, the gold standard resource for comprehensive human hereditary disease mutation data, licensed exclusively through QIAGEN.
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.

Founded and maintained by the Institute of Medical Genetics at Cardiff University, HGMD Professional contains over 352,000 detailed reports on individual gene variants, with over 45,000 new reports added in 2021 alone.

Computed ACMG/AMP Classifications

Proprietary algorithms dynamically and transparently compute ACMG/AMP classifications for every variant in the uploaded VCF file.
QCI Interpret for Hereditary Diseases can provide evidence to trigger all 28 criteria of the ACMG/AMP variant interpretation guidelines.

Once a VCF file has been uploaded to the software, within seconds, QCI Interpret returns evidence categorized into one of the 28 defined criteria set forth by the ACMG/AMP guidlines and assigns a calculated strength of the evidence.

Users can then view each piece of evidence used in the assessment through clickable hyperlinks that show the full article—not the abstract.

Enhanced Exome Support

Rapidly prioritize variants through an Interactive Filter Cascade that identifies variants impacting symptoms, pathways, and genes implicated in drug response or disease progression.
A list of gene variants can be drilled down to those most relevant to the patient test case by defining a series of filters that reflect the most important selection criteria.

The customizable Interactive Filter Cascade offers 5 different filters that prioritize variants by biological relevance, phenotype associations, and incidence in cancer, kindred, proband, and cohort studies.

On-demand Webinar | Join Dr. Georgios Stamoulis as he discusses how your lab can increase your diagnostic yield of hereditary diseases with QCI Interpret.

See what's new in the
latest QCI Interpret release

The QCI Interpret Winter 2023 Release is now available and comes with several new features, including a new Variant Triage mode for accelerated variant review and expanded bibliographic coverage for ACMG Tier 3 and Tier 4 carrier screening genes.

Trusted insights. Confident interpretations.

0 %
Increase in Efficiency
Rapid variant filtering and automated variant annotation and curation enable labs to increase workflow efficiency by 80%.
Supported Disease Classes
For every variant in any gene in any phenotype, you receive a computed ACMG pathogenicity classification.
Curated Variants Per Month
Over 5,000 new expert-curated variants are entered into the QIAGEN Knowledge Base each month.

The QIAGEN Knowledge Base

Built over 2 decades, the QIAGEN Knowledge Base leverages machine learning to rapidly index journal articles for mutations and human judgment and expertise (Augmented Molecular Intelligence) to ensure accuracy, relevance and context—every catalogued “finding” has been “touched” by a trained scientist.

The QIAGEN Knowledge Base is built on our own comprehensive ontology that uniformly models relationships between different entities, such as the relationship between a variant, the gene that it resides in, and the observed phenotype. The superior structured content ensures consistency and computability.

VCF to final report in 5 simple steps within minutes—not hours

QCI Interpret is panel- and sequencer-agnostic and can be used with any secondary analysis platform.

Upload agnostically any VCF file
Add phenotypes, filter and prioritize variants
Review pathogenicity classification
Final assessment and reportability status
Generate custom clinical report

The QCI Interpret workflow starts with a variant calling format (VCF) file and it is compatible with any NGS platform. You can chose to upload multiple-sample VCF files for different patients, or multiple single sample VCF files for samples from the same patient. Manually enter metadata to contextualize the uploaded VCF file in the hereditary workflow. 

Add any phenotypic information related to the uploaded VCF file and take advantage of QIAGEN’s phenotype driven analysis in order to minimize turnaround time and focus on the region of interest with only a couple of mouse clicks.

Use QCI Interpret’s proprietary Interactive Filter Cascade (view filter here) to access 5 different filters to triage variants with granular control:

  • Confidence Filter (industry-wide)
  • Common Variants Filter (industry-wide)
  • Predictive Deleterious Filter (pre-computed ACMG classifications; pathogenic vs. non-pathogenic)
  • Genetic Analysis Filter (include/exclude specific genotypes)
  • Biological Context Filter (exclusive to QIAGEN)

QCI Interpret uses a rules-based approach to automatically compute pathogenicity classifications (Pathogenic to Benign) according to the professional guidelines from the American College of Medical Genetics and Association for Molecular Pathology (ACMG/AMP). Simplify your data for easier analysis by filtering them into several priority levels for gradual review from high priority to low. Look further into the ones that have been classified by QCI Interpret as Pathogenic and Likely Pathogenic (see how here).

Pathogenicity classifications in QCI Interpret are accompanied by clear visibility into the evidence and criteria supporting the classifications. In addition, you can manually add a rationale for each of the rules triggered if desired and adjust the strength of the final assessment if additional data is available (see how here).

Review the literature as an essential step in the variant assessment process

QCI Interpret provides the most up-to-date, expertly curated extensive bibliography coverage (published clinical studies, including treatment and prognostic studies, functional studies, review articles, and other types) with multiple lines of evidence linking variants to a disease. Bibliography is categorized by article type for every variant detected and includes all findings that have been curated from the published literature as well as findings that have been imported from specific databases (view sample bibliography here).

Inspect and evaluate the curated data to make a final decision on the pathogenicity assessment and reportability status (allow the variant to be displayed on the final clinical report). You can easily add your own criteria for the final variant assessment in the Assessment window (see how here).

Generate a final clinical report that is patient-specific and includes clinically relevant variants, interpretations, and references specified throughout the assessment process.

View full sample report for Hereditary Disorders here


Explore QCI Interpret's capabilities

A world of evidence at your fingertips

With QCI Interpret for Hereditary, you can be confident that every clinical recommendation you make is backed by the latest peer-reviewed publications, clinical practice guidelines, FDA therapeutics, and open clinical trials, all vetted by M.D. and Ph.D.-level expert curators who do the reading for you.

Use QCI Interpret as a variant analysis, interpretation, and decision support tool to evaluate genomic variants in the context of published biomedical literature, professional association guidelines, and publicly available databases. Quickly retrieve curated variant lists obtained from whole-exome or whole-genome sequencing.

The phenotype network feature provides curated evidence supporting gene-disease relationships. View the summary of the gene-disease clinical validity and a visual diagram of the paths from symptoms provided for a case to a candidate disease.  Actively add or remove symptoms (and diseases) to dynamically update the ranking of candidate diseases for variants.

The QIAGEN Knowledge Base contains published articles that refer to the specific variants, along with the categorization of the article types: clinical cases, functional studies, population studies, reviews, and other studies.

Clinical cases are deeply curated to gather specific evidence for automated computation of an ACMG-recommended pathogenicity classification into 5 categories: Pathogenic, Likely pathogenic, VUS, Likely benign, and Benign. For each computed classification, the criteria engaged are displayed along with the supporting evidence.

Use QCI Interpret to group, filter, and prioritize genetic variants from the variant lists. QCI Interpret helps simplify the data, making them easier to analyze by filtering data into several priority levels for gradual review from high priority to low. Sort your variants by pathogenicity in search for those that are clinically relevant.  

In QCI Interpret, you can inspect and evaluate the curated data to make a final decision on the pathogenicity assessment (Pathogenic, Likely pathogenic, VUS, Likely benign, Benign) and reportability status (allow the variant to be displayed on the final clinical report). When vetting the criteria in the Assessment window, you can easily add your own criteria for the final variant assessment.

From our customers

Success stories

Çukurova University

How Dr. Atil Bisgin is accelerating the analysis and interpretation of rare genetic variants. 


How Dr. William Kearns interprets over 1,000 expanded carrier screening tests per month.

University Hospital Cologne

Why Dr. Margarete Odenthal uses QCI Interpret to evaluate pathogenic breast cancer mutations.
Christer Ericcson, PhD
Christer Ericcson, PhD Chief Scientific Officer, iCellate Medical AB
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“Current and future cancer patients, and the healthcare systems, need the fastest possible responsible realization of the promise of personalized cancer medicine. iCellate’s implementation of novel biologically based cancer sample types and cancer tests are empowered by interfacing with QIAGEN’s powerful clinical decision support software QIAGEN Clinical Insight (QCI) Interpret.”
Miguel Ángel Molina Vila, PhD
Miguel Ángel Molina Vila, PhDTechnical Director, Laboratory of Oncology, Hospital Quirón Dexeus, Pangaea Oncology
Read More
“The Molecular Oncology lab needs to deliver reliable patient reports, clearly identifying clinically relevant genetic alterations. QCI Interpret is an invaluable tool to achieve this aim.”
Hiroyuki Mano, MD, PhD
Hiroyuki Mano, MD, PhDDirector of C-CAT, National Cancer Center of Japan
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"The Center for Cancer Genomics and Advanced Therapeutics (C-CAT) and our network of hospitals will use the QCI solution because of the breadth and depth of its professionally curated knowledge base, the ability to match patients with approved treatments or clinical trials and QIAGEN’s customization of its QCI solution for C-CAT’s specific needs."
Stan Letovsky, PhD
Stan Letovsky, PhDVice President of Data Sciences and Bioinformatics, LabCorp
Read More
"Pairing [HGMD Professional] with QIAGEN's automated and scalable informatics framework facilitates our day-to-day secondary and tertiary bioinformatics analyses, and will help improve the quality of care for patients."
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See the content we
have for your variants

Want to see what content QCI Interpret for Hereditary Diseases can provide for your variants? Please complete the form below and our experts will show you the depth of content that our software provides for your specific variants.

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Product Disclaimer: QCI Interpret is an evidence-based decision support software intended as an aid in the interpretation of variants observed in genomic next-generation sequencing data. The software evaluates genomic variants in the context of published biomedical literature, professional association guidelines, publicly available databases, annotations, drug labels, and clinical-trials. Based on this evaluation, the software proposes a classification and bibliographic references to aid in the interpretation of observed variants. The software is NOT intended as a primary diagnostic tool by physicians or to be used as a substitute for professional healthcare advice. Each laboratory is responsible for ensuring compliance with applicable international, national, and local clinical laboratory regulations and other specific accredidations requirements.