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NGS Secondary and Tertiary Analysis

Deliver clear and confident precision oncology reports with QCI Interpret

The industry’s most advanced FASTQ to final report solution for precision oncology NGS testing powered by AI-enabled literature searches and state-of-the-art manual curation


QCI Interpret for Oncology

The most advanced end-to-end solution for oncology NGS analysis, interpretation and reporting

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.

QCI Interpret for Oncology

Cloud-based NGS secondary analysis that is an optional service for labs needing a FASTQ to VCF solution.

Clinical decision support software (tertiary analysis) with on-demamd variant interpretation services for labs needing a VCF to final report solution.

Offer for current users of the Alissa Clinical Informatics Platform

Automate FASTQ to final report

1. Upload raw FASTQ sequencing files

  • Select pre-configured analysis pipelines in QCI Secondary Analysis (optional service for FASTQ to VCF).
  • Generate high-quality variant calls, visualize results, and send VCF files directly to QCI Interpret.

2. Upload VCFs and enter patient data

  • Select workflow in QCI Interpret.
  • Upload variant files for a patient sample and enter relevant case details, such as patient diagnosis.

3. View list of auto-classified variants

  • View list of computed AMP/ASCO/CAP classifications for each variant.
  • Filter and rank by variants by significance.
  •  View supporting evidence.

4. Identify trials and therapeutic options

  • Match genomic profile and diagnosis with treatments and region-specific clinical trials.
  • Review curated evidence to make final decision on reportability.

5. Add oncologist-ready summaries

  • Use over 490,000 oncologist-reviewed
    variant interpretation summaries.
  • Submit rare or novel variants to QIAGEN’s variant interpretation service (optional).
  • Receive results same day (cases vary).

6. Generate and sign-off on final report

  • Build easy-to-understand, customizable reports for oncologists.
  • Include key details to guide patient treatment, such as variant therapeutic, prognostic and diagnostic relevance and co-occurring interactions.

QCI Secondary Analysis

QCI Secondary Analysis is an optional cloud-based service that processes FASTQ files to produce VCF files containing single nucleotide variants (SNV), insertion–deletion mutation (InDel) and structural variant (SV) calls. The module performs quality and adapter trimming, read mapping, deduplication, local realignment, quality control and variant calling and seamlessly connects to QCI Interpret for an integrated and automated FASTQ to report workflow.

  • Unrivalled speed – Requires less than 1 minute to process one WESvsample at 35x coverage;  can process large comprehensive cancer panels in seconds.
  • Lowest cost per sample –Costs less than $0.40 per WGS sample.
  • Accurate –Achieves 99% accuracy for more than 90% of the genome.

QCI Interpret for Oncology

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.


Explore QCI Interpret's capabilities

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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.  

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.

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, drug labels and guidelines, treatment studies, prognostic studies, reviews, and external database reports.

In QCI Interpret for Oncology you can inspect and evaluate the curated data to make a final decision on the pathogenicity/actionability assessment 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.

QCI Interpret for Oncology provides expert test interpretation with the updated new world data from basic research and clinical trials. QIAGEN’s goal is to enable customers to generate real-world insights from increasingly large genomic data sets.

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.

QCI Interpret for Oncology 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.

With its latest release, QCI Interpret for Oncology enables users to easily issue report amendments without needing to run the report again. 

  • A new ‘Addend Report’ button allows users to create a copy of the current test after a case is signed out.
  • This copied test will display ‘Addendum’ labels that are visible within the test, from the Test List page, and in the PDF report.
Sample report

QCI Interpret for Oncology
sample 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.

Over 3.5 million NGS patient cases interpreted worldwide

Discover why QCI Interpret is one of the most trusted clinical bioinformatics platforms in the world.

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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
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“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
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"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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