QCI Interpret for Oncology

QCI Interpret for Oncology, developed by QIAGEN Digital Insights, is the industry's most advanced end-to-end solution for precision oncology NGS analysis, interpretation, and reporting. Designed for clinical diagnostic laboratories, it automates the full workflow from raw FASTQ files to final oncologist-ready reports, supporting solid tumors, hematological malignancies, liquid biopsy, and hereditary cancer testing. The platform combines AI-powered literature searches with state-of-the-art expert (MD/PhD) manual curation to enable high-confidence variant interpretation at scale, reducing turnaround time and simplifying complex bioinformatics processes.

QCI Interpret for Oncology is comprised of two integrated software applications: QCI Secondary Analysis, an optional cloud-based module for FASTQ-to-VCF processing, and QCI Interpret, the clinical decision support software (CDS) for tertiary analysis and final reporting. An additional in-software option allows labs to submit rare or novel variants to QIAGEN's on-demand professional variant interpretation service, providing same-day results in most cases.

End-to-End Automated Workflow

• Upload raw FASTQ sequencing files and select pre-configured analysis pipelines in QCI Secondary Analysis to generate high-quality variant calls and send VCF files directly to QCI Interpret.
• Upload VCF files and enter patient case details, including diagnosis, within QCI Interpret to initiate tertiary analysis.
• View automatically computed AMP/ASCO/CAP classifications for each variant, with the ability to filter and rank by clinical significance and review supporting evidence.
• Match the patient's genomic profile and diagnosis with available treatments and region-specific clinical trials to identify therapeutic options.
• Access over 800,000 oncologist-reviewed variant interpretation summaries, or submit rare and novel variants to QIAGEN's variant interpretation service for on-demand expert review.
• Generate customizable, easy-to-understand final reports for oncologists that include variant therapeutic, prognostic, and diagnostic relevance as well as co-occurring interactions, then sign off on the completed report.

QCI Secondary Analysis Capabilities

• Unrivalled speed – Processes one whole exome sequencing (WES) sample at 35x coverage in under one minute; large comprehensive cancer panels can be processed in seconds.
• Vendor-agnostic – Analysis workflows are custom-tailored to panels from any vendor, ensuring broad laboratory compatibility.
• High accuracy – Achieves 99% accuracy for more than 90% of the genome.
• Performs quality and adapter trimming, read mapping, deduplication, local realignment, quality control, and variant calling for SNVs, InDels, and structural variants (SVs).
• Seamlessly connects to QCI Interpret for a fully integrated and automated FASTQ-to-report workflow.

QCI Interpret for Oncology – Key Features

• Dynamic variant classifications – Automatically computes pathogenicity and actionability based on ACMG or AMP/ASCO/CAP guidelines for every variant across more than 31,000 cancer types, with full transparency into the criteria applied.
• Evidence-based variant categorization – Classifies variants into four AMP-recommended tiers: Tier 1 (strong clinical significance, evidence levels A and B), Tier 2 (potential clinical significance, evidence levels C and D), Tier 3 (unknown clinical significance), and Tier 4 (benign or likely benign), with supporting evidence displayed for each classification.
• Oncologist-reviewed summaries and on-demand interpretation – Over 800,000 preformulated, oncologist-reviewed variant impact summaries are available in-software, with the option to submit rare or novel variants to QIAGEN's professional interpretation service.
• Panel- and sequencer-agnostic – Fully customizable to accommodate targeted panels, comprehensive genomic profiling, exomes, and genomes.
• Treatment and clinical trial matching – Matches genomic profiles and patient diagnoses with available drugs and region-specific clinical trials, including the ability to search for treatment options even when diagnosis is unknown. Provides data on clinical impact (diagnostic, prognostic, predictive), matched drugs, and therapeutic effect.
• Filter and prioritize variants – Group, filter, and prioritize genetic variants by interpretation type, alteration type, and clinical actionability to identify actionable mutations in driver genes and match driver alterations with specific drugs for personalized therapeutic management.
• Extensive bibliography coverage – The QIAGEN Knowledge Base includes published articles referencing specific variants, categorized by article type: clinical cases, functional studies, drug labels and guidelines, treatment studies, prognostic studies, reviews, and external database reports.
• Reflex for full curation (add-on) – An optional Reflex license enables cases processed using QCI Interpret One's pre-curation service to be seamlessly submitted for full manual expert curation without creating a new test.
• Somatic rereport treatment policy – An optional treatment reporting policy automatically reapplies prior treatment decisions based on variant and diagnosis-specific history, ensuring consistency in somatic workflow reporting.
• Enhanced Gene Panel View and custom Gene List Management – Users can upload and dynamically create custom gene list views, with up to five Gene Lists available, supporting both oncology and hereditary workflows.

Validation and Compliance

• A 2025 Cancer Genetics study conducted in conjunction with Mayo Clinic demonstrated high concordance between QCI Interpret's automated classifications and the ClinGen/CGC/VICC oncogenicity guidelines across real-world cancer variants.
• QIAGEN has received European IVDR certification for QIAGEN Clinical Insight Interpret, supporting regulatory compliance for clinical laboratories.

QCI Interpret for Oncology supports LIMS and EHR integration, enabling seamless connectivity with existing laboratory information systems. The platform is cloud-enabled and designed to help clinical labs of all sizes scale their NGS testing operations while maintaining the accuracy and consistency required for precision oncology reporting.