QCI Interpret for Hereditary Diseases

QCI Interpret for Hereditary Diseases, developed by QIAGEN Digital Insights, is an end-to-end NGS data analysis, interpretation, and reporting solution designed for clinical diagnostic laboratories. It streamlines the entire process from raw FASTQ files to a final clinical report, helping labs improve diagnostic yield, reduce turnaround time, and support confident variant interpretation decisions for hereditary conditions including rare and undiagnosed diseases, inherited disorders, and carrier screening applications.

The platform is comprised of two integrated software applications — QCI Secondary Analysis and QCI Interpret — that together automate and accelerate the FASTQ to final report workflow. The solution combines QIAGEN's proprietary expert (MD/PhD) curation with AI-powered machine curation to deliver high-confidence variant interpretation, and supports whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene panels from any vendor or sequencer.

End-to-End Automated Workflow

1. Upload raw FASTQ sequencing files and select pre-configured analysis pipelines in QCI Secondary Analysis to generate high-quality variant calls, visualize results, and send VCF files directly to QCI Interpret.
2. Upload VCF files and enter patient data by selecting the appropriate workflow in QCI Interpret and providing relevant case details.
3. Retrieve a list of auto-classified variants with ACMG/AMP classifications for each variant, and use AI-trained phenotype-driven ranking to filter variants by significance.
4. Review evidence and set reportability status by filtering publications to focus on phenotype-related references and evaluating curated data to make final pathogenicity assessments.
5. Generate and sign off on a final clinical report that is patient-specific and includes clinically relevant variants, interpretations, and references compiled throughout the assessment process.

QCI Secondary Analysis Capabilities

• Unrivalled speed — Processes one WGS sample at 35x coverage in less than 20 minutes.
• Vendor-agnostic — Analysis workflows are custom-tailored to panels from any vendor.
• 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, producing SNV, InDel, and structural variant (SV) calls.
• Seamlessly connects to QCI Interpret for a fully integrated and automated FASTQ to report workflow.

QCI Interpret for Hereditary — Key Features

• Dynamic variant classifications — Provides evidence to trigger all 28 criteria of the ACMG/AMP variant interpretation guidelines with full transparency, returning classifications within seconds of VCF upload.
• AI-trained phenotype-driven ranking — Trained on thousands of solved cases, this feature ranks causative variant candidates in rare diseases by incorporating variant-specific variables including computed pathogenicity, mode of inheritance, zygosity, patient symptoms, and manually curated disease-specific evidence from the QIAGEN Knowledge Base.
• Complete bibliographic coverage of the clinical exome — Combines human-certified content for more than 1,000 routinely tested genes monitored daily by the QIAGEN curation team with AI-derived literature references for remaining genes in the clinical exome, clearly distinguishing between the two content types.
• AI-powered disease-relevant literature identification — Identifies all literature, case reports, and clinical trials relevant to a patient's phenotype with one click, with the ability to filter results to show only phenotype-related references.
• Full transparency of variant assessments — Pathogenicity classifications are accompanied by clear visibility into supporting evidence and criteria, with clickable hyperlinks to full articles (not just abstracts), and the ability to manually add rationale for each rule.
• ACMG/AMP classifications with case-level context — Automatically incorporates case-level information such as inheritance models and relevant findings in associated samples; users can modify criteria and store changes for all downstream cases.
• Preset Filter Views — Enables targeted review of variants according to lab-specific standard operating procedures (SOPs), including filters for HGMD variants or pathogenic/likely pathogenic variants in ClinVar.
• Mode of Inheritance filters — Allows users to review genes based on mode of inheritance, including Dominant, Recessive, X-Linked, and None.
• 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 added beyond existing pre-specified gene panels, supporting both hereditary and oncology workflows.
• Panel- and sequencer-agnostic — Fully customizable to accommodate gene panels, exomes, and genomes.

QCI Interpret for Hereditary Diseases supports LIMS and EHR integration, enabling seamless connectivity with existing laboratory infrastructure. The platform has been recognized for its clinical-grade capabilities, with Genomics England selecting QIAGEN to support The Generation Study — a first-of-its-kind initiative to sequence the genomes of 100,000 newborns in England. QIAGEN has also received European IVDR certification for QIAGEN Clinical Insight Interpret, underscoring the platform's compliance with rigorous regulatory standards.