Variant Interpretation with QCI Interpret

Enabling seamless workflows from FASTQ to report, the software solution supports the interpretation and reporting of targeted panels, comprehensive genomic profiling, clinical exomes and genomes.

For labs using an Illumina® sequencer and Illumina BaseSpace®, raw FASTQ sequencing files can be directly uploaded to QCI Secondary Analysis. For labs using other sequencers, a bulk file uploader tool can be used to upload data to QCI Secondary Analysis.

QCI Secondary Analysis then seamlessly connects to QCI Interpret for Oncology.

The QCI Interpret for Oncology workflow starts with any of the following NGS format files: vcf, zip, gz, tgz, csv, tsv or bz2 file, and it is compatible with any NGS platform. You can choose to upload multiple-sample files for different patients, or multiple single sample files for samples from the same patient. Manually enter metadata to contextualize the uploaded file in the somatic workflow. 

Simultaneously upload SNVs and structural variants

In cases when you have separate files for small nucleotide variations (SNVs), copy number variations (CNVs) or fusions and rearrangements for the same patient, upload them at the same time for an integrative view of the small variations together with large exonic indels (see how here).

QCI Interpret for Oncology enables the filtering and prioritization of variants by interpretation type, alteration type, and clinical actionability.

The software uses rules-based approach to automatically compute actionability (Tier 1 to Tier 4) and pathogenicity (Pathogenic to Benign) classifications 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 (see how here). Look further into the ones that have been classified by QCI Interpret as clinically actionable (see how here).

Review computed actionability

Actionability and 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 lists of treatments and clinical trials

QCI Interpret allows you to search for appropriate therapeutic options by matching the genomic profile and disease diagnosis with the treatments and clinical trials.  Combination genotypes are curated from drug labels, guidelines, clinical trials records, and clinical studies. QCI Interpret offers you the opportunity to explore prognostic data, diagnostic data, treatments, and age-matched clinical trials even in the case diagnosis is unknown, or in the case when a match to a specific diagnosis cannot be made.

The treatment/trial is displayed and the Evidence field illustrates the nature of the multiple alteration matches. Look for the clinical trial close to your geographic region and search for drugs that are available in your country (see how here).

Review the literature 

QCI Interpret provides expertly-curated extensive bibliography coverage (clinical cases, functional studies, population studies, drug labels and guidelines, treatment studies, prognostic studies, reviews, and external database reports) with multiple lines of evidence linking variants to a disease. The 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 (see how here).

Assess the underlying evidence

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

Leave the heavy-lifting to QIAGEN. On top of accessing over 320,000 decision-ready interpretive comments, you can submit your variants to QIAGEN to receive customized, oncologist-reviewed interpretations and sum-mary comments for every clinically relevant variant detected. An ideal solution for labs working with rare or novel variants, QCI Interpret’s on-demand clinical curation and interpretation services does the research, curation, and interpretation for you, replacing labor intensive processes with automated simplicity.

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

QCI Interpret for Oncology enables rapid report building by providing oncologist-reviewed variant interpretation summaries. 

Each clinical report contains the following information:

• Molecular function
• Therapeutic, prognostic, and diagnostic relevance
• Variant interactions, such as effect of co-occurring variants on therapies, drug resistance and sensitivities
  • Clinical practice guideline recommendations
  • Relevant local recruiting clinical trials
  • FDA-approved drug therapies
  • Primary literature references

View full sample report here.