NGS Secondary and Tertiary Analysis

With its latest release, QCI Interpret advances its curation approaches with cutting-edge AI content extraction for thousands of rare disease genes to provide complete bibliographic coverage of the clinical exome. Therefore, with this new feature, QCI Interpret customers receive human-certified content for more than 1,000 routinely tested genes that QIAGEN’s curation team monitors daily and AI-derived literature references for the remaining genes in the clinical exome to supplement QIAGEN curated content.  In the above screen grab, the green icons indicate human-certified content and the blue icons indicated AI-derived content.

AI-trained phenotype driven ranking tested on a dataset of thousands of solved cases provides superior overall candidate ranking for causative variants in rare diseases. The new variant-ranking approach takes into account multiple variant-specific variables, including the variant’s computed pathogenicity, mode of inheritance, zygosity, patient symptoms, as well as all the manually curated, disease-specific evidence in the QIAGEN Knowledge Base. Greatly enhancing the diagnostic power of exome sequencing, the AI-trained phenotype-driven ranking feature improves the accuracy and efficiency of identifying disease-gene associations.

QCI Interpret leverages advanced AI capabilities that identify all the literature, case reports and clinical trials relevant to your patient’s phenotype with one-click. The software has a new column with “Source” icons (1) with the option to sort (2) and disease “Context” details (when present) to all references (3). The new Show Phenotype-Related References Only filter option narrows down the results to focus exclusively on phenotype-related references (4).

QCI Interpret provides 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 guidelines and assigns a calculated strength of the evidence. ACMG classifications automatically include case-level information such as inheritance models and relevant findings in associated samples, and if additional information or expertise is available, users can incorporate their data, modify criteria, and store changes for all downstream cases. Users can then view each piece of evidence used in the assessment through clickable hyperlinks that show the full article—not the abstract.

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. ‘

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 phenotype association for every variant detected and includes all findings that have been manually and AI curated from the published literature as well as findings that have been imported from specific databases. Users can  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.

QCI Interpret for Hereditary provides customizable protocols which enable labs to standardize genetic tests and analysis workflows for whole genome sequencing, exome sequencing, and gene panels. Protocols can include combinations of simple or complex filters on any set of annotation entities, can define gene lists or genomic regions, and can be locked down on the user and annotation level. Protocols can also be optimized to automatically render reports and include any user interpretations for given variants. Default protocols are provided for both germline and somatic NGS testing.  This allows all users to quickly become proficient in the system and provide a template to optimize.