Genome and exome sequencing is transforming cancer diagnostics and care. In the first installment of our Advancing Clinical NGS series, learn how molecular diagnostic labs can overcome the complexity of implementing bioinformatics workflows for cancer genome and exome sequencing.
How can whole-genome sequencing (WGS) and whole-exome sequencing (WES) be integrated into health care systems to replace the standard of care for oncology? These next-generation comprehensive precision diagnostic tests have the potential to become the best practice for oncology molecular testing in health care systems around the world.
Compared to panel sequencing, WGS and WES offer the ability to comprehensively cover the coding sequence so that either the entire genome, exome or virtual gene panels can be investigated for present and future diagnostic needs; they enable comparability and standardization across different laboratories; and they accurately measure (instead of estimate) complex biomarkers, including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). However, despite clear advantages, the implementation and wide-scale adoption of cancer genome and exome sequencing in clinical settings is lacking.
In this blog, we discuss how clinical diagnostic labs can overcome challenges of implementing WGS and WES for cancer and show how QCI Interpret for Oncology, the industry’s most advanced clinical decision support solution for precision oncology NGS testing, can be used to analyze and interpret WGS and WES panels for cancer with speed and precision.
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.
Below we highlight key features of QCI Interpret for Oncology that help labs overcome the complexity of implementing cancer genome and exome panels for precision oncology applications.
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.
QCI Interpret for Oncology also provides evidence-based variant classification based on AMP/ASCO/CAP guidelines. 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.
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.
In addition, the software 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.
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.
