Comparison of results from two commercially available in-house tissue-based comprehensive genomic profiling solutions research-use only AVENIO tumor tissue comprehensive genomic profiling kit and TruSight oncology 500 Assay

Hans-Peter Adams, Matthew C. Hiemenz, Kay Hertel, Frederike Fuhlbrück, Mara Thomas, James Oughton, Helle Sorensen, Ulrich Schlecht, Justin M. Allen, Martina Cantone, Sophie Osswald, David Gonzalez, Eli Pikarsky, Muriel De Vos, Ed Schuuring, Thomas Wieland*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

Increased adoption of personalized medicine has brought comprehensive genomic profiling (CGP) to the forefront. However, differences in assay, bioinformatics, and reporting systems and lack of understanding of their complex interplay are a challenge for implementation and achieving uniformity in CGP testing. Two commercially available, tissue-based, in-house CGP assays were compared, in combination with a tertiary analysis solution in a research-use only (RUO) context: the AVENIO Tumor Tissue CGP RUO Kit paired with navify Mutation Profiler (RUO) software and the TruSight Oncology 500 RUO assay paired with PierianDx Clinical Genomics Workspace software. Agreements and differences between the assays were assessed for short variants, copy number alterations, rearrangements, tumor mutational burden, and microsatellite instability, including variant categorization and clinical trial-matching (CTM) recommendations. Results showed good overall agreement for short variant, known gene fusion, and microsatellite instability detection. Important differences were obtained in tumor mutational burden scoring, copy number alteration detection, and CTM. Differences in variant and biomarker detection could be explained by bioinformatic approaches to variant calling, filtering, tiering, and normalization; differences in CTM, by underlying reported variants and conceptual differences in system parameters. Thus, distinctions between different approaches may lead to inconsistent results. Complexities in calling, filtering, and interpreting variants illustrate key considerations for implementation of any high-quality CGP in the laboratory and bringing uniformity to genomic insight results.
Original languageEnglish
Pages (from-to)1018-1033
Number of pages16
JournalJournal of Molecular Diagnostics
Volume26
Issue number11
Early online date24 Oct 2024
DOIs
Publication statusPublished - Nov 2024

Bibliographical note

Publisher Copyright:
© 2024 Association for Molecular Pathology and American Society for Investigative Pathology

Keywords

  • genomic profiling solutions
  • assay
  • personalized medicine
  • CGP testing

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

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