ILLUMINA TruSight Oncology 500 Sequencing Panel Validation at A Large Community Based Hospital

Document Type

Conference Proceeding

Publication Date

3-2021

Publication Title

Laboratory Investigation

Abstract

Background: With growing efficacy of targeted therapy, it is critical to have comprehensive tumor profiling. TruSight Oncology 500 (TSO500) is a hybrid capture based next generation sequencing (NGS) assay that enables comprehensive genomic profiling of tumor samples. TSO500 includes 523 cancer-related genes which provides identification of pertinent single nucleotide variants (SNV), insertions and deletions (Indels), splice variants, fusions, copy number variants (CNV), tumor mutational burden (TMB) and microsatellite instability (MSI), from genomic DNA and RNA. Design: We evaluated the performance of TSO500 using a combination of 102 formalin fixed paraffin embedded (FFPE) tumor types, 41 hematologic samples and 27 reference standard samples (Images 1A and 1B). The clinical samples were previously tested by reference laboratories using NGS. Test performance considered optimal with specimens containing at least 10% tumor cells, and nucleic acid concentration of at least 3.3 ng/µL for DNA and 4.6 ng/µL for RNA. Library preparation performed using hybrid capture based TruSight Oncology 500 Library Preparation Kit and sequenced on Nextseq 550/500. Sequenced data analyzed using TSO500 local app and analysis pipeline customized in collaboration with PierianDX. Results: For clinical samples, SNVs with at least 3 % allele frequency and at least 100X depth of coverage detected with 97% sensitivity. Indels with 3% allele frequency and depth of coverage at least 100X detected with 95% sensitivity. CNVs with 3 or greater copies detected with 94% sensitivity. RNA fusions detected with 72% sensitivity. TMB values determined without the need for matched normal DNA. Conclusions: Use of a large cancer panel, like TSO500, allows detailed and simultaneous assessment of SNVs, fusions, CNVs, in a single assay at low variant allele frequencies (VAFs) with a high degree of sensitivity and specificity. This comprehensive oncology panel can also assess biomarkers such as TMB and MSI, both of which are helpful in patients stratification for targeted and immune therapy.

Volume

101

Issue

Supplement 1

First Page

1066

Comments

United States and Canadian Academy of Pathology. USCAP 110th Annual Meeting. Never Stop Learning 2021. Virtual and interactive. March 13-18, 2021.

Last Page

1067

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