204P - Performance assessment of a comprehensive genomic profiling (CGP) NGS kit across multiple study laboratories

Background

Precision oncology is a rapidly evolving field. Reliable tools are required for comprehensive genomic profiling (CGP) in clinical and research settings. NGS provides capabilities to detect multiple alterations, but complex workflows may be difficult to implement. Roche Diagnostics and Foundation Medicine have developed the AVENIO Tumor Tissue CGP Kit, a streamlined and easy to implement Research-Use-Only CGP assay to enable translational research labs.

Methods

The AVENIO Tumor Tissue CGP Kit profiles 324 genes for cancer alterations, tumor mutation burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH)). The kit contains reagents to create libraries. A software provides access to Foundation Medicine’s bioinformatics pipeline. Five laboratories tested 160 samples, consisting of cell line and formalin fixed paraffin embedded (FFPE) tumor specimens. To assess reproducibility, 144 samples were evaluated across operators, lots, and instruments. To evaluate diagnostic sensitivity and specificity, 314 FFPE samples were tested and positive and negative predictive agreements determined against an orthogonal NGS method.

Results

Across five labs, pass rate was 98.1%. Sequencing quality metrics were high, with most samples reaching 1500x-2500x median coverage. Sites had 99.7% agreement for short variants. In the 144 sample reproducibility study, samples were highly uniform across variables, achieving >90% on-target rate. In the 314 sample concordance study, pass rate was 99.06%, with most samples achieving 2000x-2500x median coverage. Out of 314 samples, PPA to an orthogonal NGS-based method were: 98.3% short variants, 90.5% rearrangements, 94.8% copy number, 100% MSI, 100% TMB, and 96.8% gLOH. NPA reached 99.97% across short variants. Detected alterations included EGFR T7090M, BRAF V600E, KRAS 12/13 mutations, and EML4-ALK fusions.

Conclusions

CGP tests are being utilized in precision oncology, but NGS workflows and bioinformatics pipelines can be difficult to implement. The AVENIO CGP Tumor Tissue Kit is highly reproducible across sites and operators, achieving high sequencing quality metrics and diagnostic sensitivity.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

Roche Diagnostics Solutions.

Funding

Roche Diagnostics Solutions.

Disclosure

J. Choi, A. Ahmed, K. Bi, K. Kirkconnell, C. Yin, M. Shin, N. Shrestha, J. Blau, S. Li, Y. Li, G. Kumar, R. Chien, W. Wen, Z. Li: Other, Institutional, Full or part-time Employment: Roche Diagnostics. A. Fellowes, E. Pikarsky : Other, Institutional, Sponsor/Funding, Roche sponsored study: Roche Diagnostics. M. Teixeira: Other, Institutional, Sponsor/Funding, Roche Sponsored Study: Roche Diagnostics; Other,Speaker, Consultant, Advisor: AstraZeneca Produtos Farmacêuticos; Other, Speaker, Consultant, Advisor: Janssen Cilag Farmacêutica, Merck Sharp & Dohme, Novartis Farma Produtos Farmacêuticos, Roche Farmacêutica Química , Roche Sistemas De Diagnósticos Sociedade Unipessoal. I. Vogl, S.E. Trabucco: Other, Institutional, Full or part-time Employment: Foundation Medicine. M. Javey: Other, Institutional, Full or part-time Employment, Stocks: Roche Diagnostics.