131P - Benchmarking whole exome sequencing in the German network for personalized medicine

Background

Whole Exome Sequencing (WES) has emerged as an efficient tool in clinical cancer diagnostics to broaden the scope from panel-based diagnostics to screening of all genes and enabling robust determination of complex biomarkers in a single analysis.

Methods

To assess concordance, six formalin-fixed paraffin-embedded (FFPE) tissue specimens and four commercial reference standards were analyzed by WES as matched tumor-normal DNA at 21 NGS centers in Germany, each employing local wet-lab and bioinformatics. In addition, all raw data were re-analyzed with a central bioinformatic pipeline to separate wet- and dry-lab variability.

Results

The positive percentage agreement (PPA) of somatic variant calling was 76% of variants compared to a five-center consensus calling. Variant filtering was identified as the main cause for divergent variant calls. Adjusting filter criteria and re-analysis increased the PPA to 98%. Copy-number alteration (CNA) calls were concordant for 82% of genomic regions. Calls of homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI) status were concordant for 94%, 93%, and 93% respectively. Agreement of CNAs and complex biomarkers did not increase considerably using the central pipeline and the origin of variability was hence attributed to wet-lab differences.

Conclusions

In conclusion, continuous optimization of bioinformatic workflows and participating in round robin tests are recommend.

Editorial acknowledgement

Clinical trial identification

Legal entity responsible for the study

The authors.

Funding

Twist Bioscience, Qiagen, IDT, Illumina, Agilent.

Disclosure

M. Martis-Thiele: Financial Interests, Institutional, Invited Speaker: Twist. J. Siemanowski-Hrach: Financial Interests, Personal, Invited Speaker: DLS, Molecular Health, AstraZeneca, Biocartis. K. Lehmann: Financial Interests, Personal, Invited Speaker: AstraZeneca, GSK, Novartis, Menarini; Financial Interests, Personal, Advisory Board: AstraZeneca, Novartis. S. Ossowski: Financial Interests, Personal, Invited Speaker: Illumina, Oxford Nanopore. C. Schroeder: Financial Interests, Personal, Funding: BMS Stiftung Immunonkologie; Financial Interests, Personal, Research Grant: Illumina. C. Schaaf: Financial Interests, Personal, Research Grant: Illumina. P. Schirmacher: Financial Interests, Personal, Research Grant: Incyte, BMS, Gilead, Falk; Financial Interests, Personal, Speaker’s Bureau: MSD, BMS, AstraZeneca, Incyte, Astellas, Janssen, Eisai, Amgen, Boehringer Ingelheim. D. Kazdal: Financial Interests, Personal, Invited Speaker: AstraZeneca, Pfizer; Financial Interests, Personal, Advisory Board: Bristol Myers Squibb. N. Pfarr: Financial Interests, Personal, Invited Speaker: Novartis, Bayer, Roche, AstraZeneca, Illumina, BMS, MSD, PGDX/Labcorp; Financial Interests, Personal, Advisory Board: Novartis, Lilly, Roche, Janssen; Financial Interests, Personal, Sponsor/Funding: Novartis, AstraZeneca, Illumina, BMS, MSD, PGDX/Labcorp; Financial Interests, Personal, Research Grant: Illumina. J. Budczies: Financial Interests, Personal, Research Grant: German Cancer Aid; Financial Interests, Personal, Advisory Role: MSD. A. Stenzinger: Financial Interests, Personal, Advisory Board: Aignostics, AstraZeneca, Janssen, Bayer, Seattle Genetics, Pfizer, MSD, Eli Lilly, Illumina, Thermo Fisher, Amgen, Astellas, Agilent, Qlucore, QuiP, Sanofi; Financial Interests, Institutional, Advisory Board: BMS, Takeda, Novartis; Financial Interests, Personal, Invited Speaker: Roche, Incyte, Servier; Financial Interests, Institutional, Research Grant: Bayer, Chugai, BMS, Incyte, MSD. All other authors have declared no conflicts of interest.