While next-generation sequencing (NGS) is rapidly adopted in personalized medicine, the lack of standardization and straightforward data analysis solutions impede the translation of labor-intensive NGS protocols into lean sample-to-result workflows.
The IdyllaTM system has all features to facilitate this translation. Biocartis is developing an IdyllaTM Pan-Tumor NGS Prep Panel Assay, targeting single nucleotide variants, deletions and insertions that are methodically selected to be clinically actionable and future-proof. The IdyllaTM Pan-Tumor NGS Prep Panel Cartridge will automate formalin-fixed paraffin embedded (FFPE) sample preparation, DNA quality check and amplicon-based target enrichment. The enriched product can be sequenced on most mainstream desktop sequencers. Independent of the platform on which the NGS data are generated, Biocartis variant calling software provides a concise report.
Biocartis is currently performing a feasibility study that assesses the usability of incorporating the IdyllaTM system in NGS workflows in clinical diagnostic labs. Three study sites differ in sequencing expertise, sample throughput and user needs, enabling evaluation in both the centralized and decentralized NGS setting. The performance of the prototype IdyllaTM Pan-Tumor NGS Prep Panel Assay in terms of PCR- and NGS-related characteristics will be determined.
Each study site uses the IdyllaTM platform and prototype IdyllaTM Pan-Tumor NGS Prep Panel Assay to process 10 FFPE contrived or patient tumor samples with known mutational status. The resulting PCR products are collected from the IdyllaTM Cartridges, barcoded and pooled for sequencing. Variant calling is performed by the Biocartis data analysis pipeline. The workflow usability will be assessed by a questionnaire. The variant report will be matched to the known mutational status to assess preliminary assay performance.
In a preliminary evaluation, the prototype assay showed a high target specificity and a uniform coverage. All expected mutations were detected, including those with a variant allele frequency (VAF) as low as 1%. The results of the feasibility study, which is currently ongoing, will be processed by the end of April 2018. Biocartis will use the study data to assess future development possibilities, such as the introduction of commercial panels into the Cartridge. In addition, Biocartis will decide on further optimizing and expanding the prototype assay.