Challenge

Our client is a leading US biotech, providing products and services for the entire genomics workflow. They needed a new powerful application for a wet laboratory to design and evaluate quantitative polymerase chain reaction (PCR and qPCR) primers and probes. The current tool was narrow-focused, resulting in a scientific backlog for the client’s customers.

Solution

The Quantori team built a back-end service as a sophisticated bioinformatic constructor for reaction components and chemical conditions to control PCR and qPCR. Our project team consisted of DevOps specialists, software engineers, chemists, bioinformaticians, mathematicians, and analysts. The application is implemented using C# wrapped in Docker with Kubernetes for hosting, compatible with Excel, FASTA, CSV files, and allows manual input. The input of sequences is also possible through the NCBI DB. The sequences are analyzed in Quantori’s proprietary open-source application to design and evaluate required oligo-sequences. The team implemented an Oligo DWH to store oligo-assays to reuse and redesign moving forward. Specifically for the project, the team conducted profound scientific research at the intersection of genetics, biochemistry and bioinformatics, thermodynamics, complex computations, and algorithms. The team additionally carried out concurrent double-testing with golden cases and market counterparts, such as Primer3 and other custom tools, to present the most precise algorithms and boost the domain achievements. Within this ongoing project, the team created a UI to unify the application, the DWH, and other scaling systems.

Outcome

Our client received a custom-developed,unprecedented large-scale multi-attribute application, as well as redefined parameters for probes, denaturation, nucleotide sizes of DNA and primers and GVC  — content, including PCR/qPCR singleplex and multiplex regimens. We implemented thermodynamic algorithms for the oligo design with Gibbs free energy minimization and introduced analysis of the secondary structure formation for probes, primers, and genotyping design to avoid undesirable bonding. Our new solution outperformed the client’s existing tool and market equivalents in attributes variations, flexibility, and accuracy.