Active Startup Project

This project has facilitated the update of the bioinformatics platform of Mendel’s Brain, known as Mendel’s Garden. The goals were to improve all phases of the bioinformatics process:

  • Allow any sequencing file or list of genomic variants as input to the process. Mendel’s Garden automatically accepts both NGS sequencing files (FASTQ) and lists of genomic variants coming from DNA microarray hybridization or VCFs.
  • Increase the number of variants usable for polygenic risk score calculation through genomic imputation. By using genetic maps appropriate to each population, we can calculate haplotypes that allow us to infer genomic positions not present.
  • Improve the polygenic risk score calculation algorithm. We have enabled the calculation of polygenic risk scores using the PGSC_CALC tool and the use of regression models curated by PGS Catalog.
  • Automate the issuance of reports in various formats (PDF and HTML). In addition to issuing reports in HTML as we did until now, we can also issue reports in PDF using templates and Jasper Reports.
  • Enable horizontal scaling of the application through the use of software containers deployable in the cloud. The pipeline is orchestrated using Google Cloud Platform’s Cloud Functions.

Ministry of Industry, Commerce and Tourism framed within the strategic areas defined in the National Strategy for Connected Industry 4.0.