Infectious Disease services

Univerzita Komenskeho V Bratislave (UK BA)

Laboratory provides low or medium throughput screening of selected bacterial and/or viral strains from various sample material, including sample preparation to analysis by real-time PCR. The service includes insight into technology, sample preparation, and partial or full bioinformatic data processing.

Karolinska Institutet (KI)

The Unit: Clinical Genomics Stockholm (https://www.scilifelab.se/units/clinical-genomics-stockholm/) This infrastructure is part of Science for Life Laboratory (SciLifeLab) which is an academic collaboration between Swedish universities (including Karolinska Institutet) and a national research infrastructure with a focus on life science. Clinical Genomics Stockholm unit is a research infrastructure for large-scale, genomics-based analyses using next generation sequencing technologies. The unit assists in translational research projects, in the translation of genomics-based tools to routine clinical care and also aims to improve the capability for national microbial surveillance and for pandemic preparedness. The Service: Non-human genome sequencing Sequencing of bacterial or viral whole genomes with the possibility of sequence analysis and strain typing. Sequencing of SARS-CoV-2 amplicons. Sequencing of metagenome samples (with PCR-free protocol). This service encompasses: o Consultation (Project design, Target capture design) o Sample management o DNA& RNA sequencing (microbial genomes, metagenomics) o Bioinformatics (Bioinformatic analysis on data generated at CG) Equipment Our unit has access to specialized equipment that enable us to factilitate the translation of new high-throughput techniques into clinical use. These include, but are not restricted to: • Various automatic robotic systems (BRAVO NGS Workstation, Hamilton NGS Star) • Various systems for QC, quantification and fragment analyses (TapeStation, Quantification using fluorescent assay (Qubit, Quantit)) • Instrumentation for real time PCR and ddPCR (BioRad qPCR) • Instrumentation for Multispectral imaging (Saphyr optical mapper) • Sequencing platforms: o Illumina (NovaSeq 6000, NovaSeq 6000 Dx, NovaSeq X) o Nanopore (PromethION “access via NGI”) o PacBio (Revio)