SciLifeLab Genomics, KTH Royal Institute of Technology

Science for Life Laboratory is a collaboration between four universities in Stockholm and Uppsala: Stockholm University, Karolinska Institutet, KTH Royal Institute of Technology and Uppsala University. The center combines advanced technical know-how and state-of-the-art equipment with a broad knowledge in translational medicine, and molecular bioscience. SciLifeLab currently employs around 1000 people, involving platform activities and research in biology, medicine and environmental sciences.

The National Genomics Infrastructure (NGI) is a technology platform at SciLifeLab and is one of the most competitive genomics platforms in Europe. It is located at the SciLifeLab Stockholm and at Uppsala campuses. NGI is appointed the national platform for massively parallel sequencing and genotyping by the Swedish research council. 

NGI Stockholm will provide Transnational Access to de novo sequencing, using 10x Genomics chromium instruments and HiC combination approach, RAD-seq, and spatial transcriptomics. 

Technical equipment and infrastructure

NGI Stockholm operates a large number of Illumina instruments and 2 Oxford Nanopore sequencing instruments. NGI Stockholm runs its activities based on 2 NovaSeq, 3 HiSeq 2500, 5 HiSeq XTen, 2 MiSeq, and 2 Oxford Nanopore instruments. In addition, a large fleet of liquid handling robots and an automated way of extracting RNA and DNA out of FFPE samples using the Qiagen Symphony.

To analyse the data NGI collaborates with SNIC-UPPMAX supercomputing centre providing a suite of high performance computational resources. To provide a computing environment that will allow for safe production, annotation and analysis of human genetic data, NGI/UPPMAX received funding from Swedish Scientific Council over a 4-year period to establish and operate the e-infrastructure needed for secure analysis of human data.

Besides the hardware and network components, the following is also in place:

  1.  A range of maintained bioinformatics software and reference data and routines to ensure that software and reference data is not tampered with.
  2.  System administration for the resource, including, maintaining and controlling the security work. 
  3. Extensive education and training of staff and user community inexperienced with HPC, in particular in connection to sensitive personal data.

With this resource, the NGI service fully complies with the regulations for handling sensitive data, including the new GDPR. The operation of NGI Stockholm is accredited for transcriptomic and whole genome analysis (including all steps starting from receiving samples, through bioinformatics analysis and data delivery) in accordance with the ISO/IEC17025 quality system. The laboratories to perform spatial transcriptomics are fully operational from tissue handling, sectioning (fresh frozen or FFPE), high-resolution imaging, automated library preparation and software to overlap histology imaging with spatial RNA sequencing data.
NGI Stockholm staff consists of approximately 27 FTEs (60% PhDs) and the facility is run in accordance with the ISO accreditation provided by SWEDAC. During 2018, more than 40,000 samples were handled with applications in all fields of life sciences such as de novo genome sequencing, WGS re-sequencing, and RNA sequencing. In conjugation to the activities at NGI novel applications are developed by the KTH research group at SciLifeLab focusing on development of spatial in situ technologies such as spatial transcriptomics with broad applications in research and clinical routine.