Acquisition of a PacBio Sequel IIe Long Range Sequencing Instrument and Service Agreement

The Department of Biology is based on a legacy of outstanding researchers and is today one of the largest institutes at the University of Copenhagen.

The institute has a very unique research and study environment with strong basic research and versatile education in biology, biochemistry, molecular biomedicine and bioinformatics. Students and researchers work together across a vibrant and engaging environment that contributes to our impressive publication list and great funding success. The institute is headed by Professor Niels Kroer, who together with approx. 500 employees and 2 000 students continuously develop the institute's national and international position.

The PacBio Sequel IIe will be the primary instrument for establishment of the centrally located Center for DNA Analysis (CDA). The CDA will provide access to new discoveries, research methodologies and applications derived from long-read sequencing (LRS) to biomedical, clinical, biotechnological, natural science research and development in the Copenhagen area. It will ensure that non-specialists can explore these new research avenues without advanced laboratory or analytical infrastructure. The aim of the purchase is to provide infrastructure enabling a center for cross disciplinary R&D in Denmark covering LRS exploitation, experimental design, sample preparation, interpretation and analysis of results.

The equipment is necessary for the research at the section of microbiology because it is able to sequence long DNA fragments with a low sequence independent error rate from a wide range of sample types.

It is highly compatible and complementary with existing infrastructure for sequencing, sample preparation and downstream analysis facilities at the section of microbiology.

The PacBio Sequel IIe System provides circular consensus sequencing (CCS) read generation allowing for multiple sequence passe of a single molecule with a high consensus read accuracy exceeding 99.999 % (Q50) regardless of DNA sequence context or GC content, for de novo assembly and variant detection in combination with a long HIFI read lengths up to 25 Kb.

This enables low compute, data storage and data transfer requirements due to the compact nature of the sequence read format.

This is a necessary criterion for its use in the experimental samples expected. The instrument must enable low- and ultra-low DNA input protocols for high-quality sequencing of small organisms and samples with limited input DNA and provide accurate sequences from metagenomic samples and other de novo sequencing applications. The sample data provided requires assembly of high numbers of a diverse and complex populations of unculturable species and large, complex genome templates without reference directly from HiFi data necessitating a combination of very high accuracy and long read lengths currently only achievable using CCS PacBio proprietary technology. The sequence errors arising from this type of sequencing are less context dependent than any other similar and currently available LRS technologies enabling effective de novo assembly of unknown large genomes and recovery of accurate metagenome assembled genomes.

PacBio own patent US 2012/0196279 A covering the description, usage and principle of the SMRTbellTM sequencing adapters technology allowing the production of very high accuracy long-reads using circular consensus sequencing.

The instrument is intended to provide new cost effective and reliable LRS research tools to a wide range scientists, clinicians, and enterprises in biomedicine and natural sciences in the Copenhagen area that are not able to provide their own infrastructure due to cost. The instrument fits well with our market analysis as total cost of sequencing is reduced for end users. This is because initial cost for infrastructure is provided by the center and will not have to be passed on to the end user as is the case in other technologies.