Partner CAU will provide Transnational Access for 16S rRNA, metagenome, B- and T-cell receptor and HLA (“Immunogenetics”), single-cell B- and T-cell receptor, whole genome (including also de novo sequencing of non- model organisms), targeted, exome and RNA (mRNA and miRNA), and “difficult” nucleic acid (ancient DNA, liquid biopsy nucleic acid, FFPE nucleic acid) sequencing.
Technical equipment and infrastructure
CCGA at CAU currently operates three 96-capillary Sanger sequencers and seven Next Generation Sequencers (3 MiSeq, 1 NextSeq 500, 1 HiSeq 2500, 2 HiSeq 3000/4000, 2 NovaSeq and 1 IonTorrent, MinIon).
For single-cell sequencing, a microfluidics library preparation instrument has been developed in-house. Approximately 4000 samples are processed per month on the capillary Sanger sequencers and approximately 3000 samples per month on the NGS platforms. Associated to Germany’s 2nd largest University Hospital, UKSH, the infrastructure performs biological and clinical research as well as DAkkS-accredited clinical molecular genetics diagnostic testing.
The high-throughput sequencing core facility is built on top of a high-throughput pre-PCR lab. All laboratory processes are monitored by a laboratory information management system (LIMS). Where applicable, standard operation procedures and automated workflows (e.g. using Tecan, Hamilton and Perkin-Elmer pipetting robots) have been implemented.
To cope with the vast increase in data production and subsequent data processing, large investments were made into the IT infrastructure. The applicants have exclusive access to large parts of the high performance research computation cluster (HPC) of CAU, which comprises over a thousand cores. This research linux cluster will be used for the necessary analyses and extended through the project. A field programmabel gate array (FPGA) supercomputer is integrated into the linux cluster, to enable e.g. sensitive virus detection (Vy-PER). A hybrid FPGA-and-GPU supercomputer was designed and built in-house for virus detection and genome wide association testing. Extensive storage is available through several storage servers (several petabytes). The operation of the DNA/biobanking, genotyping, Sanger-sequencing and next-generation sequencing lab is certified to ISO 15189.