Research and development at UGC
Research and development at Uppsala Genome Center mainly focuses on development of long read technology applications and medical research. Below follows a short presentation of our current projects.
Uppsala Genome Center has a development project aiming to evaluate Oxford Nanopore sequencing in a service-facility setting. We focus on optimisation of consistent production of ultra-long nanopore reads for de novo projects, as well as testing direct RNA sequencing on this platform.
The Xdrop technology is a molecular method where large DNA fragments are separated into millions of droplets, after which the positive fraction of droplets are sorted, thus allowing the DNA regions of interest to be amplified. Xdrop is commercialized by the Danish company Samplix and UGC is evaluating this technology within a EU funded project.
Fine tuning HMW DNA extraction
The key to successful de novo genome sequencing is availability of intact and chemically pure High Molecular Weight (HMW) DNA, which often possess challenges for research labs. Since 2017, we have been working extensively with different methods of extraction and handling of ultra HMW-DNA. Our ambition is to provide the research community with a set of guidelines needed to succeed with projects that require high quality input material for long read technologies.
Below is represented a taste of our work with HMW DNA extraction.
HMW DNA purification on a dialysis membrane
Agarose embedded bird's blood
Plant nuclei separation on a sucrose gradient
No-Amp targeted sequencing
Enrichment of hard-to-amplify genomic regions like repeat expansions is made possible with the no-amplification (No-Amp) targeted sequencing method utilizing the CRISPR/Cas9 system. The No-Amp protocol is being developed by Pacific Biosciences and UGC is an alpha test site for this method.
The SweGen data resource
Through the SweGen project, we make available a population-based genetic variant data set for the Swedish population. The SweGen resource consists of short-read whole genome sequence data for 1000 individuals and two de novo assembled reference genomes. The variant frequency data is openly available from SweFreq - The Swedish Frequency Resource for genomics