Clinical Genomics Örebro

Infrastructure unit

Contact

Gisela Helenius, Platform Scientific Director

Bianca Stenmark, Head of Unit

Recent user publications

The publications in this database are the result of research conducted at the units of SciLifeLab – both in user projects and technology development.

Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium.

D. Shaw, R. Abad, Z. Amin-Chowdhury, (…), R. Zanella, F. Zhou, AB. Brueggemann,

Lancet Digit Health5 (9) e582-e593

Sustained Transmission of Neisseria gonorrhoeae Strains with High-Level Azithromycin Resistance (MIC ≥ 256 μg/mL) in Argentina, 2018 to 2022.

RA. Gianecini, T. Poklepovich, D. Golparian, (…), M. Unemo, J. Campos, P. Galarza,

Microbiol Spectr11 (4) e0097023

Genomic surveillance and antimicrobial resistance determinants in Neisseria gonorrhoeae isolates from Uganda, Malawi and South Africa, 2015-20.

F. Kakooza, D. Golparian, M. Matoga, (…), B. Bercot, T. Wi, M. Unemo,

J. Antimicrob. Chemother.78 (8) 1982-1991

High-level in vitro resistance to gentamicin acquired in a stepwise manner in Neisseria gonorrhoeae.

D. Golparian, S. Jacobsson, CL. Holley, WM. Shafer, M. Unemo,

J. Antimicrob. Chemother.78 (7) 1769-1778

SciLifeLab / Services / Our infrastructure / Clinical Genomics Örebro

Clinical Genomics Örebro

Clinical Genomics Örebro was established in 2019 as a collaborative effort between the Department of Laboratory Medicine and the Clinical Research Laboratory (KFL) at Örebro University Hospital together with Örebro University.

Applications

We provide expertise, method development and end-to-end service to translational research and precision diagnostics for the development of tomorrow’s diagnostics. Our current disease focus areas are:

Cancers (including solid tumors and hematological malignancies)
Rare inherited disease
Microbial diseases and surveillance

Services

Our national services within NGS and other molecular technologies include development of methods for clinical implementation or translational research with strong clinical utility. These include, but are not restricted to:

Consultation (Project design, Target capture design, Data analysis)
Sample management (Tissue processing, Resistance typing)
QC of samples for various analyses (Sequencing data, Genomic DNA/RNA)
Sequencing:
- DNA sequencing (WES, Panels, microbial genomes, metagenomics)
Other molecular technologies (Digital droplet PCR)
User access service (DNA/RNA concentration measurements, Automated electrophoresis for DNA/RNA, Sequencing)
Bioinformatics (Bioinformatic analysis (data generated at CG or elsewhere))
Clinical interpretation (Variants)

Equipment

Our node has access to specialized equipment that enable us to factilitate the translation of new high-throuput techniques into clinical use. These include, but are not restricted to:

Various automatic robotic systems (Hamilton NGS Star, Myra Liquid Handling Station, Magnis NGS Prep system)
Various systems for QC, quantification and fragment analyses (TapeStation, Quantification using fluorescent assay (Qubit, Quantit)
Instrumentation for Sanger sequencing (ABI 3500)
Instrumentation for real time PCR and ddPCR (BioRad qPCR, QX200 Droplet Digital PCR System, ABI 7500)
Sequencing platforms:
- Illumina (MiSeq, NextSeq 550 Dx, NextSeq 2000)
- Ion Torrent (Ion S5 Prime)
- Nanopore (MinION, GridION)

Accessing the Local Unit

For more information about our services, please contact us.

Clinical Genomics

If you do not find the service or technology you require, contact us directly or visit another Clinical Genomics node.

Clinical Genomics platform