Clinical Genomics Örebro

Infrastructure unit

Contact

Gisela Helenius, Platform Scientific Director

gisela.helenius@regionorebrolan.se

Bianca Stenmark, Head of Unit

bianca.stenmark@regionorebrolan.se

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.

Whole exome sequencing of FFPE samples-expanding the horizon of forensic molecular autopsies.

E. Adolfsson, D. Kling, C. Gunnarsson, J. Jonasson, H. Gréen, A. Gréen,

Int J Legal Med

GyrB in silico mining in 27 151 global gonococcal genomes from 1928-2021 combined with zoliflodacin in vitro testing of 71 international gonococcal isolates with different GyrB, ParC and ParE substitutions confirms high susceptibility.

D. Golparian, S. Jacobsson, L. Sánchez-Busó, (…), P. Galarza, M. Ohnishi, M. Unemo,

J. Antimicrob. Chemother.

Complete Reference Genome Sequence of the Extensively Drug-Resistant Strain Neisseria gonorrhoeae AT159, with Ceftriaxone Resistance and High-Level Azithromycin Resistance, Using Nanopore Q20+ Chemistry and Illumina Sequencing.

D. Golparian, S. Pleininger, S. Jacobsson, A. Indra, M. Unemo,

Microbiol Resour Announc11 (9) e0074422

Genomic surveillance and antimicrobial resistance in Neisseria gonorrhoeae isolates in Bangkok, Thailand in 2018.

D. Golparian, R. Kittiyaowamarn, P. Paopang, (…), S. Jacobsson, T. Wi, M. Unemo,

J. Antimicrob. Chemother.77 (8) 2171-2182
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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.

Services

Clinical Genomics Örebro has organized its services around focus areas including cancer, rare diseases, complex diseases and microbiology.

  • Support with project design
  • Quality control of samples prior to analysis
  • Clinical exome sequencing
  • Microbial whole-genome sequencing
  • Targeted panels (contact us for detailed information)
  • Ready-made libraries (prepared by collaborator)
  • Bioinformatics support
  • Clinical interpretation of variants

Applications

  • Cancer
  • Rare disease
  • Microbiology
  • Complex diseases
  • Informatics

Equipment

Library preparation:

  • Ion Chef
  • ACSIA
  • Various systems for QC and quantification

Sequencing systems:

  • NextSeq (Illumin)
  • MiSeq (Illumina)
  • Ion S5 (Thermo Fisher)
  • MinION (Oxford Nanopore)

Bioinformatics:

  • 48 TB Storage
  • CLC Genomics Server Software (Qiagen)
  • CLC work node 384 GB RAM, 72 cores
  • SeqSphere (Ridom GmbH)
  • Ion Reporter local server 128 GB RAM, 15 TB storage, 20 cores

Using the unit

Gisela Helenius
Platform Scientific Director
gisela.helenius@regionorebrolan.se

Bianca Stenmark
Head of Unit
bianca.stenmark@regionorebrolan.se

Last updated: 2020-06-18

Content Responsible: Scilifelab Administration()