Genomics Core Facility
The Helse Sør-Øst Genomics Core Facility has provided state-of-the-art high-throughput genomics services to study genome structure, dynamics and function. This has been achieved by building up scientific competence and easy access to the latest advanced technology and equipment. The Core Facility offers a wide repertoire of genomics services to analyse the genome, transcriptome and epigenome, and is an Illumina certified service provider for bead array and high-throughput sequencing applications, assuring the highest level of quality for our services. During the project period of 2014, we have fulfilled all our objectives and goals. A number of new technologies and protocols have been implemented, including sequencing and analysis of low input or low quality RNA using the Illumina TruSeq Stranded Total RNA-Seq and the RNA Access kit that is currently under evaluation. Both protocols allow the analysis of poor quality RNA material e.g. from FFPE samples. The TruSeq Stranded Total RNA-Seq permits the analysis also of non polyA and long non-coding RNAs. The RNA Access protocols provide RNA expression analysis down to 10g of starting material. This new protocol is based on an in-solution capture step, similar to exome capture, limiting the expression analysis to the probe content used in the capturing step e.g. all ref seq genes. For low input DNA, we have established the Agilent SureSelect QXT protocol. This allows the analysis of exome or targeted capture panel starting from 50 ng of genomic DNA. In collaboration with the Norwegian Cancer Genomics Consortium we developed and evaluated an in solution capture extended cancer panel (Agilent SureSelect), which is composed of coding regions of 900 cancer relevant genes, including selected promoters and recurrent fusion breakpoints. This pane also includes actionable cancer genes that have been identified in large international cancer sequencing efforts like TCGA and ICGC, as well as commercial and academic clinical cancer panel from University of Washington (UW-Oncoplex) and Foundation Medicine. For high sensitive detection and validation of clinical relevant mutations, we have established amplification based protocols from Illumina and Raindance. The TruSight Tumor and Thunderbolts panel can analyse 26 and 50 genes (hotspots) frequently mutated in solid tumours, respectively. These panels have been tested using DNA isolated from FFPE material and down to 20 ng of input material. The Thunderbolts panel from Raindance has also been tested for analysis of cell-free DNA in plasma and serum for detection of somatic mutation in circulation tumour DNA. Additional novel protocols for targeted resequencing are constantly being tested and adopted. The corresponding bioinformatics analysis pipelines have been further developed, and bioinformatics competence expanded. We have also implemented a Laboratory Information Management System (LIMS) to provide end-to-end workflow tracking and integration for further quality assurance of our services. The Genomics Core Facility has started a formal collaboration with the Norwegian Sequencing Centre to provide the best sequencing services to our users. The Genomics Core Facility will have a role as an specialised competence centre for cancer related projects. More information at oslo.genomics.no
The Genomics Core Facility has contributed to a large number of scientific project, many of them contributing to innovation. As a policy, the Core Facility does not request authorship or ownership for the services provided and has not been directly involved in innovation. Due to the difficulty of identifying all publications using data generated from our services, an incomplete list of publications generated from our services is included. In addition, a number of our services have contributed to the identification of novel candidate biomarkers associated with disease, as well as new molecular signatures. A subset of these candidate biomarkers are currently being investigated further and validated in extended panels of samples. The Genomics Core Facility provides sequencing infrastructure for the National personalised cancer medicine initiatives financed by NFR. Our Core Facility is leading the largest sequencing project in Norway, sequencing thousands of exomes of cancer patients. The head of the core facility is the responsible for sequencing technology aspects of the Norwegian Cancer Genomics Consortium running this project. This project has the potential of dramatically changing cancer treatment by targeting tumours based on their genetic makeup. Overall, the Genomics Core Facility has through its services contributed to the national and international competiveness of many research groups at Helse Sør-Øst.
The architecture and evolution of cancer neochromosomes.
Cancer Cell 2014 Nov 10;26(5):653-67. Epub 2014 nov 10
Performance comparison of four exome capture systems for deep sequencing.
BMC Genomics 2014;15():449. Epub 2014 jun 9
The regulatory landscape of osteogenic differentiation.
Stem Cells 2014 Oct;32(10):2780-93.
Reexpression of LSAMP inhibits tumor growth in a preclinical osteosarcoma model.
Mol Cancer 2014;13():93. Epub 2014 apr 28
Generation and characterization of an immortalized human mesenchymal stromal cell line.
Stem Cells Dev 2014 Oct 1;23(19):2377-89. Epub 2014 jun 30
Validation of miRNA genes suitable as reference genes in qPCR analyses of miRNA gene expression in Atlantic salmon (Salmo salar).
BMC Res Notes 2014;8(1):945. Epub 2014 des 23
Transcriptional profiling of adult neural stem-like cells from the human brain.
PLoS One 2014;9(12):e114739. Epub 2014 des 16
Biomarkers of histone deacetylase inhibitor activity in a phase 1 combined-modality study with radiotherapy.
PLoS One 2014;9(2):e89750. Epub 2014 feb 25
Implications of Targeted Genomic Disruption of ß-Catenin in BxPC-3 Pancreatic Adenocarcinoma Cells.
PLoS One 2014;9(12):e115496. Epub 2014 des 23
HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network.
EMBO Mol Med 2014 May;6(5):651-61. Epub 2014 mai 1
The ETS family member GABPa modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer.
Nucleic Acids Res 2014 Jun;42(10):6256-69. Epub 2014 apr 21
Brief report: importance of SOX8 for in vitro chondrogenic differentiation of human mesenchymal stromal cells.
Stem Cells 2014 Jun;32(6):1629-35.
The p.R482W substitution in A-type lamins deregulates SREBP1 activity in Dunnigan-type familial partial lipodystrophy.
Hum Mol Genet 2015 Apr 1;24(7):2096-109. Epub 2014 des 18