High-Throughput sequencing

High-throughput sequencing allows the analysis, at single based resolution, of the genome, transcriptome and epigenome. The Genomics Core Facility has established a large portfolio of protocols to study variation, somatic events, transcriptional changes and DNA-protein interaction, among others. With both the high capacity HiSeq sequencer and the MiSeq personal sequencer from Illumina, the Genomics Core Facility can provide adjustable set-ups for both larger and smaller projects. Due to the large diversity of applications and protocols prices vary considerably depending on different factors. Please contact the Genomics Core Facility for specific pricing and an advisory meeting.
 
Exome sequencing
Provides sequencing information for all protein coding genes in a genome (approximately 2% of the genome).  The Genomics Core Facility has established different protocols for exome sequencing. Today most of our services are performed using the Agilent SureSelect Human All Exon v5 in-solution capturing system, which combines good performance, updated content and price. Service for additional Agilent, Illumina and Nimblegen exome capture systems can be performed for human and other species.
 
Cancer panels
Cancer panels deliver a cost effective alternative for targeted resequencing of specific regions of the genome. We offer a number of cancer related panels from different providers.
 
  • Illumina TruSight Tumor is an amplicon-based panel optimized for the detection of low frequent somatic mutations in tumour samples from FFPE and fresh frozen material. The panel analyses mutations in 26 genes frequency mutated in solid human cancers.
  • Illumina TruSight Myeloid panel uses expert-defined content to identify somatic mutations in myeloid malignancies (AML, MDS, MPN, CML, CMML, JMML), by analyzing 15 full genes (exons only) and 39 additional genes where oncogenic hotspots are covered.
  • Illumina TruSight Cancer panel examines 94 genes associated both with common and rare human cancer.
  • Raindance Thunderbolts cancer panels offer a fast, accurate and low-cost target enrichment system for analyzing somatic mutations in fresh frozen and FFPE tumour samples, as well as liquid biopsies. Two panels are available, a Solid Cancer panel targeting 50 genes frequently mutated in solid tumours and a Myeloid panel targeting 49 genes recurrently affected in AML, MDS, MPD and myeloma. Custom panels will soon be available.
 
Extended Cancer panel
We have developed a custom in-solution SureSelect capturing extended cancer panel that detects genetic changes in 900 cancer related genes, including a limited number of common gene fusions. The panel content was developed based on mutational information of large international sequencing projects (TCGA and ICGC), as well as academic clinical sequencing panels and in collaboration with the Norwegian Cancer Genomics Consortium.
 
Targeted Resequencing
The TruSeq Custom Amplicon platform provides a fully customizable, amplicon-based assay for targeted resequencing. Researcher can define up to 1536 amplicons per reaction, covering their region of interest, and examining up to 650 kb.
 
RNA-Seq
RNA sequencing provides transcriptome profiling, capable of determining expression levels, transcriptome structure and fusion genes among others. The following protocols are established at the Genomics Core Facility
 
  • Illumina TruSeq Stranded mRNA protocol for sequencing of the protein-coding transcripts.
  • Illumina Total Stranded RNA protocol for sequencing of protein-coding and long non-coding RNAs above 150 bp (available for human, rat, mouse, yeast, E. coli and Globin depletion for blood samples).
  • Illumina TruSeq RNA Access protocol for sequencing of protein-coding transcripts for low quality samples (degraded samples, FFPE samples) and very low inputs of starting material.
 
ChIP-Seq
Chromatin immunoprecipitation combined with sequencing allows investigations of DNA-protein interactions genome-wide. This technology can be used to study chromatin states and transcription factor binding among others. The user should provide immunoprecipitated DNA and ensure the high level of specificity necessary for this experiments.
 
Small RNA-Seq
Small RNA analysis is a powerful application for the discovery and profiling of microRNAs and other non-coding small RNAs for any organism, without prior genome annotation. The TruSeq Small RNA protocol enables the most accurate detection and quantification of small RNA sequences.
 
Aditional protocols
The Genomics Core Facility can provide whole genome sequencing of small organisms as viruses or bacteria, and custom made libraries compatible with the Illumina’s sequencing system.
 
 
Contact us for a meeting to discuss the options we can provide.

 
 
 
 
 
 


News

Feb 24, 2016

The HiSeq 4000 build upon the existing HiSeq 2500 platform using the new HiSeq X patterned flow cell technology, providing unparalleled speed and performance. The dual-flow cell HiSeq 4000 System delivers the highest throughput and lowest price per sample across multiple applications. The new sequencer will provide users will faster turnaround time (run time is 3 days compared to 6-11 days in HiSeq 2500) and higher quality, more data per run and longer reads (150 bp paired-end).

Feb 15, 2016

The Oslo University Hospital Genomics and Bioinformatics Core Facilities will relocate to the new Oslo Cancer Cluster Innovation park to colocalise with the section for Molecular Pathology. The colocalisation will facilitate the technology and competence transfer from our genomics environment to accelerate the implementation of high-throughput sequencing for clinical stratification of cancer patients.


Contact Information:

oslo<at>genomics.no 

Visiting address:
Genomics Core Facility (Room 3-F8-04)
Department of Core facilities
Institute for Cancer Research
New OCCI-building 
 
Norwegian Radium Hospital 
Ullernchaussen 66, Lamell 3, 2B 
NO-0379 Oslo, NORWAY

+47 - 9183 2772 Laboratory
+47 - 9183 3425 Office

Head of Core Facility
Leonardo A. Meza-Zepeda, Dr. philos.

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