High-Throughput sequencing

High-throughput sequencing allows the analysis, at the single based resolution, of the genome, transcriptome, and epigenome. The Genomics Core Facility has established a large portfolio of protocols to study genome variation, somatic events, transcriptional changes, and DNA-protein interaction, among others. With the full line of Illumina sequencers, the Genomics Core Facility provides 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 Core Facility for specific pricing and an advisory meeting.
 
Exome sequencing
It provides sequencing information for all protein-coding genes in a genome (approximately 2% of the genome).  We have established different protocols for exome sequencing. Today most of our services are performed using the Twist CoreExome+RefSeq in-solution capturing system, which combines performance, updated content, and price. Service for additional Agilent, Illumina, and TWIST exome capture systems can be performed for humans and other species.
 
Whole genome sequencing
Standard and PCR-free Whole Genome Sequencing protocols are available using different library construction protocols. Various coverages are offered to service different needs, from Ultra-Low Pass WGS, to study copy number changes in tissue and blood (liquid biopsies), to high-coverage tumour normal sequencing for cancer. 
 
Cancer panels & Liquid Biopsies
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 Oncology 500 is a capture-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 523 genes frequency mutated in solid human cancers, as well as microsatellite instability (MSI) and tumor mutational burden (TMB).
  • AmpliSeq for Illumina offers a highly multiplexed polymerase chain reaction (PCR)-based workflow for use with targets ranging from a few to hundreds in a single run. Multiple ready-to-use panels are available, as well as custom solutions.
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  • ArcherDx LIQUIDPlex panel offers predesigned and custom panels for sensitive detection of circulating tumour DNA (ctDNA) in body fluids.   
 
Extended Cancer panel
We have developed a custom in-solution Agilent 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.
 
 
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 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 exome protocol for sequencing of protein-coding transcripts for low-quality samples (degraded samples, FFPE samples) and very low inputs of starting material.
  • Lexogen QuantSeq 3' mRNA-Seq protocol provides a cost-effective, genome-wide analysis of gene expression. QuantSeq protocol is suitable for low input (1 ng total RNA) and FFPE samples.
 
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 a high level of specificity necessary for these 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.
 
Additional protocols
The Genomics Core Facility can provide whole-genome sequencing of small organisms as viruses or bacteria, and custom-made libraries compatible with Illumina’s sequencing system.
 
 
Contact us for a meeting to discuss the options we can provide.

 
 
 
 


News

Jun 3, 2021

The Genomcis Core Facility will not be accepting new sample submissions over the summer break. Deadline for submission is 1 PM on Friday 9th of July. We will reopen again from Monday 2nd of August. The sequencing of existing projects will continue, although turnaround times may be longer than usual.

We wish all our users a good summer

Feb 8, 2021

The Genomics and Bioinformatics Core Facilities resumes the drop-in hour every Wednesday between  2:30-3:30 PM. Follow the Zoom link below.


Contact Information:

Genomics@rr-research.no

Unit Leader Core Facility
Susanne Lorenz, PhD

Susanne.Lorenz@rr-research.no

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

Leonardo.A.Meza-Zepeda@rr-research.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

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