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Hacking the Cancer Genome

Background:

Recent advances in DNA sequencing technology allow today the sequencing of whole human genomes in just a few days. These advances will make possible in a near future, the systematic access to complete DNA sequence of cancer and normal cell genomes. The full genome sequence of a cancer sample creates several hundreds billions nucleotides of genomic information that can be used to assembly and compare to a reference genome. In order to detect tumor specific rearrangements and mutations that are involved in cancer development and progression, bioinformatic tools for reconstructing the genome and integration of different types of genome-wide data are required. New algorithms and statistical approaches for analysis of sequencing data are needed to facilitate the analysis and improve our understanding of cancer genomes.

 

Master project:

Our group has for many years studied the biology and genetics of malignant bone tumors. As part of the International Cancer Genome Consortium, we are generating whole genome sequencing data of a large number of bone cancer clinical samples. The first part of the project is to participate on the development of new bioinformatics pipelines and tools for high-throughput sequencing data analysis for cancer genomes. This part will involve the use of various recent algorithms based on:

- Burrow-Wheeler transform for short sequence mapping on reference genome

- De Bruijn graph for genome assembly

- Bayesian statistics for point mutation calling

The Mater student will be part of a bioinformatics team working on the detection of cancer specific aberrations, among them

  • Genomic rearrangement, i.e. genomic translocation, inversion, deletion, insertion and duplication,
  • Point mutation and small insertion/deletion
  • Gene expression analysis
  • Epigenetic analysis of the methylome

The second part of the project will involve the development of pipelines to integrate multilevel data generated in the first part of the master project. Integration will be used to annotate and prioritize the genomics events frequently seen within bone tumors.  

 

Working environment:

Our research group combines laboratory and bioinformatic approaches to better understand the biology of cancer cells. We offer state of the art facilities in our brand new research building located at The Norwegian Radium Hospital, and an exciting, stimulating and young environment. The master student will be part of a dynamic and multidisciplinary research group with several PhD students and postdocs working on different aspects of cancer genomics and biology. The group has collaboration partners both nationally and abroad.  Our group also collaborates closely with the Bioinformatic Core Facility lead by Prof. E. Hovig.

 

For more information please contact Dr. Mohammed-Amin Madoui  (amin@genomics.no)
 

Publisert 10. aug. 2012 08:43 - Sist endret 21. sep. 2013 20:43

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