Design, analysis and applications of custom high-density oligonucleotide microarrays
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AbstractNot until recently have custom made high-density oligonucleotide microarrays been available at an affordable price. The aim of this thesis was to design microarrays and analysis algorithms for DNA repair and DNA damage detection, and to apply the methods in real experiments. Thomassen et al. have used their custom designed whole genome-tiling microarrays for detection of transcriptional changes in Escherichia coli after exposure to DNA damageing reagents. The transcriptional changes in E. coli treated with UV light or the methylating reagent MNNG were shown to be larger and to include far more genes than previously reported. To optimize the data analysis for the custom made arrays, Thomassen and coworkers designed their own normalization and analysis algorithms, and showed these more suitable than established methods that are currently applied on custom tiling arrays. Among other findings several novel stress-induced transcripts were detected, of which one is predicted to be a UV-induced short transmembrane protein. Additionally, no upregulation of the previously described UV-inducible aidB is shown. In the MNNG study several genes are shown as downregulated in response to DNA damage although having upstream regulatory sequences similar to the established LexA box A and B. This indicates that the LexA regulon also might control gene repression and that the box A and B sequence can not alone answer for the LexA controlled gene regulation. Thomassen et al. have also custom designed a microarray for oncogenic fusion gene detection. Cancer specific fusion genes are often used to subgroup cancers and to define the optimal treatment, but currently the laboratory detection procedure is both laborious and tedious. In a blinded study on six cancer cell lines proof of principle was shown by detection of six out of six positive controls. The design and analysis methods for this microarray are now being refined to make a diagnostic fusion gene detection tool.
List of papers
|1 Gard O.S. Thomassen, Alexander D. Rowe, Karin Lagesen, Jessica M. Lindvall, and Torbjørn Rognes. Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. PLoS One 2009 Jun 17;4(6):e5943. The published version of this paper is available at: https://doi.org/10.1371/journal.pone.0005943|
|2 Gard O.S. Thomassen, James A. Booth, Alexander D. Rowe, Ragnhild Weel-Sneve, Karin Lagesen, Knut I. Kristiansen, Magnar Bjørås, Torbjørn Rognes, and Jessica M. Lindvall. Transcriptome analysis of MNNG treated Escherichia coli reveals a widespread transcription of coding and non-coding RNA. Manuscript submitted.|
|3 Gard O.S. Thomassen, Ragnhild Weel-Sneve, Alexander D. Rowe, James A. Booth, Jessica M. Lindvall, Karin Lagesen, Knut I. Kristiansen, Magnar Bjørås, and Torbjørn Rognes. Tiling array analysis of UV treated Escherichia coli predicts novel differentially expressed small peptides. Manuscript submitted.|
|4 Rolf I. Skotheim, Gard O.S. Thomassen, Marthe Eken, Guro E. Lind, Francesca Micci, Franclim R. Ribeiro, Nuno Cerveira, Manuel R. Teixeira, Sverre Heim, Torbjørn Rognes, and Ragnhild A. Lothe. A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Molecular Cancer 2009, 8:5. The published version of this paper is available at: https://doi.org/10.1186/1476-4598-8-5|