Gard Thomassen

• Samarakoon, Pubudu Saneth; Fournous, Ghislain; Hansen, Lars Thomas; Wijesiri, Ashen; Zhao, Sen & A, Rodriguez Alex [Vis alle 12 forfattere av denne artikkelen] (2025). Benchmarking accelerated next-generation sequencing analysis pipelines. Bioinformatics Advances. 5(1), s. 1–13. doi: 10.1093/bioadv/vbaf085. Fulltekst i vitenarkiv Vis sammendrag

  Motivation Industry-standard central processing unit (CPU)-based next-generation sequencing (NGS) analysis tools have led to longer runtimes, affecting their utility in time-sensitive clinical practices and population-scale research studies. To address this, researchers have developed accelerated NGS platforms like DRAGEN and Parabricks, which have significantly reduced runtimes—from days to hours. However, these studies have evaluated accelerated platforms independently without sufficiently assessing computational resource usage or thoroughly investigating speedup scalability, a gap our study is designed to address. Results Corroborating previous studies, accelerated pipelines demonstrated shorter runtimes than CPU-only approaches, with Parabricks-H100 demonstrating the highest speedups, followed by DRAGEN. In mapping, DRAGEN outperformed Parabricks (L4 and A100) and matched H100 speedups. Parabricks (A100 and H100) variant calling demonstrated higher speedups than DRAGEN. Moreover, DRAGEN and Parabricks-H100 mapping showed positive trends in the coverage-based scalability analysis, while other configurations failed to scale effectively. Our profiler analysis provided new insights into the relationships between Parabricks’ performances and resource usage patterns, revealing its potential for further improvements. Our findings and cost comparison help researchers select accelerated platforms based on coverage needs, timeframes, and budget, while suggesting optimization strategies.

• Øvrelid, Egil; Bygstad, Bendik & Thomassen, Gard (2021). TSD: A Research Platform for Sensitive Data. Procedia Computer Science. 181, s. 127–134. doi: 10.1016/j.procs.2021.01.112. Fulltekst i vitenarkiv Vis sammendrag

  Digitalisation has led to a strong increase of research data, but most of these data are managed in unsatisfactory ways, and research data management has been characterized as a “wicked problem”. Several research data platforms have been launched, but security and privacy issues remain. Our research question is how can a research platform for sensitive data be built and used? Based on platform research, we propose a framework to analyze requirements. Our empirical evidence is a research platform called TSD, i.e. a platform for sensitive data. We analyze the development of TSD and offer two contributions; first, we discuss a framework to understand the architectural requirements for a research data platform, and second, we show how a research platform can be developed through a process of platformization.

• Aarestrup, FM; Albeyatti, A; Armitage, W; Auffray, C; Augello, L & Balling, Rudi [Vis alle 52 forfattere av denne artikkelen] (2020). Towards a European health research and innovation cloud (HRIC). Genome Medicine. 12(18). doi: 10.1186/s13073-020-0713-z. Fulltekst i vitenarkiv Vis sammendrag

  The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

• Lorenz, Susanne; Barøy, Tale; Sun, Jinchang; Nome, Torfinn; Vodak, Daniel & Bryne, Jan Christian [Vis alle 21 forfattere av denne artikkelen] (2016). Unscrambling the genomic chaos of osteosarcoma reveals extensive transcript fusion, recurrent rearrangements and frequent novel TP53 aberrations. OncoTarget. 7(5), s. 5273–5288. doi: 10.18632/oncotarget.6567. Fulltekst i vitenarkiv Vis sammendrag

  In contrast to many other sarcoma subtypes, the chaotic karyotypes of osteosarcoma have precluded the identification of pathognomonic translocations. We here report hundreds of genomic rearrangements in osteosarcoma cell lines, showing clear characteristics of microhomology-mediated break-induced replication (MMBIR) and end-joining repair (MMEJ) mechanisms. However, at RNA level, the majority of the fused transcripts did not correspond to genomic rearrangements, suggesting the involvement of trans-splicing, which was further supported by typical trans-splicing characteristics. By combining genomic and transcriptomic analysis, certain recurrent rearrangements were identified and further validated in patient biopsies, including a PMP22-ELOVL5 gene fusion, genomic structural variations affecting RB1, MTAP/CDKN2A and MDM2, and, most frequently, rearrangements involving TP53. Most cell lines (7/11) and a large fraction of tumor samples (10/25) showed TP53 rearrangements, in addition to somatic point mutations (6 patient samples, 1 cell line) and MDM2 amplifications (2 patient samples, 2 cell lines). The resulting inactivation of p53 was demonstrated by a deficiency of the radiation-induced DNA damage response. Thus, TP53 rearrangements are the major mechanism of p53 inactivation in osteosarcoma. Together with active MMBIR and MMEJ, this inactivation probably contributes to the exceptional chromosomal instability in these tumors. Although rampant rearrangements appear to be a phenotype of osteosarcomas, we demonstrate that among the huge number of probable passenger rearrangements, specific recurrent, possibly oncogenic, events are present. For the first time the genomic chaos of osteosarcoma is characterized so thoroughly and delivered new insights in mechanisms involved in osteosarcoma development and may contribute to new diagnostic and therapeutic strategies.

• Booth, James A.; Thomassen, Gard O Sundby; Rowe, Alexander D.; Weel-Sneve, Ragnhild; Lagesen, Karin & Kristiansen, Knut Ivan [Vis alle 9 forfattere av denne artikkelen] (2013). Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Scientific Reports. 3. doi: 10.1038/srep03053. Fulltekst i vitenarkiv Vis sammendrag

  The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.

• Løvf, Marthe; Thomassen, Gard O Sundby; Mertens, Fredrik; Cerveira, Nuno; Teixeira, Manuel & Lothe, Ragnhild A [Vis alle 7 forfattere av denne artikkelen] (2013). Assessment of Fusion Gene Status in Sarcomas Using a Custom Made Fusion Gene Microarray. PLOS ONE. 8(8). doi: 10.1371/journal.pone.0070649. Fulltekst i vitenarkiv
• Nome, Torfinn; Thomassen, Gard O Sundby; Bruun, Jarle; Ahlquist, Terje Cruickshank; Bakken, Anne Cathrine & Hoff, Andreas Midbøe [Vis alle 17 forfattere av denne artikkelen] (2013). Common fusion transcripts identified in colorectal cancer cell lines by high throughput RNA sequencing. Translational Oncology. ISSN 1944-7124. 6(5), s. 546–553. doi: 10.1593/tlo.13457. Fulltekst i vitenarkiv
• Celestino, Ricardo; Sigstad, Eva; Løvf, Marthe; Thomassen, Gard O Sundby; Kotanska-Grøholt, Krystyna & Jørgensen, Lars Hilmar [Vis alle 13 forfattere av denne artikkelen] (2012). Survey of 548 oncogenic fusion transcripts in thyroid tumors supports the importance of the already established thyroid fusions genes. Genes, Chromosomes and Cancer. ISSN 1045-2257. 51(12), s. 1154–1164. doi: 10.1002/gcc.22003. Fulltekst i vitenarkiv
• Løvf, Marthe; Thomassen, Gard O Sundby; Bakken, Anne Cathrine; Celestino, Ricardo; Fioretos, Thoas & Lind, Guro Elisabeth [Vis alle 8 forfattere av denne artikkelen] (2011). Fusion Gene Microarray Reveals Cancer Type-Specificity Among Fusion Genes. Genes, Chromosomes and Cancer. ISSN 1045-2257. 50(5), s. 348–357. doi: 10.1002/gcc.20860. Fulltekst i vitenarkiv
• Thomassen, Gard O Sundby; Sneve, Ragnhild; Rowe, Alexander D.; Booth, James; Lindvall, Jessica M. & Lagesen, Karin [Vis alle 9 forfattere av denne artikkelen] (2010). Tiling Array Analysis of UV Treated Escherichia coli Predicts Novel Differentially Expressed Small Peptides. PLOS ONE. 5(12). doi: 10.1371/journal.pone.0015356. Fulltekst i vitenarkiv Vis sammendrag

  Background Despite comprehensive investigation, the Escherichia coli SOS response system is not yet fully understood. We have applied custom designed whole genome tiling arrays to measure UV invoked transcriptional changes in E. coli. This study provides a more complete insight into the transcriptome and the UV irradiation response of this microorganism. Results We detected a number of novel differentially expressed transcripts in addition to the expected SOS response genes (such as sulA, recN, uvrA, lexA, umuC and umuD) in the UV treated cells. Several of the differentially expressed transcripts might play important roles in regulation of the cellular response to UV damage. We have predicted 23 novel small peptides from our set of detected non-gene transcripts. Further, three of the predicted peptides were cloned into protein expression vectors to test the biological activity. All three constructs expressed the predicted peptides, in which two of them were highly toxic to the cell. Additionally, a remarkably high overlap with previously in-silico predicted non-coding RNAs (ncRNAs) was detected. Generally we detected a far higher transcriptional activity than the annotation suggests, and these findings correspond with previous transcription mappings from E. coli and other organisms. Conclusions Here we demonstrate that the E. coli transcriptome consists of far more transcripts than the present annotation suggests, of which many transcripts seem important to the bacterial stress response. Sequence alignment of promoter regions suggest novel regulatory consensus sequences for some of the upregulated genes. Finally, several of the novel transcripts identified in this study encode putative small peptides, which are biologically active.

• Thomassen, Gard O Sundby; Rowe, Alexander D.; Lagesen, Karin; Lindvall, Jessica Margareta & Rognes, Torbjørn (2009). Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays. PLOS ONE. 4(6). doi: 10.1371/journal.pone.0005943. Fulltekst i vitenarkiv Vis sammendrag

  Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome's complexity and sequence composition, need to be considered in the design to ensure a high quality microarray. Secondly, since tiling projects today very often exceed the limits of conventional array-experiments, researchers cannot use established computer tools designed for commercial arrays, and instead have to redesign previous methods or create novel tools. Principal Findings Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, respectively, as well as the use of multiple copies of control probe-sets on tiling microarrays. Furthermore, a novel normalisation and background estimation procedure for tiling arrays is presented along with a method for array analysis focused on detection of short transcripts. The design, normalisation and analysis methods have been applied in various experiments and several of the detected novel short transcripts have been biologically confirmed by Northern blot tests. Conclusions Tiling-arrays are becoming increasingly applicable in genomic research, but researchers still lack both the tools for custom design of arrays, as well as the systems and procedures for analysis of the vast amount of data resulting from such experiments. We believe that the methods described herein will be a useful contribution and resource for researchers designing and analysing custom tiling arrays for both bacteria and higher organisms. © 2009 Thomassen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

• Skotheim, Rolf Inge; Thomassen, Gard O Sundby; Eken, Marthe; Lind, Guro Elisabeth; Micci, Francesca & Ribeiro, FR [Vis alle 11 forfattere av denne artikkelen] (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Molecular Cancer. 8. doi: 10.1186/1476-4598-8-5. Fulltekst i vitenarkiv Vis sammendrag

  Background The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings. Results We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies. Conclusion This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.

• Thomassen, Gard O. S.; Rosok, Oystein & Rognes, Torbjørn (2006). Computational prediction of microRNAs encoded in viral and other genomes. Journal of Biomedicine and Biotechnology. ISSN 1110-7243. doi: 10.1155/JBB/2006/95270. Fulltekst i vitenarkiv Vis sammendrag

  We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it seems that these small regulators have a more important role than has been previously thought. Most microRNAs have been detected by cloning and Northern blotting, but experimental methods are biased towards abundant microRNAs as well as being time-consuming. Computational detection methods must therefore be refined to serve as a faster, better, and more affordable method for microRNA detection. We also present data from a small study investigating the problems of computational miRNA prediction. Our findings suggest that the prediction of microRNA precursor candidates is fairly easy, while excluding false positives as well as exact prediction of the mature microRNA is hard. Finally, we discuss possible improvements to computational microRNA detection.

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• Øvrelid, Egil; Bygstad, Bendik; Breivik, Jarle; Nerland, Monika Bærøe; Westbye, Hilde & Kjekshus, Lars Erik [Vis alle 7 forfattere av denne artikkelen] (2021). Hybridundervisning: Nødvendig nyskapning eller digitalisering på ville veier? Fulltekst i vitenarkiv Vis sammendrag

  Begrepet hybridundervising har fått en sentral rolle i diskusjonen om digitalisering av høyere utdanning, spesielt under den pågående pandemien. Hybridundervising kan i videste forstand beskrives som en blanding av ulike undervisningsformer, men kan også tolkes mer spesifikt. Det vil si som undervisningsaktiviteter hvor noen studenter og lærere deltar digitalt, mens andre er fysisk tilstede. Denne utviklingen byr på store teknologiske, pedagogiske, organisatoriske og økonomiske utfordringer. I den videre utviklingen av høyere utdanning vil hybridundervisning være et sentralt tema, hvor digitaliseringsskeptikere og digitaliseringsoptimister står mot hverandre.

• Stangeland, Elin; Soligard, Lars; Thomassen, Gard O Sundby; Bianchini, Federico & Bösl, Korbinian (2020). Data Management Planning workshop for Life Science Projects. Fulltekst i vitenarkiv
• Øvrelid, Egil; Bygstad, Bendik & Thomassen, Gard O Sundby (2020). Tsd: A Research Platform For Sensitive Data. Fulltekst i vitenarkiv
• Øvrelid, Egil; Bygstad, Bendik & Thomassen, Gard O Sundby (2020). TSD: A GENERATIVE RESEARCH PLATFORM IN THE AGE OF THE PANDEMICS. Fulltekst i vitenarkiv
• Stansberg, Christine; Willassen, Nils P; Thomassen, Gard O Sundby; Hovig, Johannes Eivind & Jonassen, Inge (2020). How open databases turn out to be crucial in the fight against Covid-19. NBS-nytt. ISSN 0801-3535. 4, s. 38–43. Fulltekst i vitenarkiv
• Eide, Hans A; Fotland, Margaret Louise; Kvale, Live Håndlykken; Stangeland, Elin; Stølen, Svein & Thomassen, Gard O Sundby [Vis alle 7 forfattere av denne artikkelen] (2015). Sharing and Storing Research Data A 4-level model of the Data flow. Fulltekst i vitenarkiv
• Nakken, Sigve; Vodák, Daniel; Fournous, Ghislain; Thomassen, Gard O Sundby & Hovig, Johannes Eivind (2013). Big challenges in personalized cancer medicine. META. ISSN 1890-1956. s. 8–12. Fulltekst i vitenarkiv Vis sammendrag

  DNA sequencing technology has recently made huge leaps, making it possible to characterize all genetic changes in any cancer. Robust bioinformatics solutions for both safe data storage, as well as processing, interpretation, and sharing, are critically important before this layer of patient information could be useful to the clinic. Here, we will provide an introduction to the field of bioinformatics in personalized cancer medicine, and specifically highlight the need for computation and storage resources at a local and national level.

• Skotheim, Rolf Inge; Nome, Torfinn; Thomassen, Gard O Sundby; Johannessen, Bjarne; Bakken, Anne Cathrine & Bruun, Jarle [Vis alle 10 forfattere av denne artikkelen] (2012). Identification of Fusion Transcripts in Colorectal Cancer by Combined RNA-seq and Exon Microarray Analyses. European Journal of Cancer. ISSN 0959-8049. 48, s. S121–S121. Fulltekst i vitenarkiv
• Eike, Morten Christoph; Lærum, Hallvard; Hughes, Timothy; Håndstad, Tony; Bremer, Sara & Bergan, Stein [Vis alle 10 forfattere av denne artikkelen] (2012). GenAP: a platform for clinical genetic analysis of high-throughput sequencing data. Fulltekst i vitenarkiv Vis sammendrag

  The introduction of high-throughput sequencing (HTS) into clinical practice poses great challenges in terms of analytic resources, integration and data security. The project Norwegian clinical genetic Analysis Platform (genAP) was initiated as a response to these challenges, aiming to establish a centralised infrastructure for secure storage and analysis of human sequencing data, with possibilities for disseminated clinical use. GenAP is a collaborative project between Oslo University Hospital and the University of Oslo, with implementation of the system in a high-performance computing environment. As part of this project, we are in the process of establishing pilot HTS pipelines for a set of clinical packages, each with a defined set of targeted genes. The pilots cover diagnostic, prognostic and pharmacogenetic areas, including cardiomyopathies, breast cancer and tacrolimus dosage, respectively. Initially, the pipelines involve data for a limited set of candidate genes, but the system will be scalable to exome and whole-genome data for a large number of patients. To reduce the workload associated with manual analysis, we have sought to achieve a high degree of automation, including variant annotation and quality control, filtering and prioritisation based on public resources, identification of previously classified variants, and standardisation of report information structure for integration with existing medical journal systems. The pilot phase includes comparing the performance of HTS to conventional methods, building a database of genetic variants adapted to our patient populations and real-world testing using collaborating clinicians. The experiences gained will be used to expand to other clinical packages, and the ultimate goal is to introduce the system in the clinic. Complementing the genetic, bioinformatic and clinical issues, the project also addresses legal, ethical and organizational issues encountered when HTS is deployed in large scale clinical decision making. This presentation will demonstrate the overall architecture of our system and present initial experiences with the pilot systems.

• Eike, Morten Christoph; Lærum, Hallvard; Hughes, Timothy; Bremer, Sara; Bergan, Stein & Thomassen, Gard O Sundby [Vis alle 9 forfattere av denne artikkelen] (2012). A national platform for clinical genetic analysis of high-throughput sequencing data in Norway. Fulltekst i vitenarkiv Vis sammendrag

  The introduction of high-throughput sequencing (HTS) into clinical practice poses great challenges in terms of analytic resources, integration and data security. The project Norwegian clinical genetic Analysis Platform (genAP) was initiated as a response to these challenges, aiming to establish a centralised infrastructure for secure storage and analysis of human sequencing data that allows for disseminated clinical use. GenAP is a collaborative project between Oslo University Hospital and the University of Oslo, with implementation of the system in an established high-performance computing environment. As part of this project, we are in the process of establishing pilot HTS pipelines for a set of clinical packages, each with a defined set of targeted genes. The pilots cover diagnostic, prognostic and pharmacogenetic areas, including cardiomyopathies, breast cancer and tacrolimus dosage, respectively. Initially, the pipelines involve targeted capture and resequencing, but the system will be scalable to exome and genome data for a large number of patients. To reduce the workload associated with manual analysis, we have sought to achieve a high degree of automation, including variant annotation and quality control, filtering based on public resources, identification of previously classified variants, and standardization of report information structure for integration with existing patient journal systems. The pilot phase includes comparing the performance of HTS to conventional methods, building a database of genetic variants adapted to our patient populations and real-world testing using collaborating clinicians. The experiences gained will be used to expand to other clinical packages, and the ultimate goal is to introduce the pipelines for widespread use in the clinic. Complementing the genetic, bioinformatic and clinical issues, the project also addresses legal, ethical and organizational issues encountered when HTS is deployed in large scale clinical decision making. This presentation will demonstrate the overall architecture of our system and present initial experiences with the pilot systems.

• Løvf, Marthe; Thomassen, Gard O Sundby; Lind, Guro Elisabeth; Lothe, Ragnhild A & Skotheim, Rolf Inge (2010). An oligo microarray design for detection of known and putative oncogenic fusion transcripts. European Journal of Cancer. ISSN 0959-8049. 8(5), s. 199–199. Fulltekst i vitenarkiv
• Skotheim, Rolf Inge; Eken, Marthe; Thomassen, Gard O Sundby; Lind, Guro Elisabeth & Lothe, Ragnhild A (2009). A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. European Journal of Cancer. ISSN 0959-8049. 7(2), s. 147–148. Fulltekst i vitenarkiv
• Thomassen, Gard O Sundby & Rognes, Torbjørn (2010). Design, analysis and applications of custom high-density oligonucleotide microarrays. Universitetet i Oslo. Fulltekst i vitenarkiv Vis sammendrag

  Not 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.

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