Projects

arrayMap: Genomic array data for copy number aberration mining in cancer

arrayMap is a reference resource for mining and user friendly visualization of genomic array data sets. The website (www.arraymap.org) currently contains data from more than 40000 genomic arrays (BAC/P1, SNP, oligonucleotide ...) generated for cancer genome studies. The data is extracted eiter from reposiories (GEO, arrayExpress) or publication supplements, or directly provided by the authors of the primary studies. Details about the resource can be found in our PLoS ONE article. The resource has also been discussed in a news feature in a recent issue of the Journal of the National Cancer Institute (JNCI).

Progenetix: Oncogenomic online database and data mining software

Progenetix is the largest resource for "called" oncogenomic screening data. The website (www.progenetix.net) currently contains data from more than 29000 tumors, mostly from CGH projects. While we continuously improve on the data content, the current emphasis in on workflow development for imtegrating all accessible array CGH data resources, including raw data re-analysis.

Molecular karyotyping in Silver-Russell syndrome (SRS) patients

This project explores genomic changes in patients with growth deficiency and clinical diagnosis of "Silver-Russell syndrome", using high density SNP arrays.

  • Thomas Eggermann, Sabrina Spengler & Nadine Schoenherr, RWTH Aachen University, Aachen, Germany
  • Gerhard Binder & Michael B. Ranke, University Hospital Tübingen, Tübingen, Germany

Cytogenetic signature of Burkitt lymphomas

The translocation between the MYC oncogene region and different immunoglobuline genes in Burkitt lymphomas (BL) was one of the first specific cytogenetic changes described in a malignancy. However, this aberration is not exclusively found in BL but also occurs in other B-cell malignancies. We will attempt to determine, if from accumulated cytogenetic data in BL and other "MYC-IG" B-NHL a cytogenetic signature for BL can be extracted that matches with results from recent expression array studies.

  • Evert-Jan Boerma, Department of Pathology and Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
  • Philip Kluin, Department of Pathology and Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
  • Reiner Siebert, Institute of Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany

Computational methods for structural analysis of oncogenomic data

  • Tamer Kahveci, Department of Computer Science, University of Florida, Gainesville
  • Jun Liu, Department of Computer Science, University of Florida, Gainesville
  • Sanjay Ranka, Department of Computer Science, University of Florida, Gainesville
  • previous students: Jaaveed Mohammed, James Carter

Liu, J, J Mohammed, J Carter, S Ranka, T Kahveci, and M Baudis. 2006. Distance-based clustering of CGH data. Bioinformatics 22, no. 16: 1971-1978.

Characterization of genomic aberrations in gangliogliomas

  • Ruthild Weber & Alexander Hoischen, Department of Human Genetics, Rheinische Friedrich-Wilhelms-University, Bonn, Germany

Hoischen, A, M Ehrler, J Fassunke, M Baudis, C Landwehr, B Radlwimmer, P Lichter, J Schramm, AJ Becker, and RG Weber. 2007. Comprehensive characterization of genomic aberrations in gangliogliomas by comparative genomic hybridization (CGH), array-based CGH and interphase-FISH. accepted at Brain Pathology

Bayesian Network Analysis of Chromosomal Aberrations

  • Nadjet S. El Mehidi, Oncology Department, Royal Free and University College Medical School, London, UK
  • Sylvia Nagl, Oncology Department, Royal Free and University College Medical School, London, UK

Selected previous collaborations

Reiner Siebert and group, Kiel
Cytogenetic data mining in leukemias and lymphomas
Durig, J, S Bug, L Klein-Hitpass, T Boes, T Jons, JI Martin-Subero, L Harder, M Baudis, U Duhrsen, and R Siebert. 2007. Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32). Leukemia 21, no. 10: 2153-2163
Jo Vandesompele, Ghent
Clinical correlation of cytogenetic aberrations in childhood neuroblastoma
Vandesompele J., Baudis M., De Preter K., Van Roy N., Ambros P., Bown N., Brinkschmidt C., Christiansen H., Combaret V., Lastowska M., Nicholson J., O'meara A., Plantaz D., Stallings R., Brichard B., Van den Broecke C., De Bie S., De Paepe A., Laureys G. and Speleman F. Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. J Clin Oncol, 23(10) (2005): 2280-99. PubMed: 15800319
Alfredo Hidalgo, Mexico City
Genomic changes in cervical cancer
Hidalgo, A, M Baudis, I Petersen, H Arreola, P Pina, G Vazquez-Ortiz, D Hernandez, J Gonzalez, M Lazos, R Lopez, C Perez, J Garcia, K Vazquez, B Alatorre, and M Salcedo. 2005. Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma. BMC Cancer 1, no. 5: 77.
Xin Mao, London
Oncogenomic data mining in molecular-genetic analysis projects
Mao, X, RA Hamoudi, IC Talbot, and M Baudis. 2006. Allele-specific loss of heterozygosity in multiple colorectal adenomas: toward an integrated molecular cytogenetic map II. Cancer Genet Cytogenet 167, no. 1: 1-14.
Mao, X, RA Hamoudi, P Zhao, and M Baudis. 2005. Genetic losses in breast cancer: toward an integrated molecular cytogenetic map. Cancer Genet Cytogenet 2, no. 160: 141-151.