Service Project S02
Cancer genomics, sequencing, informatics and data integration platform
klaus.kuhn@tum.de(link sends e-mail)
Homepage(link is external)
roland.rad@tum.de(link sends e-mail)
Homepage(link is external)
Given the increasing importance of genomic analyses in basic and translational cancer research and the phenomenal developments in genetic engineering and genetic screening technologies, such as CRISPR/Cas9, transposons and RNAi, it will be a central requirement for the consortium to implement sequencing and bioinformatics, as well as data integration capabilities. S02 will be a platform for cancer genomic analyses that will provide state of the art sequencing and bioinformatics support, covering a broad spectrum of applications, including whole-exome/genome sequencing, Chip-Seq, targeted SNP resequencing, RNA-Seq, transposon insertion site sequencing, multiplexed amplicon-based sequencing of CRISPR/Cas9 targets or viral integration sites and others. All projects within this CRC will require sequencing and bioinformatics support.
A second major aim of S02 will be to characterize the genomic landscapes of mouse PDAC cell line resources and human PDAC organoid collections assembled within this consortium; and to integrate these genomic data with high-throughput drug screening, proteomic, histopathologic, clinical/prognostic information and other phenotypic data that will be produced in the different projects or collected in the clinic. These resources will be a critical experimental platform that will be extensively used by CRC members to dissect the molecular basis of various phenotypes. All data will be curated and made available through a user-friendly and intuitive biomedical data analytics and visualization platform (tranSMART, cBioPortal) that will specifically be developed for this purpose.
Publications
Peschke, K., Jakubowsky, H., Schafer, A., Maurer, C., Lange, S., Orben, F., Bernad, R., Harder, F. N., Eiber, M., Ollinger, R., Steiger, K., Schlitter, M., Weichert, W., Mayr, U., Phillip, V., Schlag, C., Schmid, R. M., Braren, R. F., Kong, B., Demir, I. E., Friess, H., Rad, R., Saur, D., Schneider, G., and Reichert, M. (2022). EMBO Mol Med 14, e14876. doi: 10.15252/emmm.202114876
Kaltenbacher, T., Loprich, J., Maresch, R., Weber, J., Muller, S., Oellinger, R., Gross, N., Griger, J., de Andrade Kratzig, N., Avramopoulos, P., Ramanujam, D., Brummer, S., Widholz, S. A., Barthel, S., Falcomata, C., Pfaus, A., Alnatsha, A., Mayerle, J., Schmidt-Supprian, M., Reichert, M., Schneider, G., Ehmer, U., Braun, C. J., Saur, D., Engelhardt, S., and Rad, R. (2022). Nat Protoc 17, 1142-1188. doi: 10.1038/s41596-021-00677-0
Schneeweis, C., Hassan, Z., Ascherl, K., Wirth, M., Koutsouli, S., Orben, F., Krauss, L., Schneider, C., Ollinger, R., Kramer, O. H., Rad, R., Reichert, M., Robles, M. S., Saur, D., and Schneider, G. (2022). Cancer Commun (Lond) 42, 360-364. doi: 10.1002/cac2.12280
Falcomata, C., Barthel, S., Ulrich, A., Diersch, S., Veltkamp, C., Rad, L., Boniolo, F., Solar, M., Steiger, K., Seidler, B., Zukowska, M., Madej, J., Wang, M., Ollinger, R., Maresch, R., Barenboim, M., Eser, S., Tschurtschenthaler, M., Mehrabi, A., Roessler, S., Goeppert, B., Kind, A., Schnieke, A., Robles, M. S., Bradley, A., Schmid, R. M., Schmidt-Supprian, M., Reichert, M., Weichert, W., Sansom, O. J., Morton, J. P., Rad, R., Schneider, G., and Saur, D. (2021). Cancer Discov 11, 3158-3177. doi: 10.1158/2159-8290.CD-21-0209
Zhang, Z., Li, H., Deng, Y., Schuck, K., Raulefs, S., Maeritz, N., Yu, Y., Hechler, T., Pahl, A., Fernandez-Saiz, V., Wan, Y., Wang, G., Engleitner, T., Ollinger, R., Rad, R., Reichert, M., Diakopoulos, K. N., Weber, V., Li, J., Shen, S., Zou, X., Kleeff, J., Mihaljevic, A., Michalski, C. W., Algul, H., Friess, H., and Kong, B. (2021). Gastroenterology 161, 1601-1614 e1623. doi: 10.1053/j.gastro.2021.07.030
Wahida, A., Muller, M., Hiergeist, A., Popper, B., Steiger, K., Branca, C., Tschurtschenthaler, M., Engleitner, T., Donakonda, S., De Coninck, J., Ollinger, R., Pfautsch, M. K., Muller, N., Silva, M., Usluer, S., Thiele Orberg, E., Bottcher, J. P., Pfarr, N., Anton, M., Slotta-Huspenina, J. B., Nerlich, A. G., Madl, T., Basic, M., Bleich, A., Berx, G., Ruland, J., Knolle, P. A., Rad, R., Adolph, T. E., Vandenabeele, P., Kanegane, H., Gessner, A., Jost, P. J., and Yabal, M. (2021). Sci Immunol 6, eabf7235. doi: 10.1126/sciimmunol.abf7235
Breunig, M., Merkle, J., Wagner, M., Melzer, M. K., Barth, T. F. E., Engleitner, T., Krumm, J., Wiedenmann, S., Cohrs, C. M., Perkhofer, L., Jain, G., Kruger, J., Hermann, P. C., Schmid, M., Madacsy, T., Varga, A., Griger, J., Azoitei, N., Muller, M., Wessely, O., Robey, P. G., Heller, S., Dantes, Z., Reichert, M., Gunes, C., Bolenz, C., Kuhn, F., Maleth, J., Speier, S., Liebau, S., Sipos, B., Kuster, B., Seufferlein, T., Rad, R., Meier, M., Hohwieler, M., and Kleger, A. (2021). Cell Stem Cell 28, 1105-1124 e1119. doi: 10.1016/j.stem.2021.03.005
Feldmann, K., Maurer, C., Peschke, K., Teller, S., Schuck, K., Steiger, K., Engleitner, T., Ollinger, R., Nomura, A., Wirges, N., Papargyriou, A., Jahan Sarker, R. S., Ranjan, R. A., Dantes, Z., Weichert, W., Rustgi, A. K., Schmid, R. M., Rad, R., Schneider, G., Saur, D., and Reichert, M. (2020). Gastroenterology 160, 346-361 e324. doi: 10.1053/j.gastro.2020.09.010
Lankes, K., Hassan, Z., Doffo, M. J., Schneeweis, C., Lier, S., Ollinger, R., Rad, R., Kramer, O. H., Keller, U., Saur, D., Reichert, M., Schneider, G., and Wirth, M. (2020). Mol Oncol 14, 3048-3064. doi: 10.1002/1878-0261.12835
Weber, J., Braun, C. J., Saur, D., and Rad, R. (2020). Nat Rev Cancer 20, 573-593. doi: 10.1038/s41568-020-0275-9