Cancer Evolution and Data Analysis (CEDA)

A bi-weekly, one hour long journal club on cancer evolution and data analysis. We're trying to get up to date with recent discoveries made from data and "upcoming" methods in cancer data analysis. Feel free to join (see schedule below). 

Location: Coffee room, building 1110, 4th floor

Time: 13.00

We stick to the one-hour time limit quite well. If you have any questions, contact das@birc.au.dk

Meetings

[2017/06/07] [Johanna Bertl] Inigo Martincorena et al.: "Universal patterns of selection in cancer and somatic tissues". Find it here: http://biorxiv.org/content/early/2017/04/29/132324 

[2017/05/17] [Elham Bavafaye Haghighi] C.J. Tokheim, N. Papadopoulos, K.W. Kinzler, B. Vogelstein, R. Karchin, Evaluating the evaluation of cancer driver genes, Proc. Natl. Acad. Sci. . 113 (2016) 14330–14335. doi:10.1073/pnas.1616440113.

[2017/05/03] [Palle Villesen]https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0694-1    (It is a subpublication of the MAQC consortium comparing RNA-seq and microarray data in a "real" example (predicting outcome from neuroblastoma samples).

[2017/04/19] [Petr Taus] Dvir Aran, Zicheng Hu, Atul J Butte. xCell: Digitally portraying the tissue cellular heterogeneity landscape.  bioRxiv 114165; doi: https://doi.org/10.1101/114165

[2017/04/05] [Guo Qianyun] Treviño, Victor, Emmanuel Martinez-Ledesma, and José Tamez-Peña. Identification of outcome-related driver mutations in cancer using conditional co-occurrence distributions. Scientific Reports 7 (2017): 43350.

[2017/03/22] [Astrid Kousholt] Alexandrov LB, Jones PH, Wedge DC, et al. Clock-like mutational processes in human somatic cells. Nat Genet. 2015;47(12):1402-1407. http://dx.doi.org/10.1038/ng.3441.

[2017/03/08] [Elham Bavafaye Haghighi] Bartsch GJ, Mitra AP, Mitra SA, et al. Use of Artificial Intelligence and Machine Learning Algorithms with Gene Expression Profiling to Predict Recurrent Nonmuscle Invasive Urothelial Carcinoma of the Bladder. J Urol. 2016;195(2):493-498. doi:10.1016/j.juro.2015.09.090.

[2017/02/22] [Guo Qianyun] Hoadley KA, Yau C, Wolf DM, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014;158(4):929-944. doi:10.1016/j.cell.2014.06.049.

[2017/02/01] [Dan Søndergaard] Sebastian Moran et al. “Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis”. The Lancet Oncology, Volume 17, Issue 10, October 2016, Pages 1386-1395, ISSN 1470-2045, http://dx.doi.org/10.1016/S1470-2045(16)30297-2.

[2017/01/18] [Søren Besenbacher] Nik-Zainal S, Davies H, Staaf J, et al. “Landscape of somatic mutations in 560 breast cancer whole-genome sequences”. Nature. 2016;534(7605):47-54. http://dx.doi.org/10.1038/nature17676.

[2016/12/21] [Jacob Malte Jensen] Ulz, Peter, et al. "Inferring expressed genes by whole-genome sequencing of plasma DNA." bioRxiv (2016).

[2016/12/07] [Astrid Kousholt] Alexandrov et al., “Deciphering signatures of mutational processes operative in human cancer.” Cell Reports (2013).

[2016/11/23] [Guo Qianyun] Vural S, Wang X, Guda C. “Classification of breast cancer patients using somatic mutation profiles and machine learning approaches. BMC Syst Biol. 2016;10(Suppl 3).” doi:10.1186/s12918-016-0306-z.

[2016/11/09] [Svend Nielsen] Sottoriva A, Kang H, Ma Z, et al. “A Big Bang model of human colorectal tumor growth.” Nature genetics. 2015;47(3):209-216. doi:10.1038/ng.3214.

[2016/10/26] [Dan Søndergaard] Greaves M, Maley CC. “Clonal evolution in cancer.” Nature. 2012;481(7381):306-313. doi:10.1038/nature10762.

 

Paper Suggestions

Valent P, Bonnet D, De Maria R, et al. Cancer stem cell definitions and terminology: the devil is in the details. Nat Rev Cancer. 2012;12(11):767-775. doi:10.1038/nrc3368.

Weigelt B, Glas AM, Wessels LFA, Witteveen AT, Peterse JL, van’t Veer LJ. Gene expression profiles of primary breast tumors maintained in distant metastases. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(26):15901-15905. doi:10.1073/pnas.2634067100.

Schmitt MW, Loeb LA, Salk JJ. The influence of subclonal resistance mutations on targeted cancer therapy. Nat Rev Clin Oncol. 2016;13(6):335-347. doi:10.1038/nrclinonc.2015.175.

Birkenkamp-demtro K, Reinert T, Vang S, et al. Genomic Alterations in Liquid Biopsies from Patients with Bladder Cancer. 2016;70:75-82. doi:10.1016/j.eururo.2016.01.007.

Hedegaard J, Lamy P, et al. Comprehensive Transcriptional Analysis of Early- Article Comprehensive Transcriptional Analysis of Early-Stage Urothelial Carcinoma. 2016:27-42. doi:10.1016/j.ccell.2016.05.004.

Lamy P, Nordentoft I, Birkenkamp-demtröder K, et al. Paired exome analysis reveals clonal evolution and potential therapeutic targets in urothelial carcinoma Abstract Greater knowledge concerning tumor heterogeneity and clonality is needed to determine. :1-30.

Shumansky K, Vang S, Hornshøj H, et al. Article Mutational Context and Diverse Clonal Development in Early and Late Bladder Cancer. 2014:1649-1663. doi:10.1016/j.celrep.2014.04.038.

Reinert T, Schøler L V, Thomsen R, et al. Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery. 2016:625-634. doi:10.1136/gutjnl-2014-308859.