Dr. Morin has assigned me the following list of papers to read.
[x] Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2015).
[x] Okosun, J. et al. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet (2013). doi:10.1038/ng.2856
[x] Tamborero, D. et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 3, (2013).
[x] Tamborero, D., López-Bigas, N. & Gonzalez-Perez, A. Oncodrive-CIS: A Method to Reveal Likely Driver Genes Based on the Impact of Their Copy Number Changes on Expression. PLoS ONE 8, e55489 (2013).
[x] Nik-Zainal, S. et al. The Life History of 21 Breast Cancers. Cell 149, 994–1007 (2012).
[ ] Greenman, C., Wooster, R., Futreal, P. A., Stratton, M. R. & Easton, D. F. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics 173, 2187–2198 (2006).
[ ] Bignell, G. R. et al. Signatures of mutation and selection in the cancer genome. Nature 463, 893–898 (2010).
[ ] Alexandrov, L. B. & Stratton, M. R. ScienceDirectMutational signatures: the patterns of somatic mutations hidden in cancer genomes. Current Opinion in Genetics & Development 24, 52–60 (2014).
[ ] Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 104, 20007–20012 (2007). (I believe there is another more recent paper describing an updated version of this algorithm)
[ ] Garraway, L. A. & Lander, E. S. Lessons from the cancer genome. Cell 153, 17–37 (2013).
[x] Newman, Aaron M., et al. "An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage." Nature medicine (2014).
[x] Leary, Rebecca J., et al. "Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing." Science translational medicine 4.162 (2012): 162ra154-162ra154.
[ ] Murtaza, Muhammed, et al. "Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA." Nature 497.7447 (2013): 108-112.
Dr. Morin has assigned me the following list of papers to read.