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Paper Review #1
"The genomic complexity of primary human prostate cancer"
Berger, et al., 2011
| Overview | Conclusions |
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Conclusions:
Berger, et al., overall did a fine job consolidating a large amount of complex data into seven pages. After all, the title of the article begins with “The genomic complexity.” The abstract and introduction concisely outlined the reason why the study was done, some take-home points of the results, and the significance and future implications of these results. I found their presentation of specific data to be helpful, considering they would never be able to include every single result and analysis. They acknowledged the complexity of whole genome sequencing, which is why it has not been done before for prostate cancer, and I appreciated their acknowledgment of the limitations and underestimations of their tests, such as the FISH assays of prostate tumors. They specifically illustrated the implications of rearrangements in a good number of genes, and I appreciated their outlining the basic functions of such genes. I would have liked a bit more explanation of specifically mentioned genes, proteins, complexes, and pathways in terms of function and how they affect prostate tumorigenesis; i.e. the PI3 kinase pathway, RNA polymerase II holoenzyme, the HSP-1 stress response complex, and the various cancer genes mentioned. It was clear that basic background knowledge of prostate cancer and certain biological mechanisms was assumed in the reader. I also would have liked to see more information concerning the seven prostate tumors themselves, especially in terms of details about the patients’ age, diagnosis, prognosis, etc. For several of the figures, I had to refer to supplementary materials just to be able to read them. In particular, I found the data in Figure 3 to be rather confusing, as I had to distill the implications of the terms depletion, enrichment, ERG-positive, and ETS-negative for all samples. The article very briefly explained the previously published data the researchers used to compare with their data, but I found this to be sufficient. The article in general successfully stated the implications, possible assumptions, and limitations of each test. Perhaps a bit of ethical discussion could have been included. Overall, I found the study to be a huge first step in the many steps to come in order to articulate the wide range of underlying genomic factors that could be used to provide better treatments/therapies for a cancer with such a high mortality rate. The article even indicates future implications for other cancers, especially hormone-driven cancers such as breast cancer.
References
Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, et al. The genomic complexity of primary human prostate cancer. Nature [Internet]. 2011 Feb 10 [cited 2011 Feb 21];470(7333): 214-220. Available from: http://www.nature.com/nature/journal/v470/n7333/full/nature09744.html
*Note: All citable information was taken from this original paper.
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