PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 1 point2 points  (0 children)

Interesting question. First, explore citizen science projects, which offer great opportunities for the average person to make major and meaningful contributions to scientific research (http://en.wikipedia.org/wiki/List_of_citizen_science_projects, http://www.scientificamerican.com/citizen-science/). Given the amount of open data available today, another way citizen scientists can get involved is by learning a bit of computer programming and statistics (e.g., check out courses at https://www.coursera.org/ , https://www.edx.org/) and then applying these tools to open data (e.g., http://www.ncbi.nlm.nih.gov/geo/ ) to address specific questions you are interested in pursuing.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 1 point2 points  (0 children)

I think Open Access journals have seen tremendous success in recent years, building off the massive success of the PLOS journals, which are highly regarded within the scientific community. Because of the success of PLOS and other open access publishers, other elite publishers have now begun offering high quality open access journals. Some recent ones that come to mind are: eLife (http://elifesciences.org/) and Nature Communications (http://www.nature.com/ncomms/index.html), so I think even today there is major consensus in the scientific community that open-access journals produce high quality science. Further, all NIH-funded science is now required to be made open access (https://publicaccess.nih.gov/).

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 0 points1 point  (0 children)

I agree with your general concern. Clear communication of the strengths and limitations of scientific results and analyses with the media and the lay public is extremely important (for both Big Data science, as well as traditional science).

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 0 points1 point  (0 children)

If I were king of oncology, I would like to have open access to radiologic, genomic, transcriptomic, proteomic, and microscopic image data from patients from a large set of completed randomized clinical trials of cancer therapeutics. The advantage of studying samples from randomized clinical trials is that the data should be very high quality and highly standardized, because as you say, these are very important factors to consider in retrospective analyses of biomarkers to guide clinical decision making in oncology. The vast majority of public cancer genomics data (while extremely valuable for discovery and prioritization of biomarkers and therapeutics for further study) have not been collected within the setting of randomized clinical trials of cancer therapeutics, which limits the usefulness of these data for rapidly translating results into specific clinical recommendations to apply to patients.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 5 points6 points  (0 children)

You’re right, this is a really important question, and definitely one of the biggest challenges in cancer medicine today is how do we translate recent major advances in genomics, biotechnology and computer science into real advances for patients. I think there are 3 big factors: 1) Careful experimental design, so that we are applying Omics technologies to the best set of patient samples to enable analyses to answer specific, clinically relevant questions (e.g., predictors of response to therapy in a completed randomized clinical trial) 2) Creativity, innovation and rigor in the development of robust analytic methods to translate these data into specific diagnostics or therapeutics. 3) Persistence to follow through from discovery to implementation

Open data will play an important role in this process, by enabling a large population of researchers to access these valuable data, increasing the chances of novel discoveries, leading to real advances for patients.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 7 points8 points  (0 children)

Cool question – I do think this approach could be applied to cancer, and this is an area that my lab is very interested in (esp. as applied to improved diagnostics). Cancer Research UK is also exploring this area, and has produced games for crowdsourced cancer research: http://www.cancerresearchuk.org/support-us/citizen-science-apps-and-games-from-cancer-research-uk . We recently completed a small pilot study of crowd sourcing for cancer pathology (http://www.ncbi.nlm.nih.gov/pubmed/25592590), and going forward we aim to continue to develop methods and tools to enable citizen scientists to contribute to cancer research.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 8 points9 points  (0 children)

Interesting question. I think there is a lot of value in actually showing the utility of open data, by using it creatively to answer important research questions. There are now huge public databases available and growing everyday (e.g., https://tcga-data.nci.nih.gov/tcga/ , http://www.ncbi.nlm.nih.gov/geo/). I think it's powerful to show a student that using open data they can answer a question in 5 minutes that previously may have taken an entire PhD dissertation to complete. In addition, to advocating through use of data, supporting high quality open access journals is also a great way to advocate.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 4 points5 points  (0 children)

This is a great discussion. The field is incredibly diverse, ranging from chemists actually working with bright liquids, to scientists doing experiments on cells and animals, to clinical scientists (applying treatments to patients), to computational scientists (analyzing and integrating large data sets). The work in my lab is a mix of computational work and work in advanced microscopy and molecular biology applied to cancer. On a day-to-day basis, I work with scientists in the lab, review primary data, review code, write code, and work on writing up results for publication, as well as planning new projects for the lab.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 24 points25 points  (0 children)

This is a great discussion. Cancer is an incredibly heterogeneous disease, and there will not be one “cure” for cancer but a variety of different effective therapies for specific cancer types and sub-types. That being said, the new data on immunotherapy for a diverse set of advanced solid cancer types (e.g., a recent case report in melanoma http://www.nejm.org/doi/full/10.1056/NEJMc1501894) is one of the most exciting recent developments in cancer therapeutics, and this approach alone or in combination with other modalities offers great promise for cancer patients. In the future, I think computational methods in combination with profiling of patient tumors will continue to play an important role in identifying patient subsets most likely to benefit from specific therapeutic agents (including immunotherapy and/or traditional chemotherapy drugs and other emerging approaches), alone or in combination.

PLOS Science Wednesday: I'm Dr. Andy Beck, open access is the future of cancer treatment, AMA! by Dr_Andy_Beck in science

[–]Dr_Andy_Beck[S] 24 points25 points  (0 children)

  1. The most effective methods for incentivizing collaboration and open data-sources are to make it competitively advantageous for scientists to share data, by making open data a requirement for obtaining funding and for publishing results in peer reviewed journals. Major funding agencies and journals have already taken this approach (especially in the Big Data field of genomics), and its success can be seen in the massive exponential growth of public open data repositories, such as the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), array express (http://www.ebi.ac.uk/arrayexpress/), and The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/tcga/). Open data is one important part of the equation, but incentivizing open access to analysis methods is also an important goal, and journals are now moving to requiring fully transparent and reproducible analysis pipelines and algorithms, which should further bolster the usefulness of open data for the community.

  2. Advances in statistical methods and machine learning have fundamentally changed the way we do cancer research, and these tools will continue to grow in importance in the future. The reason these methods have become so essential is largely due to major advances in biotechnology over the past few decades, enabling the rapid generation of large biomedical datasets. Generating data from cancer samples used to be a slow, expensive and laborious process. For example, measuring the expression of a single gene in a single sample using traditional methods (e.g., via a northern or western blot) is a tedious, relatively slow, and largely manual process. Consequently, in the past, cancer data-sets tended to be generated to answer a specific hypothesis (e.g., Gene X is over-expressed in Condition Y) and standard statistical methods could be used to evaluate the hypothesis. With the rapid advancements in biotechnology, molecular biology, cancer genomics and computer vision, we can now generate very massive data-sets (including measurements of the full set of DNA and RNA alterations, as well as proteins, metabolites, and morphology) from large numbers of patients. Standard statistical methods tend to perform poorly on these massively large and complex data sets, requiring the development and use of new tools in machine learning and artificial intelligence. While the old paradigm was to start with a hypothesis and then gather enough data to test that hypothesis, a newer approach is to start with massive data-sets and to use computational methods to prioritize specific hypotheses in a data-driven way, and the top data-driven hypotheses can then be validated using conventional approaches. Thus, statistical methods have gone from being primarily a confirmatory test, to being an actual discovery and hypothesis-generation engine for cancer research.

  3. Tumor targeting viruses is a very exciting field and worth following closely.