Data Visualizing Operations in Breast and Prostate Cancer
The skills the author demoed here can be learned through taking Data Science with Machine Learning bootcamp with NYC Data Science Academy.
Background
Clinical trials are experiments or observations done in clinical research. They are designed for participants to participate in the medical, observational or behavioral interventions. Clinical trials involve the testing of investigations including new treatments such as novel vaccines, drugs, dietary supplements, and medical devices that warrant further data studies to find out better ways to treat, and understand the progress of disease.
The primary purpose of doing clinical trials is to gain more information about the risks and effectiveness of an experimental treatment in humans. Different types of people participate in clinical trials. Some are healthy, some may have illnesses. They both play important roles in clinical trials.
People might ask: " Are the clinical trials safe? " As with any type of medical care or therapy of daily living, clinical trials can have risks. If you want to join a clinical trial, the staff will describe the risks that may cause to the participants. You can weigh the risk factors and decide whether or not you would like to participate.
Business Motivations
The process of developing a new drug from the original idea to launch a finished product often takes 12–15 years. The drug discovery begins in the laboratory.
When the researchers create a new therapy or drug, it is tested in the laboratory and on animals at first. If the initial lab research is successful, researchers will send the data to the Food and Drug Administration (FDA) to get approval to continue testing on human beings. Depending on product types and development stages, investigators enroll volunteers into small group of studies, and conduct larger scale studies progressively. Because Breast cancer rates the highest in female and prostate cancer rates the highest in male, I chose to analyze these two cancers in clinical trials.
Data
I got the data from clinicaltrials.gov. The dataset contains:
- The number of recruitment of breast cancer and prostate cancer
- Locations, latitude, longitude
- The number of total trials in breast cancer and prostate cancer
- Phases
- Durations of the clinical trials
- Sponsor.Collaborators
- Study types
- Rate of recruitment
Shiny App Data Analysis
The map below shows the concentrate of total clinical trials around the world. From the legend we can see that the darker the color on the map, the more trials are recruiting, or already completed. The map shows that the United States, Europe and China have the most clinical trials in breast and prostate cancer compared to other countries.
These two maps below show the clinical trials in both breast and prostate cancer that are recruiting now around the world. When you room in it, you can see the trials at specific cities and locations.
Histogram
I created the histograms that show the number of recruitments(active but not ready to recruiting, recruiting, completed and etc), phases, study types and top 10 sponsor collaborators. We can see the different counts between the two cancers clearly by looking at the histograms.
From the two histograms below, we can see that the three biggest cancer centers sponsor the most trials both in breast and prostate cancer. The pharmaceutical companies Roche ranks 4th in breast cancer and AstraZeneca ranks the 6th in Prostate cancer.
There are four phases in clinical trials:
First phase assesses the safety of a drug or device.
Second phase tests the efficacy of a drug or device.
Third phase involves randomized and blind testing in hundreds to thousands patients.
Fourth phase is often called Post Marketing Surveillance Trials that are conducted after a drug or device has been approved for consumer sale.
You can see that there is a large number of NA in the two histograms above, that is because some companies or research centers didn't report the integrated report to the clinicaltrials.gov.
Data on Rate of Recruitment
The boxplot above shows how fast the different sponsor collaborators recruit people for the two cancers. ROR means the rate of recruitment.
ROR = total amount of volunteers/ total number of months.
From the boxplot above, we can see that the rate of recruitment of majority pharmaceutical companies are faster than the academic institutes. In breast cancer, Bayer ranks the 1st in ROR. In prostate cancer, Ferring ranks the 1st.
The boxplot above shows how fast the people get recruited in different phases. Breast cancer is the fastest in Phase2&3, and prostate cancer is the fastest in Phase 4.
Conclusion
Clinical trials has become the hottest topic in the healthcare industry. The pharmaceutical, biotech and medical devices companies, even some governmental organizations spend millions on clinical trials every year. It uses the big data to analyze and recruit people in different types of experiments to help the industries reduce the cost and improve the efficiency of the recruitment. My Shiny app is available here. Source code is available at Github.
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Xiao Jia
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