A single cancer patient on average can generate 1 Terabyte of biomedical diagnostic and clinical data. According to a paper from GLOBCAN 2018, there will be 18.1 million new cancer cases worldwide along with 18 Exabytes of data being generated annually. Data generated from Cancer has all fours Vs (speed, variety, volume, and veracity) of Big data. We will see how Big Data analytics can be used in the field of cancer research in this blog post.
Researchers currently use this data to analyze the disease on three levels:
- Cellular
Researchers mainly look for various patterns in the data to discover genetic biomarkers that can help in predicting the tumor mutation and effective drug treatment for them.
- Patient
Using the patient medical history and DNA data, researchers can define the best therapies based on their tumor and gene type.
- Population
Population data can be analyzed to determine treatment strategies for cancer patients that differ based on their different lifestyles, geographies, and cancer types.
One of the common methods for cancer research is Genome Sequence, in which we determine the Deoxyribonucleic acid (DNA) sequence of a single, homogeneous or heterogeneous group of cancer cells. It’s an expensive and long-running process, in which we need to analyze billions of records of data to track down the DNA sequence of cancer cells.
Finding a tool to analyze the cancer data
The real challenge with these huge data sets is to find the proper tool to store it for a long time, process, analyze and visualize it.
Storage:
Since data sets are large and need to be archived for a long time, it needs to be stored in a distributed fashion so that no loss of data occurs. Some options available are HDFS (Hadoop Distributed File System), Amazon S3, Microsoft Azure, Google Cloud, IBM Cloud, and In-house servers
Data Collection/Transport Mechanism:
Organizations need to decide how they want to transport the data from the lab or on-site to their IT infrastructure. Some tools and mechanisms available are SFTP, Hadoop Distscp (Hadoop Distributed Copy), Apache Flume, Apache Sqoop, Apache Kafka, and Apache NiFi.
Processes/Analyze:
Organizations also need to think about how they are going to process or analyze the data. Some tools available are Apache Hadoop/ MapReduce, Apache Hive, Apache Spark in ML Library, R Packages on top of Spark, Vertica, and ETL tools.
Visualization:
Once you analyze the data, you might want to summarize these results as a report or visualization. Some tools available for this purpose are Tableau, Microstrategy, d3js library
Conclusion
In this blog post, we learned about how Apache Hadoop is used in research related to cancer. We also read about the different tools used to analyze cancer data.
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