Related Experiment Video
Updated: May 2, 2026

Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
Modular and cloud-based bioinformatics pipelines for high-confidence biomarker detection in cancer immunotherapy
Cu Nguyen1, Trinh Nguyen1, Gloria Trivitt2
1The Computational Genomics and Bioinformatics Branch, Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, Maryland, United States of America.
Background:
The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Center (CIMAC-CIDC) network aims to improve cancer immunotherapy by providing harmonized molecular assays and standardized bioinformatics analysis.
Results:
In response to evolving bioinformatics standards and the migration of the CIDC to the National Cancer Institute (NCI), we undertook the enhancement of the CIDC's extant whole exome sequencing (WES) and RNA sequencing (RNA-Seq) pipelines. Leveraging open-source tools and cloud-based technologies, we implemented modular workflows using Snakemake and Docker for efficient deployment on the Google Cloud Platform (GCP). Benchmarking analyses demonstrate improved reproducibility, precision, and recall across validated truth sets for variant calling, transcript quantification, and fusion detection.
Conclusion:
This work establishes a scalable framework for harmonized multi-omic analyses, ensuring the continuity and reliability of bioinformatics workflows in multi-site clinical research aimed at advancing cancer biomarker discovery and personalized medicine.
Related Concept Videos
Mouse Models of Cancer Study
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
Targeted Cancer Therapies
There are several types of targeted therapies against...
Combination Therapies and Personalized Medicine
The combination of the drug acetazolamide and sulforaphane is a good example of combination therapy to treat cancer. The cells in the interior of a large tumor often die due to the hypoxic and...
Tumor Immunotherapy

