Communications ACM (Feb. 14, 2012)
High-throughput DNA sequencing technologies are leading to a revolution in how clinicians diagnose and treat cancer. The molecular profiles of individual tumors are beginning to be used in the design of chemotherapeutic programs optimized for the treatment of individual patients. The real revolution, however, is coming with the emerging capability to inexpensively and accurately sequence the entire genome of cancers, allowing for the identification of specific mutations responsible for the disease in individual patients.
The RNA-Seq analysis pipeline (R-SAP) was developed by School of Biology Professor John McDonald and Ph.D. Bioinformatics candidate Vinay Mittal. Details of the pipeline are published in “R-SAP: A Multi-Threading Computational Pipeline for the Characterization of High-Throughput RNA-Sequencing Data” in the journal Nucleic Acids Research. (full story..) (link to paper)