National Cancer Institute (NCI) scientists have released a database of cancer-specific genetic variations identified through sequencing the whole exome, the protein-coding part of the genome, of 60 cancer cell lines. The scientists published details of the cell lines online on Monday (July 15) in Cancer Research.
“Opening this extensive data set to researchers will expand our knowledge and understanding of tumorigenesis, as more and more cancer-related gene aberrations are discovered,” Yves Pommier, chief of the Laboratory of Molecular Pharmacology at NCI, said in a statement. “This comes at a great time, because genomic medicine is becoming a reality, and I am very hopeful this valuable information will change the way we use drugs for precision medicine.”
The 60 cell lines, referred to as the NCI-60, are derived from 9 types of cancer occurring in the brain, lung, ovary, breast, prostate, colon, kidney, blood, and skin. The cell lines have historically been used to screen thousands of anti-cancer compounds.
Once the NCI researchers identified all of the cancer-specific genetic variations across the cell lines, they performed some preliminary mining of the data to demonstrate the database’s utility. The team used the Super Learner algorithm to predict the sensitivity of the cell lines to 103 anti-cancer drugs approved by the FDA as well as 207 drugs under investigation.
The NCI team has compiled the data into Excel spreadsheets and made it available to the research community through the NCI DTP, CellMiner, and Ingenuity Systems websites. The team plans to develop more intuitive user interfaces to enable broader access for data mining by the public. “One of the intents here is to enable people who don’t have a bioinformatics team to look at these data and look at biological and drug insight,” Pommier told Bio-IT World.