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High-throughput oncogene mutation detection in human cancers by mass spectrometry-based genotyping

of the tumor is conditioned around such mutations, so if you eliminate the oncogene, the tumor shrinks," Dr. Garraway said. Examples include the c-kit tyrosine kinase that drives development of gastrointestinal stromal tumors (GISTs), and certain EGFR mutations that are responsible for one form of lung cancer. These cancers can be treated with the targeted therapies Gleevec and Tarceva, respectively, which shut down the affected oncogenes.

The test involves taking a sample of fresh or frozen tumor, amplifying its DNA, and then searching for 250 known mutations in 17 oncogenes. (These include members of the ras, EGFR, pi3 and c-kit kinase families, among others.) To check performance of the genotyping, the research team tested over 1,000 tumors, representing 15 different cancer types, and then independently verified over half of the mutations they identified using traditional DNA sequencing or other methods. They found that over 92 percent of mutations identified by the mass spectrometry method were validated in this manner, and believe that much of the difference is due not to the mass spectrometry method but to limitations of the laborious sequencing test "which is not always sensitive in tumor specimens," Dr. Garraway said.

He added that the mass spectrometry test offers information that is distinct from the cancer microarray gene expression tests now being developed. "Those tests depend on gene expression while this one looks directly at problems in the genome," Dr. Garraway said.


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Source:American Association for Cancer Research


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