ISOLATE: identifying the site of origin of secondary tumors

Quon, G., Morris, Q. (2009) ISOLATE: A computational strategy for identifying the primary origin of cancers using high throughput sequencing. Bioinformatics, 25:2882-2889.

ISOLATE was our original deconvolution algorithm that we developed in the context of finding the primary site of origin of secondary tumors. In principle, because gene expression profiles of secondary tumors should retain a signature of their original cell type, these secondary tumor profiles can be compared against a panel of healthy profiles from many different tissues, and the true site of origin should be the closest (or one of the closest) tissues. However, because tumor samples are difficult to obtain without also collecting contaminating tissue from nearby sites, identification of the site of origin can be difficult because of the noise these contaminating cells introduce — so we developed ISOLATE to simultaneously identify the site of origin and characterize the mixture composition of the secondary tumor (in terms of contaminating healthy tissue and cancer cells).

Since its development, ISOLATE has been implemented much more efficiently as Step 1 of the ISOpure framework, so to run it, download ISOpure and read the README.txt file.