We have developed a simple analytical method that increases the efficiency of identifying mutant genes in cell lines after the inhibition of nonsense-mediated decay (NMD). The approach assumes that the spectra of mutant genes differ between cell lines of the same tumor origin. Thus, by analyzing more than one cell line in parallel and taking into account not only changes in mRNA levels after the inhibition of NMD, but also comparing mRNA levels between cell lines before the inhibition of NMD, the vast majority of false positives were eliminated from the analysis. In this study, we used Affymetrix oligonucleotide arrays to compare mRNA profiles of two prostate cancer cell lines, PC3 and LNCaP, before and after emetine treatment. As a result of our modified approach, from the 14,500 genes present on the array, 7 were identified as candidates from LNCaP cells and 1 was identified from PC3 cells. Sequence analysis of five of these candidate genes identified gene-inactivating mutations in four of them. Homozygous mutations were found in the synaptojanin 2 (SYNJ2) and the cleft lip and palate CLPTM1 genes. Two different heterozygous mutations in the Janus kinase 1 (JAK1) gene result in complete loss of the protein in several different prostate cancer cell lines.