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Chromosomal imbalances resulting in altered gene dosage play a role in the molecular pathogenesis of non-small cell lung cancer (NSCLC), but the target genes remain to be identified. To identify early-stage genetic events that drive progression of NSCLC, we conducted a high-resolution array comparative genomic hybridization (CGH) study, using an array of 4,046 bacterial artificial chromosome clones to screen for DNA copy number changes associated with individual genes in 36 tumors obtained from patients in early stages of NSCLC. Multiple early genetic events occurring on chromosome 5p were identified, with a minimal detection region at 5p15.33 approximately 12. The most frequent finding involved gain of 5p15.33, observed in 15 of 19 stage I (A+B) cancers (79%) and in 28 of the total 36 NSCLC cases (78%). This locus harbors the genes TERT, SLC6A19, and SLC6A18 and is a telomeric boundary at bacterial artificial chromosome (BAC) clone 91_J20. Other potential candidate genes evidencing high numbers of genomic copy number changes (> or =40% of patients) included the following genes, encountered in >50% of 19 stage I (A+B) cancers: CEP72 and TPPP (14 of 19; 74%); AHRR, EXOC3 (previously SEC6L1), SLC9A3, LOC442126, ZDHHC11, BRD9, and TRIP13 (13/19; 68%); and CLPTM1L (alias CRR9), SLC6A3 (previously DAT1), and LOC401169 (10/19; 53%). Fluorescence in situ hybridization validated the array CGH findings. The gain of 5p15.33 is thus one of the most consistent alterations in the early stages of lung cancer, and a series of genes in the critical 5p15.33 region may be used as novel biomarkers for the early detection and classification of lung cancer.

Conventional urine cytology has a poor prognostic performance for detecting bladder cancer, particularly for low-grade tumors. Fluorescence in situ hybridization (FISH) for chromosomes altered in bladder cancer and testing for antigens selectively expressed in tumors are promising alternatives. This study investigated the use of FISH for detecting aneuploidy of chromosomes 3, 7, 17, and 9p21 and reverse transcriptase PCR (RT-PCR) for the expression of melanoma associated antigen (MAGE) genes for the diagnosis of bladder cancer in voided urine specimens. The two techniques were compared with cystoscopic bladder biopsy results in 47 patients with urothelial cancer and 15 patients with benign prostatic hyperplasia. FISH detected cancer in 42 of 47 patients (89.4%). This was significantly higher than the detection rate 30 of 47 patients (64.3%) by MAGE RT-PCR (P < 0.001). The sensitivity of FISH increased with histologic grade and stage of the tumors, correctly identifying 77.8% of pTa and pTis, 94.1% of pT1, and 100% of Pt2-4 tumors. MAGE, however, showed a decreased sensitivity in high grade advanced tumors; it was positive in 66.7% of pTa and pTis, 70.6% of pT1, and 50% of Pt2-4 tumors. Together, the tests correctly identified urothelial cancer in 46 of 47 patients (97.9%). Combined FISH and MAGE RT-PCR testing may offer a promising alternative to conventional urine cytology in screening high-risk populations and in monitoring bladder cancer patients for recurrent tumor.