Genomic and expression profiles of NK-cell neoplasms. (A) Frequency of genomic aberrations analyzed by oligo-array CGH. Thirty-two clinical samples and 7 cell lines were analyzed. Each probe is aligned from chromosome 1 to 22 and p to q. The vertical axis indicates penetrance of the genomic aberration among the analyzed cases. The black area shows gain/amplification and the gray area shows loss/deletion. (B) Genomic aberration of chromosome 6q15-25, the most frequently deleted region of the whole genome except for chromosomes X and Y. Fifteen cases with a 6q deletion are described. Each deleted region is indicated as a horizontal bar. Two narrow, independently deleted regions (∼ 1.5 Mb) are observed in HANK1 and clinical case number 3, and are the most frequently deleted MCRs. The deleted region in HANK1 includes POPDC3, PREP, PRDM1, ATG5, and AIM1, and the deleted region in clinical case number 3 includes LACE1 and FOXO3. (C) Gene-expression profiles were analyzed in 7 cell lines and 11 clinical samples using oligo-microarray. Candidate genes selected by genomic analysis are described. The probe intensity was converted to a numerical value, and the z-score was calculated as described in supplemental Methods. The vertical axis indicates the difference in average value between normal NK cells (n = 3) and neoplastic samples (n = 18). TNFAIP3 (A20), FOXO3, and ATG5 possess 2 probes. A20-1: A_24_P166527, A20-2: A_24_P157926, FOXO3-1: A_32_P102062, FOXO3-2: A_23_P345575, ATG5-1: A_24_P175059, ATG5-2: A_23_P111381. Most of the candidate genes, and in particular FOXO3 and A20, were down-regulated in neoplastic samples compared with normal NK cells, whereas a negligible difference was observed for AIM1.