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Alteration of the CDKN2A (alias p16) tumor suppressor gene, located on 9p21, occurs frequently in familial and sporadic melanomas. Beside CDKN2A, other genes (e.g., CDKN2B, and ARF/p14(ARF), long considered distinct from CDKN2A) on this locus are often deleted or mutated in a large number of tumors including glioma, bladder cancer, and lung cancer. The aim of this study was to evaluate the deletion pattern of the 9p21 locus on a cell-by-cell basis in a large number of melanoma samples using fluorescence in situ hybridization (FISH). In an analysis of 81 primary lesions targeting the 9p21 region and chromosome 9 centromere, high frequency of 9p21 loss (84%) was found. Deletion of 9p21 was present in both early- and late-stage melanomas with similar frequencies. Extra 9p21 copies were rarely seen; they were always associated with polysomy 9 and were observed only in advanced stage melanomas (6 tumors). This FISH study strengthens the hypothesis that the loss of 9p21 occurs frequently in primary melanoma, that the deletion is present in early and late stages of the disease with similar frequency, and that it affects a large extent of the locus.

In order to characterize the chromosomal alterations in ameloblastomas, a combination of comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) techniques was performed on 9 tumors. Chromosomal alterations including a gain at 1q and losses at 1pter, 10q, and 22q could be detected by CGH only in 1 tumor. Interphase FISH analysis, using centromeric probes for chromosomes 1, 10, and 22 as well as region-specific probes for 1p36 and 10q26, revealed the most frequent alterations to exist in the tumor with the abnormal CGH profile. These alterations included marked to slight increases of monosomic cells for chromosome 10 (91.5%), 10q26 (35.8%), 1p36 (24.4%), and chromosome 22 (18.8%), as well as significant elevations of trisomic cells for chromosome 1 (41.2%). Moreover, FISH analysis revealed a frequent loss of chromosome 22 in all tumors examined, except for one lesion, indicating that loss of the entire or a part of this chromosome is a common event in ameloblastomas, possibly being a predisposing factor to ameloblastoma tumorigenesis.

In order to define and map chromosomal copy number alterations in salivary gland tumors (SGTs), a comparative genomic hybridization (CGH) technique was applied to two pleomorphic adenomas (PAs), one adenoid cystic carcinoma (ACC), and one basal cell adenocarcinoma (BCAC). The PAs exhibited regional copy number losses at 5q12.4-q14.1, 9q12-q21.13, and 16q11.2, as well as a gain at 20p12.1; among these, the losses at the 9q12-q21.11 and 16q11.2 regions were common to both PAs. The ACC showed overrepresentations of the entire regions of chromosomes 16 and 20, a regional gain at 22q12.3-q13.1, and no losses. In the BCAC, regional gains at 9p21.1-pter, 18q21.1-q22.3, and 22q11.23-q13.31 as well as losses at 2q24.2 and 4q25-q27 were seen; the gain at 22q12.3-q13.1 was common in both the ACC and the BCAC. These CGH data indicate that different genetic alterations are present in the different types of SGTs, and that the alterations involve several chromosomes. The discovery of common alterations in the same and/or different types of tumors might be important in the understanding of the development and progression of the SGTs.

Fluorescence in situ hybridization (FISH) was applied for the detection of the retinoblastoma tumor-suppressor gene deletion on retinoblastoma tumor cells obtained from the unilateral tumor of a 3-month-old boy. Both retinoblastoma tumor cells and peripheral lymphocytes of the patient showed one hybridization signal per cell at the retinoblastoma-1 locus, indicating that one copy of the gene was deleted. Peripheral blood lymphocytes obtained from the patient's parents had two copies per cell for the gene. Retinoblastoma nuclear phosphoprotein expression could not be detected in the tumor tissue. No copy number alterations were detected with ten different centromeric DNA probes in the tumor cells. The deletion at the RB1 locus detected by FISH suggested that this gene alteration was heritable. The parental peripheral blood lymphocytes did not show the loss of the gene; thus the first deletion may have taken place in either of the parental germ cells. The second somatic mutation of the RB1 gene was probably under the detection limit of FISH. The second allelic alterations were detected by using the polymerase chain reaction for all exons of the retinoblastoma gene.

To characterize the possible cytogenetic link between a primary tumor and its metastasis, interphase cytogenetic analysis was performed on tumor cells and cutaneous metastasis from a male patient with malignant melanoma by using fluorescence in situ hybridization. The numbers of distinct hybridization domains specific for ten different pericentromeric sequences were used as indicators of copy numbers of these chromosomes. In the primary tumor, the majority of cells had two copies of these chromosomes, but significant numbers of nuclei also were present with one and three copies. In addition, in almost all cells, both sex chromosomes were abnormal; nullisomy of the Y chromosome was associated with X disomy. The corresponding metastatic tumor cells were predominantly monosomic; only the distribution of chromosomes 11 and 7 was similar to the primary tumor. In the metastatic tumor, the sex chromosomes had a normal copy number; that is, one Y and one X were detected. These data indicate that both the initiation and the progression of this melanoma are associated with chromosome losses.