ABSTRACT
Most germ cell tumors have an isochromosome 12p (detected by metaphase cytogenetics), 12p overrepresentation (detected by fluorescence in situ hybridization [FISH]), or both. Although interphase FISH on paraffin-embedded tissue is a sensitive method of detection of 12p anomalies, use of FISH for clinical diagnostic purposes is not well defined. We describe an interphase FISH assay for detection of increased 12p copy number in germ cell tumors using a bacterial artificial chromosome-derived probe localized to 12p12.1 and a commercially available probe for the centromere of chromosome 12. Twenty-four paraffin-embedded blocks from 14 tumor cases (7 malignant mixed germ cell tumors, 2 dysgerminomas, 4 non-germ cell malignancies arising in germ cell tumors, and 1 mediastinal adenocarcinoma) and 18 normal controls were studied. Negative controls included normal lymph node, lung, and mediastinal tissue. The signals for 12p and 12cen were counted, and the ratio of the averaged signals was calculated; a ratio of 1.3 was considered positive. All germ cell tumors and non-germ cell malignancies arising in germ cell tumors were positive for 12p overrepresentation. All control cases were negative. Because germ cell tumors may metastasize with non-germ cell tumor morphology, interphase FISH may be helpful in distinguishing de novo malignancy from germ cell tumor recurrence in its various forms.
Subject(s)
Chromosomes, Artificial, Bacterial , Chromosomes, Human, Pair 12 , In Situ Hybridization, Fluorescence/methods , Neoplasms, Germ Cell and Embryonal/genetics , Adult , Humans , Male , Middle Aged , Paraffin EmbeddingABSTRACT
Inflammatory myofibroblastic tumors (IMTs) are rare soft tissue tumors occurring primarily in children and young adults. ALK gene rearrangements have been identified in this neoplasm, with fusion of the ALK gene at 2p23 to a number of different partner genes. Metaphase cytogenetic analyses of these tumors have been relatively few, however, and may help to identify additional variant partners. We report on an IMT from a 2-year-old boy with a karyotype of 45,XY,der(2)inv(2)(p23q12)del(2)(p11.1p11.2),-22. FISH showed ALK-RANBP2 fusion in this tumor. The breakpoint was cloned and the fusion was confirmed, making this the third reported case of IMT with ALK-RANBP2 fusion. In addition, we identified the ALK fusion partner in a previously reported IMT with t(2;17)(p23;q23) as CLTC, a gene reported to be involved in four other IMTs, and showed that the breakpoint involved a novel ALK-CLTC fusion. FISH evaluation of nine other IMTs identified CLTC as the fusion partner in one additional case, but RANBP2 was not involved in the remaining eight IMTs, suggesting that the variant partners involved in ALK rearrangements in IMTs are diverse.
Subject(s)
Clathrin Heavy Chains/physiology , Molecular Chaperones/physiology , Nuclear Pore Complex Proteins/physiology , Protein-Tyrosine Kinases/genetics , Soft Tissue Neoplasms/genetics , Anaplastic Lymphoma Kinase , Base Sequence , Child, Preschool , Chromosome Inversion , Clathrin Heavy Chains/genetics , DNA Mutational Analysis , Gene Deletion , Humans , Inflammation/genetics , Karyotyping , Male , Molecular Chaperones/genetics , Molecular Sequence Data , Mutation , Nuclear Pore Complex Proteins/genetics , Oncogene Proteins, Fusion/genetics , Receptor Protein-Tyrosine KinasesABSTRACT
Amelogenin has chromosome X (AMELX) and Y (AMELY) homologs that can be differentiated based on the length of polymerase chain reaction (PCR) amplification products. In addition to being useful for gender identification, analysis of amelogenin has utility for monitoring bone marrow engraftment in patients after a sex-mismatched bone marrow transplant, characterizing sex chromosome abnormalities, and for forensic purposes for analyzing mixtures of male and female DNA. Here, we describe two brothers in which PCR analysis demonstrated twofold greater AMELY products compared with AMELX products. Karyotype and X/Y fluorescence in situ hybridization analysis demonstrated a single copy of the X and Y chromosomes without any identifiable abnormalities. Oligonucleotide comparative genomic hybridization array analysis demonstrated a duplication of a portion of chromosome Yp that encompassed a region of at least 2.6 Mb but not greater than 4.0 Mb. The amplified region contains the genes AMELY, transducin (beta)-like 1 protein Y (TBL1Y), and protein kinase Y (PRKY). To our knowledge, duplication of this region has not previously been reported. The family history is unremarkable, and the brothers are without ap-parent dysmorphic features. Although this and other genetic variants involving AMELY are uncommon, one should use caution when using amelogenin for sex chromosome analysis and bone marrow engraftment analysis.
