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Cytogenetic analysis of tumor tissue detects clonal abnormalities. The information obtained from these studies is utilized for diagnosis, prognosis, and patient management.: The Working Group of the Laboratory Quality Assurance Committee of the American College of Medical Genetics provides these Standards and Guidelines for chromosome studies for solid tumors abnormalities as a resource for clinical cytogenetic laboratories.: The guidelines incorporate aspects of sample procurement, handling, processing, harvesting, analysis, quality control, and quality assurance. It is recommended that all pediatric solid tumors be studied by cytogenetic analysis when feasible due to the clinical and therapeutic implications of the genetic abnormalities. Cytogenetic analysis of certain adult solid tumors also provides information that impacts diagnosis and therapeutics. Molecular cytogenetic analysis or fluorescence in situ hybridization (FISH) may be a primary or secondary method of evaluation of the tumor tissue. FISH can document a specific molecular event, e.g. gene rearrangement, provide a rapid result to aid in the differential diagnosis or planning of therapy, clarify chromosome anomalies, or assess gene amplification.: Genetic analysis adds valuable information to the understanding of and therapeutic approach to solid tumors. Laboratories may use their professional judgment to make modifications or additions to these guidelines.

Fluorescence in situ hybridization (FISH) provides an important adjunct to conventional cytogenetics and molecular studies in the evaluation of chromosome abnormalities associated with hematologic malignancies. FISH employs DNA probes and methods that are generally not Food and Drug Administration-approved, and therefore, their use as analyte-specific reagents involves unique pre- and postanalytical requirements. We provide an overview of the technical parameters influencing a reliable FISH result and encourage laboratories to adopt specific procedures and policies in implementing metaphase and interphase FISH testing. A rigorous technologist training program relative to specific types of probes is detailed, as well as guidance for consistent interpretation of findings, including typical and atypical abnormal results. Details are provided on commonly used dual-fusion, extra signal, and break-apart probes, correct FISH nomenclature in the reporting of results, and the use of FISH in relation to other laboratory testing in the ongoing monitoring of disease. This article provides laboratory directors detailed guidance to be used in conjunction with existing regulations to successfully implement a FISH testing program or to assess current practices, allowing for optimal clinical testing for patient care.

The fragile X syndrome is characterized at the molecular level by expansion and methylation of a CGG trinucleotide repeat located within the FMR1 locus. The tissues of most full mutation carriers are mosaic for repeat size, but these mutational patterns tend to be well conserved when comparing multiple tissues within an individual. Moreover, full mutation alleles are stable in cultured fibroblasts. These observations have been used to suggest that fragile X CGG repeat instability normally is limited to a period during early embryogenesis. DNA methylation of the repeat region is also believed to occur during early development, and some experimental evidence indicates that this modification may stabilize the repeats. To study the behavior of full mutation alleles in mitotic cells, we generated human-mouse somatic cell hybrids that carry both methylated and unmethylated full mutation FMR1 alleles. We observed considerable repeat instability and analyzed repeat dynamics in the hybrids as a function of DNA methylation, repeat length and cellular differentiation. Our results indicate that although DNA methylation does correlate with stability in primary human fibroblasts, it does not do so in the cell hybrids. Instead, repeat stability in the hybrids is dependent on repeat length, except in an undifferentiated cellular background where large alleles are maintained with a high degree of stability. This stability is lost when the cells undergo differentiation. These results indicate that the determinants of CGG repeat stability are more complex than generally believed, and suggest an unexpected role for cellular differentiation in this process.

Summary The vast majority of fragile-X full mutations are heavily methylated throughout the expanded CGG repeat and the surrounding CpG island. Hypermethylation initiates and/or stabilizes transcriptional inactivation of the FMR1 gene, which causes the fragile X–syndrome phenotype characterized, primarily, by mental retardation. The relation between repeat expansion and hypermethylation is not well understood nor is it absolute, as demonstrated by the identification of nonretarded males who carry hypomethylated full mutations. To better characterize the methylation pattern in a patient who carries a hypomethylated full mutation of ∼60–700 repeats, we have evaluated methylation with the McrBC endonuclease, which allows analysis of numerous sites in the FMR1 CpG island, including those located within the CGG repeat. We report that the expanded-repeat region is completely free of methylation in this full-mutation male. Significantly, this lack of methylation appears to be specific to the expanded FMR1 CGG-repeat region, because various linked and unlinked repetitive-element loci are methylated normally. This finding demonstrates that the lack of methylation in the expanded CGG-repeat region is not associated with a global defect in methylation of highly repeated DNA sequences. We also report that de novo methylation of the expanded CGG-repeat region does not occur when it is moved via microcell-mediated chromosome transfer into a de novo methylation-competent mouse embryonal carcinoma cell line.

At the International Congress of Human Genetics (Jerusalem, September, 1981) a Workshop was held on the fragile X chromosome; it was entitled “The Fragile X Chromosome: Current Methods.” It was to focus on laboratory methods required to detect or to enhance the detection of the fragile X. The fragile site on the X chromosome is one of 13 proven fragile sites known in humans. (A diagram of these sites is provided.) The fragile site on the X is sensitive to the concentration of folic acid in the medium in which cells are cultured. Cytologically, gaps and breaks are increased at the X fragile site, which is located at band Xq27–28. To enhance expression in lymphocytes, prolongation of culture time to 96 hours, elevation of the pH, diminution of the colcemid effect, and air drying of slides are helpful. The need for methionine in low-folate media can be overridden by the addition of fluorodeoxyuridine (FUdR). Detection of the fragile X in males requires meticulous attention to methods of lymphocyte culture and metaphase preparation and then the examination of a sufficient number of mitoses, eg, 50–100 metaphases per individual. Detection of the fragile X in female carriers is often more difficult. Uniform detection of all obligate female carriers has not been achieved. Difficulty may correlate with increasing age or intelligence of females. Key methodologic advances with the fragile X include the addition of methotrexate, trifluorothymidine or, especially of FUdR to the culture medium. FUdR, for example, is helpful in demonstrating the fragile X in lymphoblastoid cell lines and fibroblasts. Both of these cell types now represent an opportunity to study the biochemistry of the fragile X. The success of the FUdR technique with skin fibroblasts heralds the feasibility of demonstrating the fragile X chromosome in cultured amniocytes. Since the Workshop, it has been reported that with FUdR the fragile X could in fact be detected in 46,XY amniotic fluid cells.

The tissue culture condition that is required for the type of chromosome breakage seen at most fragile sites, namely, the absence of folic acid and thymidine in the medium, greatly enhanced micronucleus formation in proliferating lymphocyte cultures from normal individuals. This suggests that chromosome breakage at fragile sites and the apparently spontaneous damage that gives rise to micronuclei are controlled by the same mechanism.

A cell line (FMC-Hu-1-B) was established from a biopsy of an abdominal mass of a child with non-Burkitt's lymphoma. The establishment of the cell line initially required the presence of normal bone marrow stromal cells and phytohaemagglutinin stimulated leucocyte conditioned medium. The cell line lacked Epstein-Barr virus nuclear antigen and exhibited numerous chromosomal abnormalities. Cell-surface marker analysis using a panel of monoclonal antibodies revealed only markers of the B lineage. Within the B-cell lineage FMC-Hu-1-B seemed to occupy a level of maturation equivalent to normal mature B-cells (surface membrane IgM, secretion of immunoglobulin and FMC-1 positive). However, the cells also weakly expressed the common acute lymphoblastic leukaemia antigen, normally found on early precursors of B-cells. The cells appear to secrete auto-stimulatory growth factor(s).