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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.

Section E6 of the ACMG technical standards and guidelines: Chromosome studies for acquired abnormalitie: This updated Section E6 has been incorporated into Section E: Clinical Cytogenetics of the 2005 ACMG Standards and Guidelines for Clinical Genetics Laboratories and supersedes the previous section E6

Preface: The Quality Assurance subcommittee of the ACMG Laboratory Practice committee has the mission of maintaining high technical standards for the performance and interpretation of genetic tests. In part, this is accomplished by the publication of the document “Standards and Guidelines for Clinical Genetics Laboratories,” which was published in its second edition in 1999 and is now maintained online (see http://www.faseb.org/genetics/acmg/index.html ). This subcommittee also reviews the outcome of national proficiency testing in the genetics area and may choose to focus on specific diseases or methodologies in response to those results. Accordingly, the subcommittee selected fragile X syndrome to be the first topic in a new series of supplemental sections, recognizing that it is one of the most frequently ordered genetic tests and that it has many alternative methods with different strengths and weaknesses. This document follows the outline format of the general Standards and Guidelines. It is designed to be a checklist for genetic testing professionals who are already familiar with the disease and the methods of analysis.

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.

We present clinical outcome, through several years of follow-up, of 4 mentally retarded patients, each with a small interstitial deletion in the long arm of chromosome 2, within a region on which clinical reports are infrequent. Our patient 1 was found to have del(2)(q22.3q23.3); patients 2 and 3, del(2)(q23.3q24.2); and patient 4, del(2) (q24.2q31). By comparison of our cases with each other and with those previously published with comparable interstitial deletion, we attempted to identify characteristic clinical findings. Short neck with excessive cervical skin was seen with monosomy of chromosome 2 bands q22.3-q23.3, while hypertrichosis and a peculiar high pitched cry were seen with monosomy of chromosome 2 bands q23.3-q24.2. As suggested by Moller et al. [1984: Hum Genet 68:77-86], a cleft between the first and second toes was seen with monosomy of chromosome 2 bands q24.2-q31. In addition, seizure disorder was present in patients 1 and 4 (with the more proximal and distal deletions, respectively).

Niels Tommerup , Malene B. Rasmussen , Mana M. Mehrjouy , Iben Bache , Allan Lind-Thomsen , Ana Carolina dos Santos Fonseca , Christina Halgren , Mads Bak , Peter Jacky , The International Breakpoint Mapping Consortium (IBMC) University of Copenhagen, Department of Cellular and Molecular Medicine, Copenhagen, Denmark; Universidade de Sao Paulo, Departamento de Genetica e Biologia Evolutiva, Sao Paulo, Brazil; Northwest Permanente, PC, Emeritus, OR, USA

Peripheral blood lymphocytes from clinically normal Doberman pinscher and boxer dogs were cultured for folate-sensitive and, in preliminary studies, aphidicolin-inducible fragile site expression. Both autosomal and X chromosomal fragile sites were observed in canine cells cultured under folate/thymidine depletion and in cells cultured in medium containing aphidicolin. Results from the three dogs evaluated for both folate-sensitive and aphidicolin-inducible fragile site expression showed that the frequency of fragile site expression was significantly (P less than 0.05) greater in cells cultured in medium containing aphidicolin than in cells cultured in folate/thymidine-depleted medium. Cells from the boxer dog expressed a high percentage (66.67%) of aphidicolin-inducible fragile sites in contrast to the Doberman pinscher dog in which only 21.10% of the lymphocytes expressed aphidicolin-inducible fragile sites. The frequencies of spontaneous and folate-sensitive fragile site expression did not vary significantly by breed of dog. Age of dog was significantly and positively correlated with frequency of folate-sensitive fragile site expression in dogs of the boxer breed, but not in dogs of the Doberman pinscher breed. The dog X chromosome expressed three folate-sensitive and aphidicolin-inducible fragile sites. The G-band location of these three fragile sites showed homology with three recognized constitutive common fragile sites on the human X chromosome: Xp22, Xq21, and Xq27.2. Two specific autosomal fragile sites were identified, one on the distal end of the long arm of chromosome 1 and one on the distal end of the long arm of chromosome 8. Other autosomal fragile sites were also apparent but could not be assigned reliably to specific chromosomes.

Cytogenetic investigations of the domestic dog, Canis familiaris, were performed on one Doberman pinscher and two Boxer dogs. Conventional homogeneously stained and G-banded metaphases from peripheral blood lymphocyte cultures synchronized with amethopterin and bromodeoxyuridine were studied. These procedures permitted the unequivocal identification of all canine chromosomes. A canine chromosome idiogram was constructed on the basis of the G-banding pattern at the haploid 327-band resolution level. The secondary constrictions and tapering of the telomeric regions characteristic of several canine chromosomes are described. Q-, C-, and NOR-banding were also performed and the salient features are described. This karyotype should enhance the value of the canine species in cytogenetic investigations.Key words: canine karyotype, G-banding, Q-banding, C-banding, NOR-banding, cell synchronization idiogram.

We evaluated four canine cutaneous mast cell tumors cytogenetically. All four tumors contained both hypodiploid and hyperdiploid cells, an increase in the number of metacentric chromosomes, exchange configurations, and cells showing loss of an X chromosome. All tumors contained metaphases with chromosome gaps and breaks at frequencies greater than observed spontaneous chromosome breaks in normal cultured canine peripheral blood lymphocytes. Three of the four tumors had a normal modal chromosome number of 78. The fourth tumor had a modal chromosome number of 93, which represented 15% of the cells evaluated from this tumor.

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).