Reporting of diagnostic cytogenetic results

This appendix, developed by the staff at the Clinical Cytogenetics Laboratory at the Brigham and Women's Hospital, includes a comprehensive list of current "macros" or standardized statements used to facilitate reporting of cytogenetic results. These are provided as a reference for other laboratories. The statements are organized under the general categories of constitutional or acquired abnormalities and subdivided into analysis type (GTG-banding or FISH). Multi-specimen usage macros are included that can be applied to two or more specimen types.

Central review of cytogenetics is necessary for cooperative group correlative and clinical studies of adult acute leukemia: the Cancer and Leukemia Group B experience

The Cancer and Leukemia Group B has performed central review of karyotypes submitted by institutional cytogenetics laboratories from patients with acute myeloid (AML) and acute lymphoblastic (ALL) leukemia since 1986. We assessed the role of central karyotype review in maintaining accurate, high quality cytogenetic data for clinical and translational studies using two criteria: the proportion of karyotypes rejected (i.e. inadequate), and, among accepted (i.e. adequate) cases, the proportion of karyotypes whose interpretation was changed on central karyotype review. We compared the first four years during which central karyotype review was performed with a recent 4-year period and found that the proportion of rejected samples decreased significantly for both AML and ALL. However, during the latter period, central karyotype reviews still found 8% of AML and 16% of ALL karyotypes inadequate. Among adequate cases, the karyotype was revised in 26% of both AML and ALL samples. Some revisions resulted in changing the patients' assignment to particular World Health Organization diagnostic categories and/or moving patients from one prognostic group to another. Overall, when both data on rejection rates and data on karyotype revisions made in accepted cases were considered together, 32% of AML and 38% of ALL samples submitted were either rejected or revised on central karyotype review during the recent 4-year period. These data underscore the necessity of continued central karyotype review in multi-institutional cooperative group studies.

Trisomies 8 and 9 not detected with fish in patients with mastocytosis

Mastocytosis is a rare disease characterized by proliferation of mast cells in one or several organs. With conventional cytogenetics about 35% of the patients have chromosomally abnormal clones in bone marrow cells. It has been proposed to include the mast cell disease among the myeloproliferative disorders, in which trisomy for chromosome 8 and 9 can appear in the bone marrow cells. In this study bone marrow cells from eight patients with mastocytosis, two had as well an associated hematological disease, have been examined with fluorescence in situ hybridization (FISH) for enumeration of chromosome no8 and 9. In conventional cytogenetics two patients had clones with del(20) and 47,XY,+14/45, X,-Y, respectively. None of the patients with mastocytosis had clones with trisomy 8 or 9 with either cytogenetics or FISH.

Spectral karyotyping analysis of head and neck squamous cell carcinoma

OBJECTIVES/HYPOTHESIS

The genetic content of head and neck squamous cell carcinomas is ill defined. Spectral karyotyping (SKY) is a new technique that allows the simultaneous detection of all chromosomal translocations by labeling each individual chromosome with different fluorescent agents. In the current study we used SKY to analyze cell lines and a primary tumor derived from head and neck squamous cell carcinomas (HNSCC) to delineate recurrent translocations and breakpoints.

STUDY DESIGN

Spectral karyotyping analysis of head and neck cancer.

METHODS

Two cell lines (MDA886 and MSK922) and one primary tumor in short-term culture were subjected to metaphase growth arrest with colcemide in their exponential growth phase and fixed onto glass slides. Painting probes for each of the autosomes and the sex chromosomes were generated from flow-sorted human chromosomes using sequence-independent DNA amplification. The probes were labeled using a polymerase chain reaction-based reaction and hybridized to metaphase preparations for 2 days at 37 degrees C. Biotinylated probes were detected using avidin Cy5 and digoxigenin-labeled probes with an anti-mouse digoxigenin antibody followed by goat anti-mouse antibody conjugated to Cy5.5. Chromosomes were counterstained with 4,6-diamino-2-phenyliodole (DAPI), and a minimum of five metaphases were captured and analyzed for each case. Breakpoints on the SKY-painted chromosomes were determined by comparison of corresponding DAPI banding.

RESULTS

Spectral karyotyping analysis revealed a complex pattern of chromosomal abnormalities. A total of 66 translocations were identified in the three cases, with one new recurrent translocation at (der(4)t(4;20)(q35;?)). Nine complex translocations, involving three or more chromosomes, were identified in these cases. Overall, 96 breakpoints were assigned to metaphase chromosomes and another 74 breakpoints could not be assigned. Breakpoints most commonly involved chromosomes in genetic rearrangements were 1, 3, 5, 8, 13, 16, and 17.

CONCLUSIONS

Spectral karyotyping analysis reveals the true complexity of chromosomal aberrations in cell lines derived from head and neck squamous cell carcinomas. The use of SKY, in combination with other techniques, may allow for a more complete assessment of the genetic abnormalities of head and neck cancers and serve as a starting point for gene identification.

Masked monosomy 7 in myelodysplastic syndromes is uncommon and of undetermined clinical significance

Masked monosomy 7, i.e. detected by FISH but not by conventional cytogenetics, has been reported in varying frequency in MDS. To establish the prevalence and possible clinical significance of the aberration, we studied the 123 previously karyotyped MDS patients using FISH and a DNA probe specific for chromosome 7. Metaphase cytogenetics revealed ten patients (8%) with monosomy 7 (6 RAEB and 4 RAEB-t). FISH confirmed this result and detected four more cases (4%) with masked monosomy 7 (3 RA and 1 RARS). Thus, masked monosomy 7 is less common than has been suggested, and does not seem to carry the same prognostic weight as monosomy 7 diagnosed by metaphase cytogenetics.

A multicenter investigation with interphase fluorescence in situ hybridization using X- and Y-chromosome probes

Twenty-six laboratories used X and Y chromosome probes and the same procedures to process and examine 15,600 metaphases and 49,400 interphases from Phaseolus vulgaris-leucoagglutinin (PHA)-stimulated lymphocytes. In Part I, each laboratory scored 50 metaphases and 200 interphases from a normal male and a normal female from its own practice. In Part II, each laboratory scored 50 metaphases and 200 interphases on slides prepared by a central laboratory from a normal male and a normal female and three mixtures of cells from the male and female. In Part III, each laboratory scored 50 metaphases (in samples of 5, 10, 15, and 20) and 100 interphases (in samples of 5, 10, 15, 20, and 50) on new, coded slides of the same specimens used in Part II. Metaphases from male specimens were scored as 98-99% XY with no XX cells, and 97-98% of interphases were scored as XY with 0.04% XX cells. Metaphases from female specimens were scored as 96-97% XX with 0.03% XY cells, and 94-96% of interphases were scored as XX with 0.05% XY cells. Considering the data as a model for any probe used with fluorescence in situ hybridization (FISH), a statistical approach assessing the impact of analytical sensitivity on the numbers of observations required to assay for potential mosaicisms and chimerisms is discussed. The workload associated with processing slides and scoring 50 metaphases and 200 interphases using FISH averaged 27.1 and 28.6 minutes, respectively. This study indicates that multiple laboratories can test/develop guidelines for the rapid, efficacious, and cost-effective integration of FISH into clinical service.

Retesting for fragile X syndrome in cytogenetically normal males

This case series describes four males who presented with learning and behavioural difficulties. In each case, the diagnosis of fragile X syndrome was delayed because of an initial false-negative cytogenetic result. Although most children are currently investigated for fragile X syndrome using highly sensitive and specific molecular techniques, there still remain a large number of older children who have been tested using only cytogenetic analysis. The clinical presentation of these four children and the reason for the occurrence of the false-negative results are considered. In addition, there is a discussion and illustration of how a screening checklist can be used to help clinicians to decide which children should be retested.

A five-year experience with fragile X testing. Setting laboratory standards of practice and a cost-effective protocol

During the years 1990-1994, our center tested 652 patients, with a broad range of referral indications, for fragile X syndrome using either cytogenetic analysis alone (Protocol 1) or more recently, a combination of DNA analysis and routine karyotyping (protocol 2). The overall positive rate for fragile X was 3.1% with an incidence of other chromosomal abnormalities (OCAs) of 3.2%. Breakdown of cases using each testing protocol along with percent positives is: [table: see text] Use of Protocol 2 yielded only definitive fragile X results, while more than half of the "positives" using Protocol 1 were equivocal. Historically this has been problematic for both the laboratory and physician since interpretation is often dependent on an equally equivocal clinical picture. Protocol 2 eliminates these diagnostic dilemmas without compromising detection of other chromosomal abnormalities, the incidence of which appears to be unaffected by testing method used. The overall incidence of OCA of 3.2% underscores the value of routine karyotyping in this referral group and likely reflects the phenotypic variability of fragile X and its clinical overlap with other chromosomal abnormalities. We believe that a fragile X testing protocol combining routine karyotyping with definitive molecular technology represents the most cost-effective diagnostic approach to this clinically challenging patient population.

Solid tissue culture for cytogenetic analysis: a collaborative survey for the Association of Clinical Cytogeneticists

AIMS

To survey the diagnostic service provided by UK laboratories for the culture of solid tissue samples (excluding tumours) and in particular to examine the variation in culture success rates and the problems of maternal cell overgrowth.

METHODS

Twenty seven laboratories took part in a collaborative survey during 1992. Each laboratory submitted data on up to a maximum of 60 consecutive specimens (n = 1361) over a six month period.

RESULTS

Skin specimens, the largest category received (n = 520), were the most problematic (51% success rate). Culture success rates were significantly lower (43%) when skin specimens (n = 140) were transported dry to the laboratory. Success rates for skin specimens also varied, depending on the origin of the specimen, from 18% for intra-uterine deaths (IUD) (n = 94) to 85% for neonatal deaths (n = 33) and 83% for live patients (n = 54). Culture of selected extra-fetal tissues from IUD, stillbirths and following elective termination of pregnancy (TOP) gave comparable success rates to those achieved for skin samples from neonatal deaths and live births. Skewed sex ratios, female > male, were identified for products of conception (POC) (n = 298) and placental biopsy specimens (n = 97).

CONCLUSIONS

By appropriate selection, transport and processing of tissues, and in particular by avoiding relying solely on skin samples from IUD, stillbirths and TOP, an increase in culture success rates for solid tissue samples submitted for cytogenetic analysis could be achieved. The high risk of maternal cell contamination from POC and placental biopsy specimens was also identified in this survey.

Statistical methods in interphase cytogenetics: an experimental approach

In situ hybridization (ISH) techniques on interphase cells, or interphase cytogenetics, have powerful potential clinical and biological applications, such as detection of minimal residual disease, early relapse, and the study of clonal evolution and expansion in neoplasia. Much attention has been paid to issues related to ISH data acquisition, i.e., the numbers, colors, intensities, and spatial relationships of hybridization signals. The methodology concerning data analysis, which is of prime importance for clinical applications, however, is less well investigated. We have studied the latter for the detection of small monosomic and trisomic cell populations using various mixtures of human female and male cells. With a chromosome X specific probe, the male cells stimulated monosomic subpopulations of 0, 1, 5, 10, 50, 90, 95, 99, and 100%. Analogously, when a (7 + Y) specific probe combination was used, containing a mixture of chromosome No. 7 and Y-specific DNA, the male cells simulated trisomic cell populations. Probes specific for chromosomes Nos. 1, 7, 8, and 9 were used for estimation of ISH artifacts. Three statistical tests, the Kolmogorov-Smirnov test, the multiple-proportion test, and the z'-max test, were applied to the empirical data using the control data as a reference for ISH artifacts. The Kolmogorov-Smirnov test was found to be inferior for discrimination of small monosomic or trisomic cell populations. The other two tests showed that when 400 cells were evaluated, and using selected control probes, monosomy X could be detected at a frequency of 5% aberrant cells, and trisomy 7 + Y at a frequency of 1%.(ABSTRACT TRUNCATED AT 250 WORDS)

Centromere index derivation by a novel and convenient approach

A previous study has shown the utility of a graphics arts tool in deriving chromosome measurements for relative length determination. It is our hypothesis that the same approach also can be used accurately for centromere index determination. Results based on a study of 50 cells and comparisons with values cited in An International System for Human Cytogenetic Nomenclature (ISCN) are consistent with this hypothesis. Chromosome morphometry is an important adjunct to conventional cytogenetics in suboptimal banded preparations and/or inadequate specimens such as samples from cancer patients.

Cytogenetic guidelines for fragile X studies tested in routine practice

Several organizations have proposed guidelines for fra(X) studies on peripheral blood lymphocytes. To evaluate these guidelines, we reviewed 1,033 consecutive specimens referred for fra(X) analysis. Each specimen was cultured with medium 199 and RPMI 1640 with 5-fluorodeoxyuridine or excess thymidine. The karyotype and expression of fra(X) were established from 20 GTL- or QFQ-banded cells and by screening of up to 130 more banded cells. We found anomalies other than fra(X) in 37 (3.6%) of the patients. We found 4% or more fra(X) cells in 38 (3.7%) cases from 36 unrelated families, including 33 (3.9%) of 850 males and 5 (2.7%) of 183 females. Another 4 females had 1 to 3% fra(X) cells. Six specimens were fra(X)-positive in only one stress system, and 32 were positive in 2 systems. To find the first 2 fra(X) cells in males, we needed to study up to 36 cells in 31 cases, 50 in one case, and 57 in another. To find the first 2 fra(X) cells in females, we needed to study up to 17 cells in 4 cases and 57 in another. A strong family history of fra(X) occurred in 5 patients, and each one was fra(X)-positive. Some manifestations of the fragile X syndrome occurred in 507 cases, 17 (3%) of which were fra(X)-positive. Abnormalities considered unlikely to be the fragile X syndrome occurred in 103 cases, 3 (3%) of which were fra(X)-positive. Use of chromosome breakage and fra(3)(p14) as quality control indicators of the fra(X) stress systems was found to be unreliable.(ABSTRACT TRUNCATED AT 250 WORDS)

Traditional and molecular cytogenetics

Traditional cytogenetic methods have relied on tissue culture techniques to generate adequate mitotic cells for the analysis of chromosome disorders for prenatal diagnosis. Chromosome banding techniques allow the evaluation of mitotic cells for structural and numerical aberrations and define the nature of any rearrangement. With the advent of fluorescent in situ hybridization methodology, which combines the molecular technologies of chromosome-specific probes and in situ molecular hybridization, it has become possible to analyze chromosomal numerical and structural aberrations from interphase cells. The use of molecular cytogenetic techniques should greatly increase the speed and diagnostic resolution of clinical specimens.

Fetal cells in the maternal circulation

The analysis of fetal cells from the maternal circulation would be the least invasive method of prenatal diagnosis. Potential fetal cell types to enter the maternal circulation are lymphocytes, trophoblast cells and nucleated erythrocytes. With conventional methods, such as cytology and interphase or metaphase cytogenetics, the ratio of fetal to maternal cells was overestimated in the past. Currently most groups use polymerase chain reaction-based Y-sequence analysis for the detection of fetal cells in pregnancies with male fetuses, either with or without prior enrichment of fetal cells. For fetal cell separation, fluorescence-activated cell sorting and immunomagnetic beads have been applied, and recently our group has used discontinuous density gradient centrifugation for this purpose. We have shown that the transferrin receptor antigen alone is not sufficient for enrichment of fetal nucleated erythrocytes. Despite some initial promising results with fluorescence in situ hybridization, the reproducibility and reliability of the techniques are still limited, mainly due to the lack of very specific cell markers and the very low and variable concentrations of fetal cells among numerous maternal cells.

Chromosome analysis guidelines preliminary report

These guidelines have been developed by the Association of Cytogenetic Technologists (ACT) for chromosome analysis. In formulating its recommendations, the task force reviewed guidelines established by several states and regional genetics groups. Draft guidelines prepared by the task force were reviewed by a panel of expert consultants, all of whom are laboratory directors and well known in their respective fields of expertise. The intention of the task force was to reflect procedures that are believed to be generally accepted by cytogenetic laboratories as basic criteria for effective chromosome analysis and that are consistent with existing cytogenetic quality assurance guidelines. It is important to stress that the primary purpose of the task force at this time is to establish guidelines for chromosome analysis. While the present guidelines address issues other than chromosome analysis, they do so incidentally and only in general terms. A more comprehensive discussion of other technical aspects of cytogenetics can be found in the forthcoming second edition of the ACT Cytogenetics Laboratory Manual. It is important to note that these guidelines are not intended to prescribe appropriate analyses for all individual circumstances. That determination is appropriately a matter for the judgment of the laboratories concerned. ACT, its members, and the task force that assisted in preparation of these guidelines make no warranty and assume no liability with respect to the information contained herein.

In situ hybridization analysis of isodicentric X-chromosomes with short arm fusion

We present here an alternative approach to the study of mosaic cell lines containing dicentric chromosomes. The approach is based on chromosome-specific non-radioactive in situ hybridization with centromere (alpha satellite DNA) probes. The hybridization analysis may be used as an alternative to the C-band analysis, while at the same time to some extent replacing the Q-band analysis as well. The advantage of using in situ hybridization is mainly that it allows the very fast screening of a large number of metaphases. We illustrate this new application of the technique by using it for the analysis of two cases of isodicentric X-chromosomes. The approach is expected to be generally applicable, so that it may be applied to the scoring of other types of chromosomal mosaicism as well.