Utility of multicolor fluorescent in situ hybridization in clinical cytogenetics

Combining Multicolor FISH with Fluorescence Lifetime Imaging for Chromosomal Identification and Chromosomal Sub Structure Investigation

Understanding the structure of chromatin in chromosomes during normal and diseased state of cells is still one of the key challenges in structural biology. Using DAPI staining alone together with Fluorescence lifetime imaging (FLIM), the environment of chromatin in chromosomes can be explored. Fluorescence lifetime can be used to probe the environment of a fluorophore such as energy transfer, pH and viscosity. Multicolor FISH (M-FISH) is a technique that allows individual chromosome identification, classification as well as assessment of the entire genome. Here we describe a combined approach using DAPI as a DNA environment sensor together with FLIM and M-FISH to understand the nanometer structure of all 46 chromosomes in the nucleus covering the entire human genome at the single cell level. Upon DAPI binding to DNA minor groove followed by fluorescence lifetime measurement and imaging by multiphoton excitation, structural differences in the chromosomes can be studied and observed. This manuscript provides a blow by blow account of the protocol required to perform M-FISH-FLIM of whole chromosomes.

Spectral imaging to visualize higher-order genomic organization

A concern in the field of genomics is the proper interpretation of large, high-throughput sequencing datasets. The use of DNA FISH followed by high-content microscopy is a valuable tool for validation and contextualization of frequently occurring gene pairing events at the single-cell level identified by deep sequencing. However, these techniques possess certain limitations. Firstly, they do not permit the study of colocalization of many gene loci simultaneously. Secondly, the direct assessment of the relative position of many clustered gene loci within their respective chromosome territories is impossible. Thus, methods are required to advance the study of higher-order nuclear and cellular organization. Here, we describe a multiplexed DNA FISH technique combined with indirect immunofluorescence to study the relative position of 6 distinct genomic or cellular structures. This can be achieved in a single hybridization step using spectral imaging during image acquisition and linear unmixing. Here, we detail the use of this method to quantify gene pairing between highly expressed spliceosomal genes and compare these data to randomly positioned in silico simulated gene clusters. This is a potentially universally applicable approach for the validation of 3C-based technologies, deep imaging of spatial organization within the nucleus and global cellular organization.

Overview of Clinical Cytogenetics

Chromosome analysis is one of the first approaches to genetic testing and remains a key component of genetic analysis of constitutional and somatic genetic disorders. Numerical or unbalanced structural chromosome abnormalities usually lead to multiple congenital anomalies. Sometimes these are compatible with live birth, usually resulting in severe cognitive and physical handicaps; other times they result in miscarriage or stillbirth. Chromosome rearrangements also occur as somatic changes in malignancies. Identification of constitutional chromosomal anomalies (anomalies present in most or all cells of the body and/or the germline) can provide important information for genetic counseling. In this unit, we introduce chromosomal microarray analysis (CMA), which is a relatively recent addition to cytogenetic technologies, and has become the recommended first-tier testing method for patients with developmental delay, intellectual disability, autism, and/or multiple congenital anomalies. We also discuss non-invasive prenatal testing/screening (NIPTS), which uses circulating cell-free fetal DNA (cfDNA) from maternal plasma to rapidly screen for autosomal and sex-chromosome aneuploidies. Cytogenetic analysis of tumors is helpful in diagnosis and in monitoring the effects of treatment. The protocols in this chapter cover the clinical study of chromosomes in nonmalignant tissues.

Karyotyping human and mouse cells using probes from single-sorted chromosomes and open source software

Multispectral karyotyping analyzes all chromosomes in a single cell by labeling them with chromosome-specific probes conjugated to unique combinations of fluorophores. Currently available multispectral karyotyping systems require the purchase of specialized equipment and reagents. However, conventional laser scanning confocal microscopes that are capable of separating multiple overlapping emission spectra through spectral imaging and linear unmixing can be utilized for classifying chromosomes painted with multicolor probes. Here, we generated multicolor chromosome paints from single-sorted human and mouse chromosomes and developed the Karyotype Identification via Spectral Separation (KISS) analysis package, a set of freely available open source ImageJ tools for spectral unmixing and karyotyping. Chromosome spreads painted with our multispectral probe sets can be imaged on widely available spectral laser scanning confocal microscopes and analyzed using our ImageJ tools. Together, our probes and software enable academic labs with access to a laser-scanning spectral microscope to perform multicolor karyotyping in a cost-effective manner.

Overview of clinical cytogenetics

This unit provides an introduction to clinical cytogenetics. It opens with indications for prenatal and postnatal chromosome analysis, followed by a brief discussion of the applications of fluorescence in situ hybridization (FISH). It suggests tissue sources for prenatal and postnatal analysis, and closes with a review of numerical and structural chromosome abnormalities. This unit provides an introduction to clinical cytogenetics.

Multicolor Fluorescence In Situ Hybridization (FISH) approaches for simultaneous analysis of the entire human genome

The ability to generate chromosome-specific paints and employ combinatorial labeling strategies has made it possible to differentiate all 24 human chromosomes in a single metaphase spread. Such technology is particularly useful when there is a limited number of metaphase spreads for analyses and when interchromosomal rearrangements are ill-defined or very complex. There are three systems currently available for simultaneous FISH analysis of all human chromosomes: spectral karyotyping (SKY), Multiplex FISH (M-FISH), and Rx-FISH. This overview discusses each of these systems and the recent advances which have made them possible.

Premature ovarian failure in a patient with a complex chromosome rearrangement involving the critical region Xq24, characterized by analysis using fluorescence in situ hybridization by chromosome microdissection

OBJECTIVE

To characterize a complex chromosome rearrangement previously detected by G-banding in peripheral blood lymphocytes as 46,X, inv(X)(p11;q2?), inv(4)(q?),ins(8)(q?) in a patient with primary amenorrhea.

DESIGN

Case report.

SETTING

University faculty of medicine and hospital.

PATIENT(S)

A 16-year-old girl with primary amenorrhea.

INTERVENTION(S)

Microdissection of chromosomes labeled by fluorescence in situ hybridization and by reverse painting.

MAIN OUTCOME MEASURE(S)

Use of commercial whole-chromosome painting probes for the detection of the aberrant chromosomes 4, 8, and X. Fluorescence probes of the isolated derivative chromosomes are self-generated.

RESULT(S)

The use of whole-chromosome painting probes allowed reliable identification of all chromosomes involved in the complex chromosome rearrangements. The DNA of those chromosomes was amplified and fluorescence labeled by polymerase chain reaction using degenerated oligonucleotide primers. These probes revealed breakpoints of the complex chromosome rearrangement by hybridization on normal and original chromosomes in 4q31.1, 8q24.1, Xp22.1, Xp11.4, and Xq24.

CONCLUSION(S)

We report on an Indian patient who has premature ovarian failure with primary amenorrhea as well as a hormone level increased for LH and FSH but decreased for TSH. She has a balanced complex translocation with three breakpoints in the X chromosome that were located by fluorescence in situ hybridization by chromosome microdissection, but no breakpoints localized in the critical regions for premature ovarian failure on the X chromosome. The breakpoint in Xq24 may be associated with the amenorrhea.

Myxoinflammatory fibroblastic sarcoma showing t(2;6)(q31;p21.3) as a sole cytogenetic abnormality

Myxoinflammatory fibroblastic sarcoma (MIFS) is a rare, low-grade sarcoma characterized by distinctive, large, and bizarre Reed--Sternberg--like cells associated with an intense inflammatory infiltrate. The biology of MIFS is still poorly understood, and only two previous cases had been studied cytogenetically. In the present case, analysis of MIFS in the foot of a 53-year-old man revealed the chromosome translocation t(2;6)(q31;p21.3) as the only cytogenetic abnormality. This finding is distinct from the two cases previously reported. Additional studies are needed to verify whether any of these chromosome rearrangements are involved recurrently in MIFS.

Severe suppression of Frzb/sFRP3 transcription in osteogenic sarcoma

Deciphering the molecular basis of cancer is critical for developing novel diagnostic and therapeutic strategies. To better understand the early molecular events involving osteogenic sarcoma (OGS), we have initiated a program to identify potential tumor suppressor genes. Expression profiling of total RNA from ten normal bone cell lines and eleven OGS-derived cell lines by microarray showed 135-fold lower expression of FRZB/sFRP3 mRNA in OGS cells compared to bone cells; this down-regulation of Frzb/sFRP3 mRNA expression was found to be serum-independent. Subsequently, fourteen OGS biopsy specimens showed nine-fold down-regulation of Frzb/sFRP3 mRNA expression compared to expression in eight normal bone specimens as determined by microarray. FRZB /sFRP3 protein level was also found to be at a very low level in 4/4 OGS cell lines examined. Quantitation by RT-PCR indicated approximately 70% and approximately 90% loss of Frzb/sFRP3 mRNA expression in OGS biopsy specimens and OGS-derived cell lines respectively, compared to expression in bone (p<0.0001). Hybridization experiments of a cDNA microarray containing paired normal and tumor specimens from nineteen different organs did not show any significant difference in the level of Frzb/sFRP3 mRNA expression between the normal and the corresponding tumor tissues. Exogenous expression of FRZB/sFRP3 mRNA in two OGS-derived cell lines lacking endogenous expression of the mRNA produced abundant mRNA from the exogenous gene, eliminating degradation as a possibility for very low level of FRZB/sFRP3 mRNA in OGS specimens. Results from PCR-based experiments suggest that the FRZB/sFRP3 gene is not deleted in OGS cell lines, however, karyotyping shows gross abnormalities involving chromosome 2 (location of the FRZB gene) in five of twelve OGS-derived cell lines. Together, these data suggest a tumor-suppressive potential for FRZB/sFRP3 in OGS.

Molecular cytogenetic analysis of chromosomes 1 and 19 in glioma cell lines

Deletions of chromosome 1p and 19q arms are frequent genetic abnormalities in primary human gliomas and are especially common in oligodendrogliomas. However, the chromosome 1p and 19q status of many glioma cell lines has not been established. Using homozygosity mapping, fluorescence in situ hybridization (FISH), and comparative genomic hybridization to arrayed BAC (CGHa), we screened 17 glioma cell lines for chromosome 1 and 19 deletions. Sequence tagged site polymorphisms were used to evaluate the cell lines for regions of chromosome 1p and 19q homozygosity. Cell lines A172, U251, TP265, U118, SW1088, U87, SW1783, and D32 contained significant regions of 19q homozygosity. In addition, A172, U87, TP483, D37, U118, MO67, and TP265 contained significant regions of 1p homozygosity. FISH probes localized to 1p36.32 and 19q13.33 as well as CGHa were used to determine which cell lines had deletions of 1p and/or 19q. Cell lines A172, U87, TP483, TP265, H4, U251, and D37 were deleted for portions of 1p. CGHa and homozygosity mapping of these cell lines define a 700-kilobase (Kb) common deletion region that is encompassed by a larger deletion region previously mapped in sporadic gliomas. This common deletion region is localized at 1p36.31 and includes CHD5, a putative tumor suppressor gene. Cell line A172 was observed to have a deletion between 19q13.33 and 19q13.41, while U87 was observed to have a smaller deletion of 19q13.33. Cell lines A172 and U87 contain 1p and 19q deletions similar to those found in sporadic gliomas and will be useful cellular reagents for evaluating the function of putative 1p and 19q glioma tumor suppressor genes.

A class I transgene reveals regulatory events on chromosome 1 marking peripheral T cell differentiation and memory

T cells respond to external signals by altering patterns of gene expression. Our characterization of a transgenic mouse revealed a genetic locus that is specifically regulated in T cells. Elucidation of the factors controlling the expression of the marker transgene may reveal basic regulatory mechanisms used by T cells as they differentiate from naive to primed/memory T cells. Although endogenous MHC class I K(q) expression is normal in these animals, expression of the K(b) transgene differentiates naive from primed/memory T cells. K(bHigh) T cells bear the phenotypic and functional properties of primed/memory T cells, while K(bLow) T cells have naive phenotypes. The transition from K(bLow) to K(bHigh) appears to involve signals resulting from engagement of the TCR. We show that transgene integration has occurred on chromosome 1, between D1Mit365 and D1Mit191. The gene regulatory mechanisms directing expression of the locus marked by the transgene are distinct from those controlling other known T cell-related genes within this locus. Stimulation of K(bHigh) T cells results in the up-regulation of both the endogenous K(q) gene and the K(b) transgene. However, the same stimuli induce increased expression of only K(q) on K(bLow) T cells. This indicates that even though the transcription factors necessary for class I expression are present in K(bLow) T cells, the K(b) gene appears not to be accessible to these factors. These findings suggest a change in chromatin structure at the transgene integration site as cells progress from a naive to a primed/memory differentiation state.

Common neonatal syndromes

The process of diagnosis of genetic syndromes in the newborn period is carried out in the context of parental anxiety and the grief following an often-unexpected outcome after a long pregnancy. The nursery staffs invariably have a strong interest in giving the family proper information about prognosis. This article is intended to focus on an approach to the diagnosis of genetic syndromes and to discuss specific syndromes that may be seen with some frequency in the nursery.

Role of multiplex FISH in identifying chromosome involvement in myelodysplastic syndromes and acute myeloid leukemias with complex karyotypes: a report on 28 cases

Chromosomal abnormalities are found by conventional cytogenetic (CC) analysis in about 50% of myelodysplastic syndromes (MDS) and 70% of acute myeloid leukemias (AML). When cytogenetic abnormalities are complex, multiplex fluorescence in situ hybridization (M-FISH) can help clarify complex chromosomal abnormalities and identify rearrangements with prognostic value or cryptic translocations, which could be preliminary steps in identifying new genes. We studied by M-FISH 28 cases of MDS and AML with complex chromosomal abnormalities, 10 of them were therapy-related. M-FISH allowed the characterization of unidentified chromosomal material in 26 cases (93%). One or several unbalanced rearrangements were observed in 27 cases (96%), generally interpreted as deletions or additional material by CC. Among those translocations, 4 involved 3 chromosomes. Eighteen cryptic translocations undetected by CC were found in 13 cases. By FISH analysis using locus specific probes, TP53 deletion, additional copies of MLL, and additional copies or deletions of RUNX1/AML1 were observed in 16, 4, and 3 cases, respectively. Thus, M-FISH is an important tool to characterize complex chromosomal abnormalities which identified unbalanced and cryptic translocations in 96% and 46% of the cases studied, respectively. Complementary FISH helped us identify involvement of TP53, MLL, and RUNX1/AML1 genes in 82% of cases, confirming their probable role in leukemogenesis.

Primary amenorrhea in a woman with a cryptic complex chromosome rearrangement involving the critical regions Xp11.2 and Xq24

OBJECTIVE

To characterize a complex chromosome rearrangement (CCR) previously detected by G-banding in peripheral blood lymphocytes, as 46,X,-2,-11,-22,-X,+mar 1+mar2+mar3+mar4 in a patient with primary amenorrhea.

DESIGN

Case report.

SETTING

University faculty of Medicine and hospital.

PATIENT(S)

A 36-year-old woman with primary amenorrhea.

INTERVENTION(S)

Fluorescence in situ hybridization (FISH).

MAIN OUTCOME MEASURE(S)

Use of commercially available M-FISH probe (24 colors simultaneously) and whole chromosome painting probes for chromosomes 2, 11, 22, and X to characterize the CCR.

RESULT(S)

The use of conventional and multiple FISH allowed the redefinition of the CCR, showing a cryptic insertion of chromosome 11 in marker 3 previously suspected by M-FISH. The combination of G-banding and FISH data revealed that four chromosomes and seven breakpoints, including 2q21, 2q31, 11q22.1, 11q22.3, 22q13.3, Xp11.21, and Xq24, were implicated in this CCR.

CONCLUSION(S)

This report confirms the importance of a combination of G-banding and FISH (M-FISH and conventional FISH) techniques to characterize the de novo CCR. These techniques also were useful in defining two possible critical chromosome regions, Xp11.21 and Xq24, in which genes of potential interest for a primary amenorrhea could be located.

Molecular cytogenetic analysis of complex chromosomal rearrangements in patients with mental retardation and congenital malformations: delineation of 7q21.11 breakpoints

Constitutional de novo complex chromosomal rearrangements (CCRs) are a rare finding in patients with mild to severe mental retardation. CCRs pose a challenge to the clinical cytogeneticist: generally CCRs are assumed to be the cause of the observed phenotypic abnormalities, but the complex nature of these chromosomal changes often hamper the accurate delineation of the chromosomal breakpoints and the identification of possible imbalances. In a first step towards a more detailed molecular cytogenetic characterization of CCRs, we studied four de novo CCRs using multicolor fluorescent in situ hybridization (M-FISH), comparative genomic hybridization (CGH), and FISH with region specific probes. These methods allowed a more refined characterization of the breakpoints in three of the four CCRs. The occurrence of 7q breakpoints in three out of these four CCRs and in 30% of reported CCRs suggested preferential involvement of this chromosomal region in the formation of CCRs. Further analysis of these 7q breakpoints revealed a 2 Mb deletion at 7q21.11 in one patient and involvement of the same region in a cryptic insertion in a second patient. This particular region contains at least 5 candidate genes for mental retardation. The other patient had a breakpoint more proximal to this region. The present data together with these from the literature provide evidence that a region within 7q21.11 may be prone to breakage and formation of CCRs.

Comparison of M-FISH and conventional cytogenetic analysis in accelerated and acute phases of CML

FISH and multicolor FISH (M-FISH) techniques have greatly enhanced the resolution of conventional cytogenetic analysis, thus enabling the identification of novel regions of rearrangement in hematological malignancies. We report on the analysis of cells from 24 chronic myelogenous leukemia (CML) patients, in either accelerated phase (14 cases) or blast crisis (10 cases) aimed at searching for previously unidentified additional abnormalities related to disease evolution. Indeed, in 6 of 24 cases (25%) M-FISH allowed a more precise description of chromosomal aberrations, the finding of cryptic rearrangements, characterization of markers, identification of additional material and a better interpretation of complex aberrations. However, new recurrent aberration did not emerge from M-FISH analysis.

Molecular genetics of pediatric soft tissue tumors: clinical application

The application of molecular genetics to pediatric soft tissue tumors has grown tremendously over the last decade. It has resulted in the identification of novel genes that have provided us with an increased understanding of oncogenesis. Furthermore, these findings have identified diagnostic and potentially prognostic factors for patient management. Molecular diagnostic techniques, such as reverse transcription PCR (RT-PCR) and fluorescence in situ hybridization (FISH), have become important tools for evaluating pediatric soft tissue tumors. By detecting characteristic fusion genes, these techniques have greatly increased the diagnostic accuracy of histopathological classification. One of the exciting promises of the development of these molecular techniques is their ability to detect micrometastasis and minimal residual disease. Monitoring of minimal residual disease in pediatric soft tissue tumors by quantitative RT-PCR may provide important prognostic information. Furthermore, the potential development of targeted therapy based on the understanding of the molecular pathology of a specific soft tissue tumor may complement existing treatments and improve disease outcome.

Analysis of marker or complex chromosomal rearrangements present in pre- and post-natal karyotypes utilizing a combination of G-banding, spectral karyotyping and fluorescence in situ hybridization

The significance of complex chromosomal rearrangements presents a diagnostic dilemma. In the past, the use of G-banding coupled with fluorescence in situ hybridization (FISH) has been the standard approach. The recent development of spectral karyotyping (SKY) and multicolor FISH (M-FISH) has resulted in an increased accuracy of identification of marker or other complex chromosomal rearrangements. However, owing to the additional cost and time associated with SKY or M-FISH, and the restricted availability of such imaging facilities in many centers, it is not feasible to perform these procedures routinely on every sample. In addition, the identification of an aberration by SKY or M-FISH will often require confirmation by FISH. A practical approach is needed to take advantage of the complementary strengths of each method. In our center we utilize an algorithm that dictates the use of routine G-banding for the initial preliminary evaluation of a patient, followed by SKY characterization if marker chromosomes or complex translocations are detected by the G-banding analysis. According to this algorithm, FISH is used to verify the results once the origin of the abnormal chromosome has been determined by SKY. To demonstrate the effectiveness of this algorithm, we have analyzed both amniocyte and lymphocyte slides, using a combination of G-banding, SKY, and FISH. Our results confirm that an algorithm which selectively uses SKY or M-FISH will provide an efficient and improved method for pre- and post-natal chromosomal analysis.

Further characterization of human fetal osteoblastic hFOB 1.19 and hFOB/ER alpha cells: bone formation in vivo and karyotype analysis using multicolor fluorescent in situ hybridization

We have previously generated an immortalized human fetal osteoblastic cell line (hFOB) using stably transfected temperature sensitive SV40 T-antigen (Harris et al. [1995a] J. Bone. Miner. Res. 10:178-1860). To characterize these cells for phenotypic/genotypic attributes desired for a good cell model system, we performed karyotype analysis by multicolor fluorescent in situ hybridization (M-FISH), their ability to form bone in vivo without developing cell transformation, and finally their ability to form extracellular matrix formation in vitro. The karyotype analysis of hFOB cells revealed structural or numeric anomalies involving 1-2 chromosomes. In contrast, the human osteosarcoma MG63 cells displayed multiple, and often complex, numeric, and structural abnormalities. Subcutaneous injection of hFOB cells in the presence of Matrigel into nude mice resulted in bone formation after 2-3 weeks. Electron microscopic analysis of the extracellular matrix deposited by hFOB cells in culture revealed a parallel array of lightly banded fibrils typical of the fibrillar collagens such as type I and III. These results demonstrate that the hFOB cell line has minimal chromosome abnormalities, exhibit the matrix synthetic properties of differentiated osteoblasts, and are immortalized but non-transformed cell line. These hFOB cells thus appear to be an excellent model system for the study of osteoblast biology in vitro.

Utility of subtelomeric fluorescent DNA probes for detection of chromosome anomalies in 425 patients

PURPOSE

A complete set of subtelomeric fluorescent DNA probes, except the acrocentric p-arms, was developed in 1996, was optimized in 1998, and is commercially available. These and other fluorescence in situ hybridization (FISH) probes have been used to detect anomalies of the subtelomere regions among groups of patients with idiopathic mental retardation (MR), developmental delay (DD), and/or nonspecific dysmorphic features (NDF), and individuals with multiple miscarriages (MM) who were karyotypically normal by standard G-banding techniques.

METHODS

A total of 425 patients were analyzed, of whom 372 had idiopathic MR/DD/NDF and 53 were involved in MM. An effort was made to select individuals for this study who were either normal karyotypically or who had subtle chromosomal anomalies that were inconclusive by banded chromosome analysis, although this was not always possible.

RESULTS

Anomalies involving the subtelomere regions were detected at a frequency of 6.8% in the MR/DD/NDF group. The cryptic or subtle anomalies are estimated to be about 3.4%. It was necessary to use M-FISH, chromosome, and locus specific FISH probes to clarify some of the abnormalities. No abnormalities were detected in the MM group. Deletion variants were present for 2qter, 7pter, and Xpter/Ypter subtelomeric regions ranging from <1 to 9.6%.

CONCLUSIONS

The subtelomeric FISH probes are instrumental in the detection of subtelomeric anomalies in a significant proportion, although no more than 50% are subtle, of patients with idiopathic MR/DD/NDF. In some cases, however, it was necessary to use other FISH probes to clarify the nature of these abnormalities. No subtelomeric abnormalities were detected in our group of 53 MM patients, suggesting a relatively low frequency of occurrence in this patient population.

Unique case of mosaicism involving two morphologically similar marker chromosomes of different centric origin in a patient with developmental delay

A five-year-old Caucasian male presented with developmental delay, minor dysmorphic features, and hyperactivity. Cytogenetic analysis showed the presence of a marker chromosome in the majority of cells analyzed. Fluorescence in situ hybridization (FISH) analyses using several alpha satellite probes, including D13Z1/D21Z1, did not reveal any signal on the marker chromosome. Subsequent multicolor FISH (M-FISH) indicated the marker to be derived from chromosome 13, and FISH with a chromosome 13 paint confirmed this finding. The absence of D13Z1/D21Z1 signal on the marker suggested that it was analphoid in nature. Comparative genomic hybridization (CGH) was utilized to further characterize the region of chromosome 13 from which the marker originated, and unexpectedly revealed a gain of chromosomal material at both the centromeric regions of chromosomes 3 and 13. In view of the CGH results, extensive FISH studies with D3Z1 and D13Z1/D21Z1 were performed and revealed the presence of four cell lines comprising one normal cell line (50.5%), a cell line with a chromosome 3 derived marker (19%), a cell line containing a marker derived from chromosome 13 (20%), and a cell line with both markers (10.5%). As the two markers appeared morphologically similar by GTG banding, all 47,XY metaphases in the initial analysis were thought to comprise only a single marker. This is the first report, to our knowledge, of the presence of a chromosome 3 and a chromosome 13 marker in mosaic condition in a congenital disorder. In light of our experience, we urge caution in interpreting karyotypes with marker chromosomes. Our case illustrates the limitations of fluorescent DNA probes and sampling errors.

Primary myelodysplastic syndrome with normal cytogenetics: utility of 'FISH panel testing' and M-FISH

The myelodysplastic syndromes (MDS) are a clinically heterogeneous group of hematologic disorders. Cytogenetic analysis is crucial as it can provide both diagnostic and prognostic information. Herein, 32 cytogenetically normal patients with primary MDS were analyzed both by multiple FISH probes on interphase nuclei (FISH panel testing) and by M-FISH (metaphase nuclei). One patient had a chromosome 13q-arm deletion, while the remaining 31 patients had normal results. These findings confirm standard cytogenetics as an excellent technique in identifying the common chromosomal abnormalities associated with MDS and suggest limited utility for either a FISH panel test or M-FISH in primary MDS.

Molecular cytogenetics

In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

Limitations of chromosome classification by multicolor karyotyping

Multicolor karyotyping technologies, such as spectral karyotyping (SKY) (Schröck et al.1996; Liyanage et al. 1996) and multiplex (M-) FISH (Speicher et al. 1996), have proved to be extremely useful in prenatal, postnatal, and cancer cytogenetics. However, these technologies have inherent limitations that, in certain situations, may result in chromosomal misclassification. In this report, we present nine cases, which fall into five categories, in which multicolor karyotyping has produced erroneous interpretations. Most errors appear to have a similar mechanistic basis.

Hyperspectral imaging: a novel approach for microscopic analysis

BACKGROUND

The usefulness of the light microscope has been dramatically enhanced by recent developments in hardware and software. However, current technologies lack the ability to capture and analyze a high-resolution image representing a broad diversity of spectral signatures in a single-pass view. We show that hyperspectral imaging offers such a technology. METHODS AND RESULTS We developed a prototype hyperspectral imaging microscope capable of collecting the complete emission spectrum from a microscope slide. A standard epifluorescence microscope was optically coupled to an imaging spectrograph, with output recorded by a CCD camera. Software was developed for image acquisition and computer display of resultant X--Y images with spectral information. Individual images were captured representing Y-wavelength planes, with the stage successively moved in the X direction, allowing an image cube to be constructed from the compilation of generated scan files. This prototype instrument was tested with samples relevant to cytogenetic, histologic, cell fusion, microarray scanning, and materials science applications.

CONCLUSIONS

Hyperspectral imaging microscopy permits the capture and identification of different spectral signatures present in an optical field during a single-pass evaluation, including molecules with overlapping but distinct emission spectra. This instrument can reduce dependence on custom optical filters and, in future imaging applications, should facilitate the use of new fluorophores or the simultaneous use of similar fluorophores.

Detection of diagnostically critical, often hidden, anomalies in complex karyotypes of haematological disorders using multicolour fluorescence in situ hybridization

Multicolour fluorescence in situ hybridization (M-FISH) simultaneously detects all 24 human chromosomes in unique fluorescent colours. The identification of diagnostically critical gene rearrangement(s) in complex karyotypes of haematological disorders continues to be a challenge. We present five cases in which t(9;11), complex t(8;22), t(12;21) and t(11;14) were detected primarily using M-FISH and were confirmed using locus-specific probes. We conclude that M-FISH can be effective in complete characterization of critical gene rearrangements in haematological disorders.

Application of multicolor fluorescent in situ hybridization for enhanced characterization of chromosomal abnormalities in congenital disorders

OBJECTIVE

To determine the efficacy of multicolor fluorescent in situ hybridization (M-FISH), which paints each chromosome in a unique color, for identification of congenital derivative and marker chromosomes. MATERIAL, METHODS AND CASES: Commercially available M-FISH probes were used to label each chromosome in a specific fluorescent color. Six representative cases involving derivative chromosomes, markers, and subtle anomalies were analyzed by M-FISH.

RESULTS

Three familial, rather subtle derivative chromosomes were identified by M-FISH with relative ease. A small ring that was unidentifiable by banded-chromosome analysis was identified by M-FISH. A case of a subtle telomeric anomaly could not be resolved without the use of telomeric-specific probes. The M-FISH results were confirmed by individual chromosome-specific painting probes.

CONCLUSION

M-FISH was helpful for identifying a wide range of congenital chromosomal anomalies. However, for subtle chromosomal abnormalities, use of locus-specific probes may be necessary.

New molecular techniques for chromosome analysis

The advent of molecular genetic technology has significantly advanced knowledge about the structure of chromosomes and their behaviour during meiosis and mitosis, as well as delineating cytogenetic aberrations that cannot be identified by conventional chromosome analysis. Molecular cytogenetics, the visualization of genetic loci using the dynamic recombinant technology of fluorescence in situ hybridization (FISH), now provides the obstetrician and gynaecologist with increasingly important diagnostic and prognostic information heretofore unavailable. The technical principles underlying FISH are briefly discussed. Emphasis is placed on the clinical applications of FISH and technologies derived from FISH, in particular comparative genome hybridization, microdissection FISH and multiplex FISH. These technologies play increasingly significant roles in preimplantation and prenatal genetic diagnosis, in the identification of microdeletion syndromes, cryptic translocations and marker chromosomes, and in defining chromosome mosaicism. FISH and related technologies also constitute essential diagnostic modalities in follow-up of organ transplantation, in a variety of haematological disorders and in determining the amplification of oncogenes associated with specific forms of cancer and neoplasia.

The application of fluorescence in-situ hybridization to prenatal diagnosis

Fluorescence in-situ hybridization has become essential in prenatal diagnosis for identifying chromosome aberrations as well as in preimplantation genetic diagnosis and the analysis of fetal cells in maternal blood. Comparative genome hybridization, multicolor fluorescence in-situ hybridization and telomere probes provide technical approaches for the characterization of fetal chromosome anomalies not possible by conventional karyotyping.

Inherited interstitial deletion of chromosomes 5p and 16q without apparent phenotypic effect: further confirmation

We describe two families in which an inherited interstitial deletion is present without apparent associated phenotypic abnormalities. The first deletion was discovered in a 19-year-old male with a previously diagnosed peroxisomal disorder. High-resolution chromosome analysis was interpreted as 46,XY,del(5)(p14.1p14.3). The patient's phenotypically normal mother had the same interstitial deletion. Chromosome 5p14 deletion has been reported in a three-generation family without phenotypic anomalies. We hypothesize that the affected son's phenotype may be coincidental or represent unmasking of an autosomal recessive peroxisomal disorder in the deleted region. The second interstitial deletion was detected by amniocentesis for advanced maternal age. High-resolution chromosome analysis was interpreted as 46,XX,del(16)(q13q22). The same deletion was found in the healthy mother and a normal brother. The pregnancy was carried to term and resulted in the birth of a normal girl. We report these cases as further evidence that rare, unbalanced deletion of specific chromosomal regions may result in no phenotypic effect. Consequences may result from expression of an autosomal recessive disorder on the homologous chromosome. Identification of such deletions is especially important for prenatal diagnosis and genetic counselling.