Multiplex-FISH for pre- and postnatal diagnostic applications

Two familial intrachromosomal insertions with maternal dup(6)(p22.3p25.3) or dup(2)(q24.2q32.1) in recombinant offspring

In this study, we describe two patients with a recombinant chromosome secondary to a maternal intrachromosomal insertion. Patient 1 was a girl with dup(6)(p22.3p25.3). Patient 2 was a boy with dup(2)(q24.2q32.1). Both familial rearrangements were characterized by means of GTG-bands, fluorescence in-situ hybridization, and comparative genomic hybridization microarray analyses. Patient 1 had an ∼23 Mb gain that involved the bands 6p22.3-6p25.3. Patient 2 had an ∼23 Mb gain (cytobands 2q24.2-2q32.1) and a further ∼1.9 Mb gain of 2p16.2-p16.3. The phenotype of each patient was in agreement with the typical 6p duplication or 2q24.2q32.1 duplication syndrome. The compound macular lesion in patient 1 suggests that retinal anomalies may be a part of the 6p trisomy phenotype. Among the 70 intrachromosomal insertions compiled here (including 68 from the literature), four were submicroscopic unbalanced insertions inherited from a balanced carrier and 66 were detectable on banded chromosomes (with or without array comparative genomic hybridization or other high-resolution assessment) and therefore spanned at least 5 Mb. Pericentric insertions are found in most chromosomes, whereas the paracentric ones are mainly observed in large and medium chromosome arms. That the former outnumber the latter in almost a 2 : 1 ratio appears to be related to the technique of diagnosis, size of the insertion, and size of the involved chromosome. Regardless of the apparent excess of carrier mothers, carriers of an intrachromosomal insertion beget almost twice as many children with a duplication than with a deletion.

[Strategies to identify supernumerary chromosomal markers in constitutional cytogenetics]

Supernumerary marker chromosomes (SMCs) are defined as extrastructurally abnormal chromosomes which origin and composition cannot be determined by conventional cytogenetics. SMCs are an heterogeneous group of abnormalities concerning all chromosomes with variable structure and size and are associated with phenotypic heterogeneity. The characterisation of SMCs is of utmost importance for genetic counselling. Different molecular techniques are used to identify chromosomal material present in markers such as 24-colour FISH (MFISH, SKY), centromere specific multicolour FISH (cenMFISH) and derivatives (acroMFISH, subcenMFISH), comparative genomic hybridisation (CGH), arrayCGH, and targeted FISH techniques (banding techniques, whole chromosome painting...). Based on the morphology of SMC with conventional cytogenetic and clinical data, we tried to set up different molecular strategies with all available techniques.

Copy number variant analysis of human embryonic stem cells

Differences between individual DNA sequences provide the basis for human genetic variability. Forms of genetic variation include single-nucleotide polymorphisms, insertions/duplications, deletions, and inversions/translocations. The genome of human embryonic stem cells (hESCs) has been characterized mainly by karyotyping and comparative genomic hybridization (CGH), techniques whose relatively low resolution at 2-10 megabases (Mb) cannot accurately determine most copy number variability, which is estimated to involve 10%-20% of the genome. In this brief technical study, we examined HSF1 and HSF6 hESCs using array-comparative genomic hybridization (aCGH) to determine copy number variants (CNVs) as a higher-resolution method for characterizing hESCs. Our approach used five samples for each hESC line and showed four consistent CNVs for HSF1 and five consistent CNVs for HSF6. These consistent CNVs included amplifications and deletions that ranged in size from 20 kilobases to 1.48 megabases, involved seven different chromosomes, were both shared and unique between hESCs, and were maintained during neuronal stem/progenitor cell differentiation or drug selection. Thirty HSF1 and 40 HSF6 less consistently scored but still highly significant candidate CNVs were also identified. Overall, aCGH provides a promising approach for uniquely identifying hESCs and their derivatives and highlights a potential genomic source for distinct differentiation and functional potentials that lower-resolution karyotype and CGH techniques could miss. Disclosure of potential conflicts of interest is found at the end of this article.

Characterisation of supernumerary chromosomal markers: a study of 13 cases

Marker chromosomes are defined as 'structurally abnormal chromosomes in which no part can be identified' (ISCN 1995). Supernumerary marker chromosomes (SMC) are 'additional markers' whose origin and composition cannot be determined by conventional cytogenetics. Molecular cytogenetic methods are necessary to identify these additional chromosomal markers. In one third, the SMCs are clinically well-defined in the literature, the remaining two thirds present a major problem for genetic counselling in prenatal diagnosis. At present, different molecular cytogenetic methods are used to determine the origin of SMCs. In this work, we studied 13 SMCs detected by RHG-banding, completed by C-banding and/or NOR-staining. 24-color FISH was used as the primary technique when the chromosomal origin was unknown. Targeted FISH procedures with specific probes (whole chromosome painting, centromeric probe, locus-specific identifier, BAC, etc.) were then performed to confirm and/or specify the chromosomal material present in the SMC. Seven SMCs were found to be associated with phenotypic abnormalities. Five derived from autosomes and two from gonosomes; these are: der(12)t(4;12), dic(15), i(18p), r(19), der(22)t(11;22), r(X), and der(Y). Two markers, r(8) and idic(15), were identified during investigations of infertile couples. Three cases seemed to be phenotypically normal. Four were discovered prenatally: r(2) and r(19) referred for elevated maternal serum markers, der(13/21) referred for advanced maternal age. The fourth SMC, der(14/22), was found during familial investigation following the identification of the same marker in an infertile son. The precise characterisation of the SMCs is of utmost importance for genetic counselling, especially in prenatal diagnosis.

Subtelomeric chromosome rearrangements in children with idiopathic mental retardation: applicability of three molecular-cytogenetic methods

AIM

To identify cryptic subtelomeric rearrangement, a possible cause of idiopathic mental retardation by means of multiprobe telomere fluorescent in situ hybridization (T-FISH).

METHODS

Hundred patients (median age 3.0 years) with mental retardation and dysmorphic features were screened using specific T-FISH probes. Multiplex ligation-dependent probe amplification and comparative genomic hybridization were used for the confirmation of results.

RESULTS

Telomere fluorescent in situ hybridization revealed 11 subtelomeric abnormalities in 10 patients (10%; 95% CI, 5.0-17.5). Four of these had only a deletion of subtelomere 2q, which was apparently a normal variant. Among 6 true aberrations (6%; 95% CI, 2.5-12.5) we found 2 de novo subtelomeric deletions and 4 unbalanced subtelomeric rearrangements (one de novo). All clinically significant subtelomeric rearrangements were confirmed by multiplex ligation-dependent probe amplification. Comparative genomic hybridization was used to investigate the whole genome of patients in whom a subtelomeric anomaly was found, confirming some, but not all subtelomeric rearrangements.

CONCLUSION

Telomere fluorescent in situ hybridization and multiplex ligation-dependent probe amplification are both very useful and interchangeable methods for detection of unbalanced chromosome rearrangements, but T-FISH also detects balanced rearrangements. In our experiment the resolution power of comparative genomic hybridization was too low for subtelomeric screening compared with T-FISH and multiplex ligation-dependent probe amplification.

Multiplex-FISH (M-FISH): technique, developments and applications

Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.

Breakpoint locations within chromosomes 1, 2, and 4 of patients with increased radiosensitivity

The exposure to low LET-radiation leads to a relative homogeneous distribution of initial damage at the DNA. Subsequent repair and post-repair mechanisms might lead to a selection of specific breakpoint locations along chromosomes. Cells from patients with increased radiosensitivity may have more specific breakpoints due to impaired repair mechanisms. We tested whether cells from patients with increased radiosensitivity had an increase in specific breakpoint clusters. Structural chromosomal aberrations of in vitro irradiated lymphocytes from 11 healthy individuals and another 3 patients with increased radiosensitivity were examined. The chromosome pairs 1, 2, and 4 were treated using the three-color FISH technique. The breakpoints were analyzed by means of computerized imaging software. In total, 1752 chromosomal breakpoints had been considered, 498 from healthy individuals, and 1254 from patients with increased radiosensitivity. For both groups there was a non-homogeneous breakpoint distribution along the chromosomes and a trend towards increased breaks in the telomere-proximal region. Also, both groups had distinct locations with increased breaks. No evidence for significant breakpoint patterns across all patients with increased radiosensitivity was found.

American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation

The following are the recommendations of the American College of Medical Genetics (ACMG) Professional Practice and Guidelines Committee, which was convened to assist health care professionals in making decisions regarding cytogenetic diagnostic testing and counseling for mental retardation (MR) and developmental delay (DD). This document reviews available evidence concerning the value of conventional and molecular cytogenetic testing for the identification of chromosomal anomalies that play a role in the etiology of MR/DD, and, based on this evidence, specific recommendations for each method of testing are provided.

Small Reciprocal Insertion detected by Spectral Karyotyping (SKY) and delimited by Array-CGH Analysis

A 5.4-year-old male propositus is reported with mild dysmorphic features including hypoplasia of the radial part of both hands affecting thenar, thumb and fingers 2-3, incomplete syndactyly of fingers 3-4, single palmar creases, brachymesophalangia of toes 3-5, dissociated retardation of bone age, telecanthus, spina bifida occulta, cryptorchidism, muscular hypotonia, and borderline mental retardation. His karyotype was unbalanced, 46,XY,der(16)ins(4;16)(q26q28.1; q12.1q12.2)pat. In the propositus' father who had brachydactyly of fingers 2-5 and brachymesophalangia of toes 3-5 the insertion was reciprocal, 46,XY,rep ins(4;16)(q26q28.1;q12.1q12.2). Insertions are rare, reciprocal insertions most unusual. The characterization of the insertion in the propositus and the detection of its reciprocity in the father were achieved by the application of spectral karyotyping (SKY). Further examination of the propositus' unbalanced genome by array-CGH analysis delimited the chromosomal locations of the deletion/insertion rearrangement on a 0.5-2 Mb resolution level and allowed to design specific BAC FISH analyses that pinpointed the borders of the affected segments. The rearrangement involved a segment of 7.7 Mb between RP11-1030 g22 and RP11-52k8 at the chromosomal regions 4q26 and 4q28.1, respectively, and a segment of 2.8 Mb between RP11-242n20 at 16q12.1 and RP11-324d17 at 16q12.2. A simple molecular genetic explanation of the phenotype cannot be given. A relation to the Townes Brocks gene (SALL1) located 340 kb proximal of the 16q12 deletion/insertion is unlikely. Possibly more relevant is an overlap of the 16q12 deletion/insertion with a small deletion of the syntenic chromosomal region in the mouse that causes a developmental disorder of digits ("Fused toes").

Molecular cytogenetic characteristics of the human hepatocellular carcinoma cell line HCCLM3 with high metastatic potential: comparative genomic hybridization and multiplex fluorescence in situ hybridization

The HCCLM3 cell line was established at the authors' institute from the lung metastatic lesions of BALB/c nude mice bearing human hepatocellular carcinoma (HCC) from the metastatic HCC cell line MHCC97-H. It has been shown to have a high potential for lung metastases and extensive metastases when the cells are inoculated subcutaneously or orthotopically in athymic nude mice. In the present study, the molecular cytogenetic characteristics of this cell line were evaluated with conventional G-banding, comparative genomic hybridization, and multiplex fluorescence in situ hybridization. A hyperdiploid karyotype of 53-58 chromosomes with 10 marker chromosomes was identified. The chromosomal aberrations such as i(X)(q10), der(Y)t(Y;18)(q12;p11), der(3)t(3;20) (p25;q13), der(4)t(4;8)(q31;q22)5, der(9)t(9;13)(p21;q22), der(14)t(14;22)(p13;q13), and der(15) t(15;21)(q11;q22) were described for the first time in human HCC cells. The analysis of this cell line through a combination of molecular cytogenetic techniques provides information on the possible molecular mechanisms involved in the metastatic process of HCC.

Sequential application of interphase-FISH and CGH to single cells

A comprehensive genomic analysis of single cells is needed for numerous scenarios in tumor genetics, clinical diagnostics and forensic application. PCR protocols were developed which allow an unbiased amplification of the whole genome of a single cell for subsequent analyses by comparative genomic hybridization (CGH). However, verification of single-cell CGH results has been impossible as the procedure naturally involves the destruction of the respective cell. Here we show that the genome of individual cells can be analyzed by two different single cell techniques applied sequentially to the same cell. In a first step, interphase fluorescence in situ hybridization (FISH) is applied. After evaluation of the interphase-FISH signals, cells of interest can be selected for a further analysis. Single cells are collected by laser microdissection, the DNA is amplified by linker-adaptor PCR and subjected to CGH-analysis. This strategy offers new opportunities for a sophisticated selection of cells based on interphase-FISH signals. Furthermore, the sequential application of two different single-cell approaches to the same single-cell represents the only option to control and verify the single-cell CGH results. We demonstrate the feasibility of this approach with a series of experiments including cells from pre- and postnatal diagnostics, for example, cells with trisomies 13, 18, or 21, respectively, leukemia and tumor cells and tissue sections.

Preimplantation genetic diagnosis for aneuploidy screening in patients with unexplained recurrent miscarriages

OBJECTIVE

To determine the aneuploidy rate in embryos of women with idiopathic recurrent miscarriages and to evaluate whether preimplantation genetic diagnosis for aneuploidy screening could be a feasible approach to improve the possibility of successful pregnancy in these couples.

DESIGN

Prospective cohort study.

SETTING

Tertiary university referral center.

PATIENT(S)

Women (n = 49) with recurrent idiopathic miscarriages.

INTERVENTION(S)

In vitro fertilization with preimplantation genetic diagnosis for aneuploidy screening.

MAIN OUTCOME MEASURE(S)

Ongoing pregnancy rate (PR) and aneuploidy rate.

RESULT(S)

The aneuploidy rate was, respectively, 43.85% and 66.95% in the younger and older group. The ongoing PR per cycle was 25.71% in the younger and 2.94% in the older patients.

CONCLUSION(S)

There is no therapeutic evidence to prescribe IVF with or without preimplantation genetic diagnosis for aneuploidy screening for this heterogeneous group of patients.

Characterization of a small supernumerary marker chromosome as r(8) at prenatal diagnosis by MFISH

OBJECTIVE

To identify the mosaic marker chromosome detected in amniotic fluid cells of a 26-year-old woman, with raised triple test values and an ultrasound scan, which showed a fetus with echogenic bowels.

METHODS

Routine karyotyping with G- and C-banding was carried out for both, amniotic fluid at 18 weeks of gestation as well as fetal blood at 22(+6) weeks. Peripheral blood of both parents was karytoyped. MFISH and the all centromeric human probe were used on fetal lymphocytes to identify the marker chromosome.

RESULTS

Both parents had a normal karyotype. Amniotic fluid culture showed a de novo supernumerary marker chromosome (SMC) in 14 of the 30 colonies from four different cover slip cultures. The marker was confirmed in 50% of the fetal lymphocytes. G- and C-banding provided little information except that the marker had some heterochromatic material. The all centromeric human probe also showed the presence of a centromere along with a rim of euchromatic material. MFISH identified this ring marker to be belonging to chromosome 8.

CONCLUSIONS

SMCs with chromosome 8 have been shown to be variable phenotypes. Presence of only heterochromatic material seems to have no discernable phenotypic effects, but, with the presence of euchromatic material, mental and physical developmental delay has been reported. The parents opted to go ahead with the pregnancy and an apparently normal female baby was born at 40 weeks with no complications.

Molecular cytogenetic characterization of two small chromosome 8 derived supernumerary mosaic markers

Two small supernumerary mosaic marker chromosomes (SMC) were identified by conventional cytogenetics, one prenatally, the other postnatally. Fluorescence in situ hybridization (FISH) techniques, including 24-color FISH, were applied to identify both SMCs and better characterize their constitution. Patient 1: a 29 year-old man, whose wife had a spontaneous abortion, was found to have a small ring of the pericentromeric region of chromosome 8 (47,XY,+r(8)(p11q11)/46,XY). Patient 2: a 37 year-old woman had amniocentesis. The fetus was found to have a SMC; its presence was confirmed postnatally. Several FISH techniques (24-color, whole chromosome paints, centromeres, telomeres, band 8p22) led to the identification of a small analphoid marker. The marker was an inversion-duplication for part of the short arm of chromosome 8 (47,XY,+inv dup (8)(p23pter)/46,XY). The 24-color FISH allowed us to conclude that both markers originated exclusively from chromosome 8. However, the structure and content of the markers were elucidated using other molecular cytogenetic techniques, showing their complementarity.

Will the new cytogenetics replace the old cytogenetics?

With the advent of array-based comparative genomic hybridization technology, the analog cytogenetic analysis that has been used for the past 100 years could be replaced by the quantitative, microarray-based molecular analysis. Major advantages of the new array-based cytogenetic technologies are the high resolution and the high throughput. This technology is the first to offer an autonomous whole-chromosome analysis in one hybridization reaction for the detection of submicroscopic gains/losses. However, as with any new technology, it needs to be validated with regard to its performance in various applications (e.g. clinical genetic testing and cancer applications), comparative cost, and the data interpretation.

Identification of 14 rare marker chromosomes and derivatives by spectral karyotyping in prenatal and postnatal diagnosis

Extra structurally abnormal chromosomes (ESACs) and cryptic rearrangements are often associated with mental retardation and phenotypic abnormalities. In some cases their characterisation, using standard cytogenetic techniques and fluorescence in situ hybridization (FISH), is difficult and time consuming, where a fast and accurate identification is essential, especially when such chromosomal aberrations are found in prenatal diagnosis. A recent molecular technique, spectral karyotyping (SKY), based on the spectral signature of 24 chromosome-specific painting probes labelled with different combinations of five fluorochromes, allows the simultaneous visualisation of all human chromosomes in different colours. We used SKY analysis on 14 cases with rare ESACs or cryptic unbalanced rearrangements found at pre- or postnatal diagnosis. SKY analysis permitted the classification of chromosome rearrangements in all 14 cases analysed in combination with FISH analysis.

Karyotyping of human metaphase II oocytes by multifluor fluorescence in situ hybridization

OBJECTIVE

To quantify aneuploidy in inseminated, injected, and noninjected oocytes from infertility patients using Multifluor fluorescence in situ hybridization (M-FISH).

DESIGN

Prospective study.

SETTING

Reproductive biology group, academic unit of pediatrics, obstetrics, and gynecology.

PATIENT(S)

Forty-eight patients undergoing ovarian stimulation and either intracytoplasmic sperm injection (ICSI) or conventional in vitro fertilization (IVF).

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

M-FISH karyotyping of 67 metaphase II oocytes, including noninjected in vitro matured oocytes, and injected inseminated-failed fertilized oocytes.

RESULT(S)

Thirty-nine percent of oocytes were aneuploid, with nondisjunction of chromosomes in 34% of oocytes and predivision of chromatids in 10%. There was no difference in aneuploidy rates between ICSI noninjected in vitro matured oocytes and injected, failed fertilized oocytes. Chromosomes most frequently involved in aneuploidy were 15, 18, 19, 22, and X. In seven injected ICSI MII oocytes, the prematurely condensed sperm chromatin was karyotyped by M-FISH.

CONCLUSION(S)

M-FISH was used to diagnose aneuploidy at maternal meiosis I in 39% of oocytes, and M-FISH karyotyping of sperm was demonstrated.

Telomeres: a diagnosis at the end of the chromosomes

In recent years, subtelomeric rearrangements have been identified as a major cause of mental retardation and/or malformation syndromes. So far, over 2500 subjects with mental retardation have been tested and reported of whom approximately 5% appeared to have a subtelomeric rearrangement. In this review, the clinical aspects of each known (submicroscopic) subtelomeric deletion will be presented and the various methods available for detecting subtelomeric abnormalities will be discussed. Not only will the patients and their families benefit from a good collection and report of the various telomeric abnormalities and their clinical phenotype, but it will also give more insight into the aetiology of mental retardation and malformation syndromes.

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.

Advances in molecular cytogenetics for the evaluation of mental retardation

Recent years have witnessed rapid advances in molecular cytogenetics and its impact in studying mental retardation (MR). We review new molecular cytogenetic methods, including interphase fluorescence in situ hyrbridization (FISH), comparative genomic hybridization (CGH), multicolor karyotyping, telomere FISH, primed in situ labeling (PRINS), genotyping, microdissection, and microarray for the evaluation of MR. These new methods are very useful in two major aspects: further characterization of chromosome abnormalities as detected with routine banding analysis, including additions, duplications, deletions, translocations, markers, or complex aberrations; and screening for "hidden" chromosome aberrations in patients with an apparently normal karyotype. These new methods have great diagnostic potential in prenatal, postnatal, and preimplantational settings. Although powerful, at this point, they are primarily research tools in nature. It is essential that these new methods be used in conjunction with standard methods in order to maximize obtainable information for better management of patients with MR.

Usefulness of high-resolution comparative genomic hybridization (CGH) for detecting and characterizing constitutional chromosome abnormalities

Comparative genomic hybridization (CGH) is a technique for detection of chromosomal imbalances in a genomic DNA sample. We here report the application of the recently developed method of high-resolution CGH on DNA samples from 66 children having various degrees of delayed psychomotor development with or without clear dysmorphic features and congenital malformations. In 5 of 50 patients with apparently normal karyotypes, a deletion or duplication was revealed by CGH. Only one of these cases had a subtelomeric rearrangement. In one of seven cases with a de novo apparently balanced translocation, deletions were found. In all nine cases where the origin of a marker chromosome or additional chromosomal material was difficult to determine, CGH gave a precise identification. The following findings were from cases having a deletion or duplication as the sole chromosomal imbalance; dup(2)(p16p21), del(4)(q21q21), del(6)(q14q15), del(6)(p12p12), dup(6)(q24qter), and dup(15)(q11q13). One case had dup(9)(p11pter) combined with a very small subtelomeric deletion on 6q. In our hands, CGH is highly useful not only for identifying known chromosomal imbalances, but also for finding elusive deletions or duplications in the large group of children with developmental delay with or without congenital abnormalities. In such cases, the diagnostic yield of CGH appears to be higher than what has been reported from subtelomeric FISH screening.

Recent advances in prenatal screening and diagnosis of genetic disorders

In any pregnancy, there is an approximate 3% to 5% chance that a fetal complication will occur. The most familiar prenatal diagnostics cannot be performed until the fetus is well into gestation, and most involve invasive procedures along with their inherent risks. In light of these facts, many noninvasive prenatal screening and diagnostic tests have been developed, the newest using recombinant deoxyribonucleic acid (DNA) technology in the examination of fetal cells. Through these procedures, genetic coding errors and chromosomal disruptions may be detected. This article discusses the currently available prenatal and screening diagnostic tests for genetic disorders with a focus on the latest technology.

Prenatal diagnosis: molecular genetics and cytogenetics

The technologies developed for the Human Genome Project, the recent surge of available DNA sequences resulting from it and the increasing pace of gene discoveries and characterization have all contributed to new technical platforms that have enhanced the spectrum of disorders that can be diagnosed prenatally. The importance of determining the disease-causing mutation or the informativeness of linked genetic markers before embarking upon a DNA-based prenatal diagnosis is, however, still emphasized. Different fluorescence in situ hybridization (FISH) technologies provide increased resolution for the elucidation of structural chromosome abnormalities that cannot be resolved by more conventional cytogenetic analyses, including microdeletion syndromes, cryptic or subtle duplications and translocations, complex rearrangements involving many chromosomes, and marker chromosomes. Interphase FISH and the quantitative fluorescence polymerase chain reaction are efficient tools for the rapid prenatal diagnosis of selected aneuploidies, the latter being considered to be most cost-effective if analyses are performed on a large scale. There is some debate surrounding whether this approach should be employed as an adjunct to karyotyping or whether it should be used as a stand-alone test in selected groups of women.

Radiation-induced chromosome aberrations: insights gained from biophysical modeling

Enzymatic misrepair of ionizing-radiation-induced DNA damage can produce large-scale rearrangements of the genome, such as translocations and dicentrics. These and other chromosome exchange aberrations can cause major phenotypic alterations, including cell death, mutation and neoplasia. Exchange formation requires that two (or more) genomic loci come together spatially. Consequently, the surprisingly rich aberration spectra uncovered by recently developed techniques, when combined with biophysically based computer modeling, help characterize large-scale chromatin architecture in the interphase nucleus. Most results are consistent with a picture whereby chromosomes are mainly confined to territories, chromatin motion is limited, and interchromosomal interactions involve mainly territory surfaces. Aberration spectra and modeling also help characterize DNA repair/misrepair mechanisms. Quantitative results for mammalian cells are best described by a breakage-and-reunion model, suggesting that the dominant recombinational mechanism during the G(0)/G(1) phase of the cell cycle is non-homologous end-joining of radiogenic DNA double strand breaks. In turn, better mechanistic and quantitative understanding of aberration formation gives new insights into health-related applications.

Modern molecular cytogenetic techniques in genetic diagnostics

During the past decade, fluorescence in situ hybridization (FISH) has become an important complementing application in genetic diagnostics. The use of variable FISH techniques enhances the thorough interpretation of numerical and complex chromosome aberrations, bridging the gap between conventional chromosome banding analysis and molecular genetic DNA studies. This review gives a brief overview of the different molecular cytogenetic FISH techniques and applications currently used in routine genetic diagnostics and focus on their advantages and limitations.

Identification of de novo chromosome rearrangements: five cases analyzed with differential chromosome painting

We report on five cases of de novo structural chromosome rearrangements that were difficult to identify by conventional G-banding analysis. In all five cases, differential chromosome painting (DCP) provided evidence for the presence of an additional segment and its origin. A combination of DCP with subsequent conventional fluorescence in situ hybridization (FISH) analysis using adequate locus-specific probes and reexamination of G-banding patterns resulted in successful identification of the rearrangements. Their karyotypes were finally interpreted as 46,XY,der(1)(qter --> q42.1::p36.3 --> qter) in case 1; 46,XY,der(8)(8pter -->8q24.3::8q24.3 --> 8q23.2::?p11.2 --> ?ps) in case 2; 47,XY,+der(10)(pter --> q11) in case 3; 46,XX,der(3)(17pter --> 17p11.2::3p26 --> 3qter) in case 4; and 46,XY,dup(1) (pter --> q32::q25 --> qter) in case 5.

Cytogenetic characterization of complex karyotypes in seven established melanoma cell lines by multiplex fluorescence in situ hybridization and DAPI banding

We report the use of multiplex fluorescence in situ hybridization (M-FISH) to resolve chromosomal aberrations in seven established melanoma cell lines with hypotriploid to hypertetraploid complex karyotypes. By simultaneous identification of all human chromosomes in single FISH experiments using a set of 52 directly labeled, whole chromosome painting probes, cryptic chromosomal translocations and the origin of unclear chromosomal material in structural rearranged and marker chromosomes could be identified, refining the tumor karyotypes in all seven cell lines. The number of structural aberrations in each cell line assigned with combined M-FISH and DAPI banding analysis ranged from 15 to 45. Altogether, 275 breakpoints could be assigned to defined chromosomal regions or bands. The chromosome arms 1p, 6q, 7p, 9p, and 11q which are known to be nonrandomly associated with melanoma tumorigenesis, were frequently involved in chromosomal breaks and/or copy number changes. This study also demonstrated the practical usefulness of combining M-FISH with conventional cytogenetic banding techniques for the characterization of complex tumor karyotypes with massive genomic alterations.

Subtelomeric rearrangements detected in patients with idiopathic mental retardation

A screening for submicroscopic rearrangements was performed in 111 patients with idiopathic mental retardation (MR) using fluorescence in situ hybridization (FISH) probes from the subtelomeric regions of all chromosome arms. Ten cryptic rearrangements were found (9%): five de novo deletions; one unbalanced de novo translocation; three unbalanced inherited translocations; and one unbalanced recombinant chromosome, inherited from a parent with a pericentric inversion. In addition, 50 of the patients were screened for interstitial rearrangements with spectral karyotyping (SKY), but no aberrations were found. However, SKY detected the subtelomeric rearrangement in three of the four unbalanced translocations. Dysmorphic features were present in all patients with detected subtelomeric rearrangements.

Additional dark G-band in the p-arm of chromosome 19 due to a paracentric inversion with a breakpoint in the pericentromeric heterochromatin

Paracentric inversions in chromosome 19 have rarely been described. Here we present an inv(19)(p11p13.1) with a breakpoint in the pericentromeric heterochromatin which leads to an additional dark G-band in the p-arm of chromosome 19. The rearranged chromosome segregated in two generations of a family without any phenotypic effects. A detailed characterization of the inv(19) by molecular cytogenetic techniques is presented.

Karyotyping mouse chromosomes by multiplex-FISH (M-FISH)

Karyotyping of mouse chromosomes is a skillful art, which is laborious work even for experienced cytogeneticists. With the growing number of mouse models for human diseases, there is an increasing demand for automated mouse karyotyping systems. Here, such a karyotyping system for mouse chromosomes based on the multiplex-fluorescence in-situ hybridization (M-FISH) technology is shown. The system was tested on a number of individual mice with numerical and structural aberrations and its reproducibility and robustness verified. Mouse M-FISH should be a valuable tool for the analysis of chromosomal rearrangements in mice.

Facilitating haplotype analysis by fully automated analysis of all chromosomes in human-mouse hybrid cell lines

Recent evidence suggests that haplotype analysis is essential in recognizing genetic factors involved in the tendency toward a particular disease or pharmacogenetic phenotype, as well as to identify genes involved in multigenic disorders. Because of the increasing need for efficient haplotype tests, a new hybrid system, called conversion technology, was developed. Conversion technology aims at converting the diploid chromosome content into a haploid state so that hybrids contain a single copy of any desired chromosome. A number of mutations can now be identified easily, as they are no longer obscured by the normal sequence present on the other copy of the chromosome. However, the efficient use of this hybrid system depends on a complete analysis of both human and mouse chromosome complements in order to assess the stability of the hybrid cells and to accurately determine their human chromosome content. We describe a new multicolor FISH-based method capable of analyzing both genomes simultaneously in a single hybridization. This new technique should become an instrumental part of inexpensive, reliable haplotype tests.

Classifying by colors: FISH-based genome analysis

In recent years a fascinating evolution of different multicolor fluorescence in situ hybridization (FISH) technologies could be witnessed. The various approaches to cohybridize multiple DNA probes in different colors opened new avenues for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. These developments had a remarkable impact on microscopy design and the usage of highly sensitive area imagers. In addition, they led to the introduction of new fluorochromes with appropriate filter combinations, refinements of hybridization protocols, novel probe sets, and innovative software for automated chromosome analysis. This paper attempts to summarize the various multicolor approaches and discusses the application of the individual technologies.

Molecular cytogenetics

Refinements in cytogenetic techniques over the past 30 years have allowed the increasingly sensitive detection of chromosome abnormalities in haematological malignancies. In particular, the advent of fluorescence in situ hybridization techniques has provided significant advances in both diagnosis and research of leukaemias. The application of new multicolour karyotyping techniques has allowed the complete dissection of complex chromosome rearrangements and provides the prospect of identifying new recurrent chromosome rearrangements. Both comparative genomic hybridization and interphase fluorescence in situ hybridization avoid the use of metaphase chromosomes altogether and have allowed the genetic analysis of previously intractable targets. Recent developments in comparative genomic hybridization to DNA microarrays provide the promise of high resolution and automated screening for chromosomal imbalances. Rather than replacing conventional cytogenetics, however, these techniques have extended the range of cytogenetic analyses when applied in a complementary fashion.

Comparative genomic hybridisation in mentally retarded patients with dysmorphic features and a normal karyotype

Segmental aneusomy for small chromosomal regions has been shown to be a common cause of mental retardation and multiple congenital anomalies. A screening method for such chromosome aberrations that are not detected using standard cytogenetic techniques is needed. Recent studies have focused on detection of subtle terminal chromosome aberrations using subtelomeric probes. This approach however excludes significant regions of the genome where submicroscopic rearrangements are also liable to occur. The aim of the present study was to evaluate the efficiency of comparative genomic hybridisation (CGH) for screening of submicroscopic chromosomal rearrangements. CGH was performed in a cohort of 17 patients (14 families) with mental retardation, dysmorphic features and a normal karyotype. Five subtle unbalanced rearrangements were identified in 7 patients. Subsequent FISH studies confirmed these results. Although no interstitial submicroscopic rearrangement was detected in this small series, the study emphasises the value of CGH as a screening approach to detect subtle chromosome rearrangements in mentally retarded patients with dysmorphic features and a normal karyotype.

New concepts to improve resolution and sensitivity of molecular cytogenetic diagnostics by multicolor fluorescence in situ hybridization

BACKGROUND

Routine application of multicolor fluorescence in situ hybridization (M-FISH) technology for molecular cytogenetic diagnostics has been hampered by several technical limitations. First, when using chromosome-specific painting probes, there is a limit in cytogenetic resolution of approximately 2-3 Mb, which can mask hidden structural abnormalities that have a significant clinical effect. Second, using whole chromosome painting probes, intrachromosomal rearrangements cannot be detected and the exact localization of breakpoints is often not possible.

METHODS

We suggest the use of multiplex-labeled region or locus- specific probes in combination with an optimal probe design to improve the sensitivity and resolution of the M-FISH technology. To allow the application of this assay in routine diagnostics, we developed a multipurpose image analysis system.

RESULTS

goldFISH was applied to the study of cryptic translocations in mental retardation patients and to the study of high-resolution breakpoint mapping in non-small cell lung cancer patients. For an individual with mental retardation, who had an apparently normal karyotype by G-banding, we detected an unbalanced translocation involving chromosomes 2 and 7.

CONCLUSIONS

In combination with optimally designed probe kits, goldFISH overcomes most of the present limitations of the M-FISH technology and results in virtually 100% reliability for detecting interchromosomal and intrachromosomal rearrangements.

A classification efficiency test of spectral karyotyping and multiplex fluorescence in situ hybridization: identification of chromosome homologies between Homo sapiens and Hylobates leucogenys

Two digital fluorescence microscopy systems, spectral karyotyping (SKY) and multiplex fluorescence in situ hybridisation (M-FISH), are used with multicolour probe sets to assist in the detection of chromosome aberrations. We have compared the resolution of the two methods in their ability to identify karyotype rearrangements, which have occurred during the divergence of Homo sapiens and Hylobates leucogenys in evolution. A 24-color human paint kit distinguishes 74 conserved autosomal segments in H. leucogenys, some of which are difficult to resolve. We examined the extent to which the SKY and M-FISH techniques are able to detect the smallest of these bands. We have found this to be a rigorous test of multicolour chromosome classification systems. We conclude from our results that both systems are able invariably to classify the majority of conserved segments but differ in the efficiency of detection of small inserts.

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.

Karyotype of the abortus in recurrent miscarriage

OBJECTIVE

To assess the chromosomal aberrations in the abortus in recurrent miscarriage and the live birth rate after a euploid or aneuploid miscarriage.

DESIGN

Retrospective analysis.

SETTING

Tertiary referral unit in university hospital.

PATIENT(S)

One hundred sixty-seven patients with 3 to 16 miscarriages before 20 weeks.

INTERVENTION(S)

Material collected at curettage from 167 abortuses was analyzed by standard G-banding techniques.

MAIN OUTCOME MEASURE(S)

The incidence of aberrations and the outcome of the subsequent pregnancy were assessed according to the embryonic karyotype.

RESULT(S)

In this study 125 specimens were successfully karyotyped. Of these, 29% (36 of 125) had chromosome aberrations; 94% of the aberrations were aneuploidy, and 6% were structural. The most prevalent anomalies were chromosome 16, 18, and 21 trisomies, triploidy, and monosomy X. After an aneuploid miscarriage, there was a 68% subsequent live birth rate (13 of 19) compared to the 41% (16 of 39) rate after a euploid abortion.

CONCLUSION(S)

The low (29%) incidence of aberrations indicates that alternative mechanisms may be responsible for the majority of recurrent miscarriages. These figures provide a basis for assessing the efficacy of therapy for recurrent miscarriage. If further studies confirm that patients with karyotypically abnormal fetuses have a good prognosis, an informed decision can be made as to whether further investigations and treatment should be undertaken.

Small marker chromosome identification in metaphase and interphase using centromeric multiplex fish (CM-FISH)

Multicolor karyotyping procedures, such as multiplex fluorescence in situ hybridization (M-FISH), spectral karyotyping, or color-changing karyotyping, can be used to detect chromosomal rearrangements and marker chromosomes in prenatal diagnosis, peripheral blood cultures, leukemia, and solid tumors, especially in cases where G-banding is not sufficient. A regular M-FISH analysis requires relatively large amounts of labeled DNA (microgram quantities), is not informative in interphase nuclei, hybridization can take up to 2 to 3 days, and unlabeled human chromosome-painting probes are not available commercially. Unique probes (plasmids, PAC), specific for centromeric or subtelomeric chromosomal regions, can replace the painting probes in M-FISH to address specific issues, such as the identification of marker chromosomes and aneuploidies. A set of plasmid probes carrying repetitive sequences specific for the alpha-satellite region of all human chromosomes were combined in a metaphase assay and an interphase assay, allowing identification of aneuploidies in one hybridization step, on a single cytogenetic slide. The fluorophore-dUTP and the labeled antibodies required to label and detect the DNA probes can be prepared in any laboratory. All DNA probes can be easily isolated and labeled using common molecular cytogenetic procedures. Because of the repetitive nature of the probes, hybridization time is short, usually less than 1 hour, and the analysis can be performed with nonspecialized image-processing software.

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.

Evaluation of 24-color multifluor-fluorescence in-situ hybridization (M-FISH) karyotyping by comparison with reverse chromosome painting of the human breast cancer cell line T-47D

Multifluor-fluorescence in-situ hybridization (M-FISH) chromosome paints for all the chromosomes in the human complement labeled with different combinations of fluorochromes is a recent technological development enabling assignment of chromosomal material to rearranged chromosomes. Little data is available on the accuracy and limitations of the approach to the analysis of complex karyotypes, which are characteristic of many malignant diseases. Here we compare M-FISH analysis of the breast-cancer-derived cell line T-47D with a previous analysis by reverse chromosome painting analysis of flow-sorted chromosomes from the same material. This demonstrated a high degree of concordance. It also illustrated the limitations of M-FISH analysis, including difficulties identifying small regions of chromosomal material and intrachromosomal rearrangements. Confirmation of selected aberrations using less-complex mixtures of painting probes and further definition of abnormalities using single copy markers may be required. The detailed karyotype description possible by M-FISH analysis contrasts with the definition in the original G-banding analysis. This and the level of concordance with reverse FISH painting supports the utility of the approach in the definition of complex karyotypes.