Applications of combined DNA microarray and chromosome sorting technologies

Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder

Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.

DNA probes for FISH analysis of C-negative regions in human chromosomes

Fluorescent in situ hybridization (FISH) is a powerful technology for studying the chromosome organization and aberrations as well as for searching the homology between chromosomal regions in mammals. Currently, FISH is used as a simple, rapid, and reliable technique for analyzing chromosomal rearrangements and assigning chromosomal breakpoints in modern diagnosing of chromosomal pathology. In addition to cloned DNA fragments, the DNA probes produced by sequence-independent polymerase chain reaction are widely used in FISH assays. As a rule, the DNA probes generated from a genomic or chromosomal DNA by whole genome amplification are enriched for repetitive elements and, consequently, efficient FISH analysis requires that repetitive DNA hybridization is suppressed. The linker-adapter polymerase chain reaction (LA-PCR) using the genomic DNA hydrolyzed with HaeIII and RsaI restriction endonucleases allows the repetitive DNA fraction in DNA probe to be decreased and gene-rich DNA to be predominantly amplified. The protocol described here was proposed for production of the DNA probes for enhanced analysis of the C-negative regions in human chromosomes.

Isolation of single, intact chromosomes from single, selected ovarian cancer cells for in situ hybridization and sequencing

The first step towards effective therapy of cancer is to reveal molecular profiles of all cell clones propelling tumor growth. The specific aim of this project was to develop a technology helping us to isolate patient's single, living cells based upon their cancer-specific, cell surface biomarkers, to reveal their molecular profiles, and to isolate, from these selected cells, intact chromosomes for in situ hybridization (FISH) and for next generation sequencing (NGS). We attained this aim, while probing the cells from the ovarian cancer patients. Ovarian cancer is the most deadly of all gynecological cancers. In most of the patients with the advanced stages of this cancer, the gene for epidermal growth factors receptor (EGFR) is mutated, as the deletion variant III, resulting in the truncated transcripts and products. From these patients, we collected cells from peritoneal fluid, blood, lymph, and biopsies. We genetically engineered fluorescent and superparamagnetic single chain variable fragments (scFvs) targeting EGFRwt and EGFRvIII. Using these scFvs, we isolated single, living ovarian cancer cells and analyzed their transcripts and products. We further genetically engineered scFv targeting dsDNA. Using these scFvs, we isolated the entire single, intact chromosomes from the selected, single ovarian cancer cells for NGS and for liquid phase FISH. This novel work-flow opens new routes not only for molecular profiling of the entire spectrum of cancer cell clones in the diagnosed patient, one cell clone at a time, but also for manufacturing targeted contrast for in vivo imaging and for designing and guiding targeted delivery of therapeutic genes in cancer therapy.

Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics

Genomic rearrangements can result in losses, amplifications, translocations and inversions of DNA fragments thereby modifying genome architecture, and potentially having clinical consequences. Many genomic disorders caused by structural variation have initially been uncovered by early cytogenetic methods. The last decade has seen significant progression in molecular cytogenetic techniques, allowing rapid and precise detection of structural rearrangements on a whole-genome scale. The high resolution attainable with these recently developed techniques has also uncovered the role of structural variants in normal genetic variation alongside single-nucleotide polymorphisms (SNPs). We describe how array-based comparative genomic hybridisation, SNP arrays, array painting and next-generation sequencing analytical methods (read depth, read pair and split read) allow the extensive characterisation of chromosome rearrangements in human genomes.

Array painting: a protocol for the rapid analysis of aberrant chromosomes using DNA microarrays

Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.

Phylogenomic analysis by chromosome sorting and painting

Chromosome sorting by flow cytometry is the principle source of chromosome-specific DNA not only for chromosome painting, but also for many other types of genomic analysis such as library construction, discovery and isolation of genes, chromosome specific direct DNA selection, and array painting. Chromosome sorting coupled with chromosome painting is a rapid method for global phylogenomic comparisons. These two techniques have made notable contributions to our knowledge of the evolution of the mammalian genome. The flow sorting of multiple species allows reciprocal painting and permits the delineation of subchromosomal homology and the definition of chromosomal breakpoints. Chromosomes are valuable phylogenetic makers because rearrangements that become fixed at the species level are considered rare events and apparently tightly bound to the speciation process. This chapter covers the preparation of a single chromosome suspension from cell cultures, bivariate chromosome flow sorting, preparation of chromosome paints by degenerate oligonucleotide primed-PCR and the fluorescence in-situ hybridization and detection of whole chromosome specific probes.

Mouse chromosome engineering for modeling human disease

Chromosomal rearrangements are frequently in humans and can be disease-associated or phenotypically neutral. Recent technological advances have led to the discovery of copy-number changes previously undetected by cytogenetic techniques. To understand the genetic consequences of such genomic changes, these mutations need to be modeled in experimentally tractable systems. The mouse is an excellent organism for this analysis because of its biological and genetic similarity to humans, and the ease with which its genome can be manipulated. Through chromosome engineering, defined rearrangements can be introduced into the mouse genome. The resulting mouse models are leading to a better understanding of the molecular and cellular basis of dosage alterations in human disease phenotypes, in turn opening new diagnostic and therapeutic opportunities.

Getting it right: designing microarray (and not 'microawry') comparative genomic hybridization studies for cancer research

The development of high-resolution microarray-based comparative genomic hybridization (aCGH), using cDNA, bacterial artificial chromosome (BAC) and oligonucleotide probes, is providing tremendous opportunities for translational research by facilitating detailed analysis of entire cancer genomes in a single experiment. However, this technology will only fulfil its promise if studies incorporating aCGH are designed with a full understanding of its current limitations and the strategies available to circumvent them. While there have been several excellent reviews on the current status of this technology, there is currently very little guidance available regarding the appropriate design of experiments incorporating aCGH (including the strengths and weaknesses of each platform), and how best to combine the results obtained from aCGH with other 'omic' technologies, including gene expression. In this review, we present the key design issues that need to be considered in order to optimize aCGH studies, including sample selection, the definition of appropriate experimental objectives, arguments for and against the various microarray platforms that are currently available, and methods for data validation and integration. It is envisaged that future well-designed aCGH studies will enhance our understanding of the genetic basis of cancer, and lead to the identification of novel predictive and prognostic cancer biomarkers, as well as molecular therapeutic targets in cancer.

Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases

BACKGROUND

Array Comparative Genomic Hybridization (a-CGH) is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA).

METHODS AND FINDINGS

CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5%) of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872) with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524) abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs) of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance.

CONCLUSIONS

This large set of clinical results demonstrates the significantly improved sensitivity of CMA for the detection of clinically relevant genomic imbalances and highlights the need for comprehensive genetic counseling to facilitate accurate clinical correlation and interpretation.

Array painting using microdissected chromosomes to map chromosomal breakpoints

Molecular characterization of breakpoints of chromosomal rearrangements is a successful strategy for the identification of candidate disease genes. Mapping translocation breakpoints and rearranged chromosomal boundaries is labor intensive and/or time consuming. Here, we present a novel and rapid procedure to map such chromosomal breakpoints by hybridizing amplified microdissection derived DNA of aberrant chromosomes to arrays containing genomic clones. We illustrate the potential of the technique by molecularly delineating the breakpoints in five small supernumerary marker chromosomes (sSMC) and mapping the breakpoints of five different chromosomal translocations.

Array-based comparative genomic hybridization in clinical diagnosis

The sequencing of the human genome and development of high-throughput microarray technologies have enhanced the detection of copy number alterations in cancer research and the study of constitutional chromosomal abnormalities. Microarray-based comparative genomic hybridization (array CGH) has integrated molecular and traditional cytogenetics and has begun to impact the clinician's approach to medical genetics. Clinical applications of array CGH may define new genetic syndromes, expand the phenotype of existing syndromes and characterize a genomic signature of some cancers. As array CGH becomes the initial diagnostic approach for the investigation of constitutional and acquired chromosomal abnormalities, the combination of bioinformatics, robotics and microarray technology will set the stage for a new generation of high-resolution and high-throughput tools for genetic analysis, diagnosis and gene discovery.

A high-resolution map of synteny disruptions in gibbon and human genomes

Gibbons are part of the same superfamily (Hominoidea) as humans and great apes, but their karyotype has diverged faster from the common hominoid ancestor. At least 24 major chromosome rearrangements are required to convert the presumed ancestral karyotype of gibbons into that of the hominoid ancestor. Up to 28 additional rearrangements distinguish the various living species from the common gibbon ancestor. Using the northern white-cheeked gibbon (2n = 52) (Nomascus leucogenys leucogenys) as a model, we created a high-resolution map of the homologous regions between the gibbon and human. The positions of 100 synteny breakpoints relative to the assembled human genome were determined at a resolution of about 200 kb. Interestingly, 46% of the gibbon–human synteny breakpoints occur in regions that correspond to segmental duplications in the human lineage, indicating a common source of plasticity leading to a different outcome in the two species. Additionally, the full sequences of 11 gibbon BACs spanning evolutionary breakpoints reveal either segmental duplications or interspersed repeats at the exact breakpoint locations. No specific sequence element appears to be common among independent rearrangements. We speculate that the extraordinarily high level of rearrangements seen in gibbons may be due to factors that increase the incidence of chromosome breakage or fixation of the derivative chromosomes in a homozygous state.

It is commonly accepted that mammalian chromosomes have undergone a limited number of rearrangements during the course of more than 100 million years of evolution. Surprisingly, some species have experienced a large increase in the incidence of rearrangements, including translocations (exchange between two non-homologous chromosomes), inversions (change of orientation of one chromosomal segment), fissions, and fusions. Within the primate order, gibbons exhibit the most strikingly unstable chromosome pattern. Gibbon chromosomal structure greatly differs from that of their most recent common ancestor with humans from which they diverged over 15 million years ago. The authors are interested in the mechanisms causing this extraordinary instability. In this study, they employed modern techniques to compare the human and white-cheeked gibbon chromosomes and to localize all the regions of disrupted homology between the two species. Their findings indicate that the molecular mechanism of gibbon chromosomal reshuffling is based on the same principles as in other mammalian species. To explain the 10-fold higher incidence of gibbon chromosomal rearrangements, it will be necessary to pursue future studies into other biological factors such as inbreeding and population dynamics.

Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells

Array-based comparative genomic hybridisation (aCGH) has diverse applications in cancer gene discovery and translational research. Currently, aCGH is performed primarily using high molecular weight DNA samples and its application to formalin-fixed and paraffin-embedded (FFPE) tissues remains to be established. To explore how aCGH can be reliably applied to archival FFPE tissues and whether it is possible to apply aCGH to small numbers of cells microdissected from FFPE tissue sections, we have systematically performed aCGH on 15 pairs of matched frozen and FFPE astrocytic tumour tissues using a well-established in-house human 1 Mb BAC/PAC genomic array. By spiking tumour DNA with normal DNA, we demonstrated that at least 70% of tumour DNA was required for reliable aCGH analysis. Using aCGH data from frozen tissue as a reference, it was found that only FFPE astrocytic tumour tissues that supported PCR amplification of >300 bp DNA fragment provided high quality, reproducible aCGH data. The presence of necrosis in a tissue specimen had an adverse effect on the quality of aCGH, while fixation in formalin for up to 96 h of fresh tissue did not appear to affect the quality of the result. As little as 10-20 ng DNA from frozen or FFPE tissues could be readily used for aCGH analysis following whole genome amplification (WGA). Furthermore, as few as 2000 microdissected cells from haematoxylin-stained slides of archival FFPE tissues could be successfully used for aCGH investigations when WGA was used. By careful assessment of DNA integrity and review of histology, to exclude necrosis and select specimens with a high proportion of tumour cells, it is feasible to preselect archival FFPE tissues adequate for aCGH analysis. With the help of microdissection and WGA, it is also possible to apply aCGH to histologically defined lesions, such as carcinoma in situ.

Factors affecting flow karyotype resolution

BACKGROUND

One of the major factors which influences the chromosome purity achievable particularly during high speed sorting is the analytical resolution of individual chromosome peaks in the flow karyotype, as well as the amount of debris and fragmented chromosomes. We have investigated the factors involved in the preparation of chromosome suspensions that influence karyotype resolution.

METHODS

Chromosomes were isolated from various human and animal cell types using a series of polyamine buffer isolation protocols modified with respect to pH, salt concentration, and chromosome staining time. Each preparation was analyzed on a MoFlo sorter (DAKO) configured for high speed sorting and the resolution of the flow karyotypes compared.

RESULTS

High resolution flow cytometric data was obtained with chromosomes optimally isolated using hypotonic solution buffered at pH 8.0 and polyamine isolation buffer (with NaCl excluded) between pH 7.50 and 8.0. Extending staining time to more than 8 h with chromosome suspensions isolated from cell lines subjected to sufficient metaphase arrest times gave the best result with the lowest percentage of debris generated, tighter chromosome peaks with overall lower coefficients of variation, and a 1- to 5-fold increase in the yield of isolated chromosomes.

CONCLUSIONS

Optimization of buffer pH and the length of staining improved karyotype resolution particularly for larger chromosomes and reduced the presence of chromosome fragments (debris). However, the most interesting and surprising finding was that the exclusion of NaCl in PAB buffer improved the yield and resolution of larger chromosomes.

Comparative genomic hybridization

Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

Chromosome sorting in tetraploid wheat and its potential for genome analysis

This study evaluates the potential of flow cytometry for chromosome sorting in durum wheat (Triticum turgidum Desf. var. durum, 2n = 4x = 28). Histograms of fluorescence intensity (flow karyotypes) obtained after the analysis of DAPI-stained chromosomes consisted of three peaks. Of these, one represented chromosome 3B, a small peak corresponded to chromosomes 1A and 6A, and a large peak represented the remaining 11 chromosomes. Chromosomes sorted onto microscope slides were identified after fluorescence in situ hybridization (FISH) with probes for GAA microsatellite, pSc119.2, and Afa repeats. Genomic distribution of these sequences was determined for the first time in durum wheat and a molecular karyotype has been developed for this crop. Flow karyotyping in double-ditelosomic lines of durum wheat revealed that the lines facilitated sorting of any arm of the wheat A- and B-genome chromosomes. Compared to hexaploid wheat, flow karyotype of durum wheat is less complex. This property results in better discrimination of telosomes and high purities in sorted fractions, ranging from 90 to 98%. We have demonstrated that large insert libraries can be created from DNA purified using flow cytometry. This study considerably expands the potential of flow cytogenetics for use in wheat genomics and opens the possibility of sequencing the genome of this important crop one chromosome arm at a time.

The evolution of eutherian chromosomes

The gross organization of the genome of Eutheria (placental mammals) into chromosomes follows a simple architecture that, with some minor changes, is almost completely conserved for more than 100 million years in various species of almost all extant mammalian orders. Recent molecular cytogenetic results--especially those from the assumed oldest clade, the Afrotheria--suggest an ancestral karyotype that would calculate the "default" frequency of gross rearrangements to less than two changes within 10 million years of mammalian evolution. The main changes are the fission, movement and subsequent fusion of large chromosome segments or of chromosome arms. Reciprocal translocations are the exception. Chromosome numbers may have increased or decreased significantly in this fusion/fission process but, in most instances, the main architecture still remains evident. There are, however, some exceptions in mammals with extremely derived karyotypes.

Overrepresentation of small supernumerary marker chromosomes (sSMC) from chromosome 6 origin in cases with multiple sSMC

Small supernumerary marker chromosomes (sSMC) in human are defined as additional centric derivatives smaller than chromosome 20. In the majority of the cases only one sSMC is present, leading to a more or less stable karyotype of 47,XX,+mar or 47,XY,+mar. In approximately 1.4% of sSMC cases two or up to seven markers of different chromosomal origin are reported. According to the literature a sSMC(6) was present in 33% of the patients with multiple sSMC while sSMC(6) are observed in <1% of cases with a single sSMC. Currently there is no explanation for this striking observation. Here we report on one more unique case with two sSMC, one derived from #5 and the other from #6. Using microdissection/reverse painting, subcentromere-specific multicolor FISH (subcenM-FISH) and multicolor banding (MCB), they could be described as min or r(6)(::p11.1 --> q11.1::) and r(5)(::p11.1 approximately 12 --> q10::q10 --> p11.1 approximately 12::), respectively. Reversed array CGH using the DNA of the microdissected sSMC as probe confirmed the FISH results and enabled the rapid mapping of the breakpoints.