A novel source of highly specific chromosome painting probes for human karyotype analysis derived from primate homologues

[From conventional cytogenetics to microarrays. Fifty years of Philadelphia chromosome]

In 1960 Ph-chromosome was found associated with the presence of chronic myelogenous leukemia. In these 50 years an increasing number of cytogenetic abnormalities have been found associated with hematological malignancies. The presence of these abnormalities is not only important for the diagnosis of the patient, but it also contributes to the prognosis of patients with leukemia or lymphoma. For this reason the WHO classification of hematological disease has included these studies for the correct characterization of leukemias and lymphomas. In addition, the use of FISH and micromatrix methodologies have refined the genetic lesions present in these malignancies. The cytogenetic changes observed also provide further information in relation to the therapy.

Comparing microarrays and next-generation sequencing technologies for microbial ecology research

Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.

Cytogenetic characterization of NCI-H69 and NCI-H69AR small cell lung cancer cell lines by spectral karyotyping

Small cell lung cancer (SCLC) shows an excellent sensitivity to chemotherapy, but commonly develops resistance after a few months. An early identification of a genomic marker in drug discovery may help to select patients who would respond to treatment in clinical trials. Herein, we characterized the parental NCI-H69 (sensitive) and NCI-H69AR (anthracycline-resistant) cell lines by G-banding and spectral karyotyping (SKY). In the H69 cell line, SKY allows us to redefine three alterations that are not well characterized by G-banding and to confirm seven. For H69AR, SKY redefined 10 chromosomal alterations and confirmed four observed by G-banding. Fluorescence in situ hybridization confirmed the amplification of the MYCN gene (dmin or hsr) in these two cell lines, although only the H69AR cell line showed MYCN amplification in the form of homogeneously staining regions. It should be noted that a new derivative chromosome appears in the H69AR cell line, a der(16)t(3;16;18;5;18), characterized by SKY as showing 18q amplification. Amplification of genes located in this region may correlate with resistance to anticancer therapies. We suggest that the 18q marker may have a broader application in SCLC. In conclusion, SKY provides a useful complementary technique to routine cytogenetics for the accurate characterization of SCLC cell lines and could provide some relevant information concerning regions involved in chemoresistance.

FISH glossary: an overview of the fluorescence in situ hybridization technique

The introduction of FISH (fluorescence in situ hybridization) marked the beginning of a new era for the study of chromosome structure and function. As a combined molecular and cytological approach, the major advantage of this visually appealing technique resides in its unique ability to provide an intermediate degree of resolution between DNA analysis and chromosomal investigations while retaining information at the single-cell level. Used to support large-scale mapping and sequencing efforts related to the human genome project, FISH accuracy and versatility were subsequently capitalized on in biological and medical research, providing a wealth of diverse applications and FISH-based diagnostic assays. The diversification of the original FISH protocol into the impressive number of procedures available these days has been promoted throughout the years by a number of interconnected factors: the improvement in sensitivity, specificity and resolution, together with the advances in the fields of fluorescence microscopy and digital imaging, and the growing availability of genomic and bioinformatic resources. By assembling in a glossary format many of the "acronymed" FISH applications published so far, this review intends to celebrate the ability of FISH to re-invent itself and thus remain at the forefront of biomedical research.

Pericentromeric euchromatin is conserved in minute human supernumerary chromosomes: a study using cross-species colour segmenting (RxFISH)

Investigation of marker chromosomes is one of the most challenging areas of clinical cytogenetics, especially in the prenatal scenario. A range of techniques including microdissection/reverse painting, SKY and M-FISH are available for the investigation of larger markers (>3 Mb). All these techniques rely on hybridization of unique, homologous sequences with simultaneous suppression of repeat sequences. In contrast, RxFISH is based on hybridization of cross-species syntenic sequences; repeat sequences do not hybridize due to species divergence. We have used RxFISH to analyse a group of the smallest, i.e. minute, supernumerary marker chromosomes. Our results suggest that even the smallest marker chromosomes often contain conserved pericentric euchromatin. More detailed characterization of pericentric genetic content is needed to assess the clinical significance of minute supernumerary markers.

Biomedical applications and studies of molecular evolution: a proposal for a primate genomic library resource

The anticipated completion of two of the most biomedically relevant genomes, mouse and human, within the next three years provides an unparalleled opportunity for the large-scale exploration of genome evolution. Targeted sequencing of genomic regions in a panel of primate species and comparison to reference genomes will provide critical insight into the nature of single-base pair variation, mechanisms of chromosomal rearrangement, patterns of selection, and species adaptation. Although not recognized as model "genetic organisms" because of their longevity and low fecundity, 30 of the approximately 300 primate species are targets of biomedical research. The existence of a human reference sequence and genomic primate BAC libraries greatly facilitates the recovery of genes/genomic regions of high biological interest because of an estimated maximum neutral nucleotide sequence divergence of 25%. Primate species, therefore, may be regarded as the ideal model "genomic organisms". Based on existing BAC library resources, we propose the construction of a panel of primate BAC libraries from phylogenetic anchor species for the purpose of comparative medicine as well as studies of genome evolution.

Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates

We demonstrate that the nuclear topological arrangement of chromosome territories (CTs) has been conserved during primate evolution over a period of about 30 million years. Recent evidence shows that the positioning of chromatin in human lymphocyte nuclei is correlated with gene density. For example, human chromosome 19 territories, which contain mainly gene-dense and early replicating chromatin, are located toward the nuclear center, whereas chromosome 18 territories, which consist mainly of gene-poor and later replicating chromatin, is located close to the nuclear border. In this study, we subjected seven different primate species to comparative analysis of the radial distribution pattern of human chromosome 18- and 19-homologous chromatin by three-dimensional fluorescence in situ hybridization. Our data demonstrate that gene-density-correlated radial chromatin arrangements were conserved during higher-primate genome evolution, irrespective of the major karyotypic rearrangements that occurred in different phylogenetic lineages. The evolutionarily conserved positioning of homologous chromosomes or chromosome segments in related species supports evidence for a functionally relevant higher-order chromatin arrangement that is correlated with gene-density.

New t(11;12)(q12;q11) characterized by RxFISH in a patient with T-cell large granular lymphocyte leukemia

Chromosomal abnormalities in patients with large granular lymphocyte leukemia (LGLL) are rare. Herein we present a novel cytogenetic abnormality t(11;12)(q12;q11) in a patient with LGLL identified by cross-species color banding (RxFISH). The application of RxFISH allowed the rapid and easy identification of a chromosome rearrangement that was not recognized by conventional cytogenetics. Therefore, RxFISH is a suitable complement to, but not a replacement for, conventional cytogenetics.

Establishment and characterization of chromosomal aberrations in human cholangiocarcinoma cell lines by cross-species color banding

Cholangiocarcinoma (CC), a malignant neoplasm of the biliary epithelium, is usually fatal because of difficulty in early diagnosis and lack of availability of effective therapy. Furthermore, little is known about the genetics and biology of CC. Only a few reports concerning cytogenetic studies of CC have been published, and few cell lines have been established. We recently established four CC cell lines, designated as SCK, JCK, Cho-CK, and Choi-CK, and report the first application of cross-species color banding (RxFISH) and multiple chromosome painting for the characterization of the chromosomal rearrangements of these CC cell lines. Each cell line had unique modal karyotypic characteristics and showed a variable number of numerical and structural clonal cytogenetic aberrations. Chromosomes 3, 6, 7, 8, 12, 14, 17, and 18 were commonly involved in structural abnormalities. Homogeneously staining regions were determined in SCK and JCK, and double minute chromosomes were found in Cho-CK. The chromosomal aberrations of the four CC cell lines were effectively analyzed by RxFISH and FISH with multiple chromosome painting probes. The nonrandom rearrangements suggest candidate regions for isolation of genes related to CC.

Cross-species color banding in ten cases of myeloid malignancies with complex karyotypes

Cross-species color banding is a multiple-color fluorescence in situ hybridization (FISH) technique using probes developed from other animal species. Hybridization to human metaphases produces color banding patterns specific for each homologous chromosome pair. The technique has been evaluated in a complementary manner with G-banding and chromosome painting in a series of 10 myeloid malignancies with complex or unresolved karyotypes. Color banding detected the majority of chromosomal abnormalities, which had been identified by G-banding and in each case revealed chromosomal changes that G-banding had not identified. Painting was necessary to confirm these abnormalities due to the limitation of only seven colors in the color-banded karyotype. At the same time, painting fortuitously uncovered cryptic abnormalities in 6 of 10 cases that had not been detected by color banding. Insertions were visible by painting only. This study has demonstrated that in the analysis of complex karyotypes, the application of color banding revealed the involvement of the long arm of chromosome 3, indicating a poor risk, in two cases not identified by G-banding. Therefore, these techniques applied together have revealed cryptic chromosomal abnormalities with prognostic significance, which in some cases may have implications for patient management.

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.