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https://www.readbyqxmd.com/read/27910033/cytogenetic-resources-and-information
#1
Etienne De Braekeleer, Jean-Loup Huret, Hossain Mossafa, Philippe Dessen
The main databases devoted stricto sensu to cancer cytogenetics are the "Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer" ( http://cgap.nci.nih.gov/Chromosomes/Mitelman ), the "Atlas of Genetics and Cytogenetics in Oncology and Haematology" ( http://atlasgeneticsoncology.org ), and COSMIC ( http://cancer.sanger.ac.uk/cosmic ).However, being a complex multistep process, cancer cytogenetics are broadened to "cytogenomics," with complementary resources on: general databases (nucleic acid and protein sequences databases; cartography browsers: GenBank, RefSeq, UCSC, Ensembl, UniProtKB, and Entrez Gene), cancer genomic portals associated with recent international integrated programs, such as TCGA or ICGC, other fusion genes databases, array CGH databases, copy number variation databases, and mutation databases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910032/cytogenetic-nomenclature-and-reporting
#2
Marian Stevens-Kroef, Annet Simons, Katrina Rack, Rosalind J Hastings
A standardized nomenclature is critical for the accurate and consistent description of genomic changes as identified by karyotyping, fluorescence in situ hybridization and microarray. The International System for Human Cytogenomic Nomenclature (ISCN) is the central reference for the description of karyotyping, FISH, and microarray results, and provides rules for describing cytogenetic and molecular cytogenetic findings in laboratory reports. These laboratory reports are documents to the referring clinician, and should be clear, accurate and contain all information relevant for good interpretation of the cytogenetic findings...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910031/recurrent-cytogenetic-abnormalities-in-multiple-myeloma
#3
Nelson Chun Ngai Chan, Natalie Pui Ha Chan
Multiple myeloma is a heterogeneous disease. Its chromosomal abnormalities have been extensively studied with a view to accurate prognostication and personalized therapy. Here, we describe the techniques commonly employed for elucidating chromosomal aberrations, prognostic impact of recurrent chromosomal abnormalities, and recently updated risk stratification systems.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910030/recurrent-cytogenetic-abnormalities-in-non-hodgkin-s-lymphoma-and-chronic-lymphocytic-leukemia
#4
Edmond S K Ma
Characteristic chromosomal translocations are found to be associated with subtypes of B-cell non-Hodgkin lymphoma (NHL), for example t(8;14)(q24;q32) and Burkitt lymphoma, t(14;18)(q32;q21) and follicular lymphoma, and t(11;14)(q13;q32) in mantle cell lymphoma. Only few recurrent cytogenetic aberrations have been identified in the T-cell NHL and the best known is the ALK gene translocation t(2;5)(p23;q35) in anaplastic large cell lymphoma. Since lymph node or other tissue is seldom submitted for conventional cytogenetics study, alternative approaches for translocation detection are polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910029/recurrent-cytogenetic-abnormalities-in-acute-lymphoblastic-leukemia
#5
Mary Shago
Both B-cell and T-cell acute lymphoblastic leukemia (ALL) exhibit recurrent cytogenetic alterations, many with prognostic implications. This chapter overviews the major recurrent categories of cytogenetic abnormalities associated with ALL, with an emphasis on the detection and characterization of these cases by G-band and FISH analyses.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910028/recurrent-cytogenetic-abnormalities-in-myeloproliferative-neoplasms-and-chronic-myeloid-leukemia
#6
John Swansbury
The commonest types of myeloproliferative neoplasm (MPN) have remarkably similar recurrent chromosome abnormalities, but with varying incidence and prognostic implications. After a clear decade of treatment of chronic myeloid leukemia (CML) with tyrosine kinase inhibitors, the differing prognostic implications of abnormalities additional to the Ph chromosome are being revealed. This chapter provides a description of the main chromosome abnormalities in MPN and CML and their clinical implications in a time of rapid changes in both the application of new diagnostic techniques and the introduction of targeted therapies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910027/recurrent-cytogenetic-abnormalities-in-acute-myeloid-leukemia
#7
John J Yang, Tae Sung Park, Thomas S K Wan
The spectrum of chromosomal abnormality associated with leukemogenesis of acute myeloid leukemia (AML) is broad and heterogeneous when compared to chronic myeloid leukemia and other myeloid neoplasms. Recurrent chromosomal translocations such as t(8;21), t(15;17), and inv(16) are frequently detected, but hundreds of other uncommon chromosomal aberrations from AML also exist. This chapter discusses 22 chromosomal abnormalities that are common structural, numerical aberrations, and other important but infrequent (less than 1 %) translocations emphasized in the WHO classification...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910026/recurrent-cytogenetic-abnormalities-in-myelodysplastic-syndromes
#8
Meaghan Wall
Cytogenetic analysis has an essential role in diagnosis, classification, and prognosis of myelodysplastic syndromes (MDS). Some cytogenetic abnormalities are sufficiently characteristic of MDS to be considered MDS defining in the appropriate clinical context. MDS with isolated del(5q) is the only molecularly defined MDS subtype. The genes responsible for many aspects of 5q- syndrome, the distinct clinical phenotype associated with this condition, have now been identified. Cytogenetics forms the cornerstone of the most widely adopted prognostic scoring systems in MDS, the international prognostic scoring system (IPSS) and the revised international prognostic scoring system (IPPS-R)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910025/cytogenetics-for-biological-dosimetry
#9
Michelle Ricoul, Tamizh Gnana-Sekaran, Laure Piqueret-Stephan, Laure Sabatier
Cytogenetics is the gold-standard in biological dosimetry for assessing a received dose of ionizing radiation. More modern techniques have recently emerged, but none are as specific as cytogenetic approaches, particularly the dicentric assay. Here, we will focus on the principal cytogenetic techniques used for biological dosimetry: the dicentric assay in metaphase cells, the micronuclei assay in binucleated cells, and the premature condensed chromosome (PCC) assay in interphase cells. New fluorescence in situ hybridization (FISH) techniques (such as telomere-centromere hybridization) have facilitated the analysis of the dicentric assay and have permitted to assess the dose a long time after irradiation by translocation analysis (such as by Tri-color FISH or Multiplex-FISH)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910024/multicolor-karyotyping-and-fluorescence-in-situ-hybridization-banding-mcb-mband
#10
Thomas Liehr, Moneeb A K Othman, Katharina Rittscher
Multicolor fluorescence in situ hybridization (mFISH) approaches are routine applications in tumor as well as clinical cytogenetics nowadays. The first approach when thinking about mFISH is multicolor karyotyping using human whole chromosome paints as probes; this can be achieved by narrow-band filter-based multiplex-FISH (M-FISH) or interferometer/spectroscopy-based spectral karyotyping (SKY). Besides, various FISH-based banding approaches were reported in the literature, including multicolor banding (MCB/mBAND) the latter being evaluated by narrow-band filters, and using specific software...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910022/high-resolution-fiber-fluorescence-in-situ-hybridization
#11
Christine J Ye, Henry H Heng
High resolution fiber-Fluorescence in situ hybridization (FISH) is an advanced FISH technology that can effectively bridge the resolution gap between probe hybridizing on DNA molecules and chromosomal regions. Since various types of DNA and chromatin fibers can be generated reflecting different degrees of DNA/chromatin packaging status, fiber-FISH technology has been successfully used in diverse molecular cytogenetic/cytogenomic studies. Following a brief review of this technology, including its major development and increasing applications, typical protocols to generate DNA/chromatin fiber will be described, coupled with rationales, as well as technical tips...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910021/quantitative-fluorescence-in-situ-hybridization-qfish
#12
Ivan Y Iourov
Fluorescence in situ hybridization (FISH) has a wide spectrum of applications in current molecular cytogenetic and cancer research. This is a unique technique that can be used for chromosomal DNA analysis in all cell types, at all stages of the cell cycle, and at molecular resolution. Recent developments in microscopy and imaging systems have allowed quantification of digital FISH images (quantitative FISH or QFISH) and have provided a new way for molecular cytogenetic analysis at single-cell level. QFISH can be applied for studying chromosome imbalances in interphase nuclei or metaphase spreads, measuring relative DNA content at chromosomal loci and identifying parental origin of homologous chromosomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910020/cytoplasmic-immunoglobulin-light-chain-revelation-and-interphase-fluorescence-in-situ-hybridization-in-myeloma
#13
Sarah Moore, Jeffrey M Suttle, Mario Nicola
The cytogenetic analysis of plasma cell myeloma (PCM) allows stratification of patients so that prognosis may be determined and appropriate therapeutic options can be discussed. Owing to the patchy nature of the disease in the bone marrow (BM), the low proliferative activity of plasma cells and the cryptic nature of some PCM-associated cytogenetic changes, karyotypic analysis in this disease should be augmented with targeted interphase fluorescence in situ hybridization (FISH). Immunofluorescent revelation of cytoplasmic immunoglobulin light chains, together with interphase FISH (cIg-FISH), allows the identification of plasma cells within a sample so that they may be scored preferentially...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910017/fluorescence-in-situ-hybridization-probe-preparation
#14
Doron Tolomeo, Roscoe R Stanyon, Mariano Rocchi
The public human genome sequencing project utilized a hierarchical approach. A large number of BAC/PAC clones, with an insert size approximate from 50 kb to 300 kb, were identified and finely mapped with respect to the Sequence Tagged Site (STS) physical map and with respect to each other. A "golden path" of BACs, covering the entire human genome, was then selected and each clone was fully sequenced. The large number of remaining BACs was not fully sequenced, but the availability of the end sequence (~800-1000 bp) at each end allowed them to be very precisely mapped on the human genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910016/applications-of-fluorescence-in-situ-hybridization-technology-in-malignancies
#15
Montakarn Tansatit
The molecular characterization of nonrandom recurrent cytogenetic abnormalities has identified numerous disease-related genes involved in hematologic and lymphoid malignancies. Cytogenetic analysis has become essential for disease diagnosis, classification, prognostic stratification, and treatment guidance. Fluorescence in situ hybridization (FISH) has greatly enhanced the field and enabled a more precise determination of the presence and frequency of genetic abnormalities. The advantages of FISH compared to standard cytogenetic analysis are that FISH can be used to identify genetic changes that are too small to be detected under a microscope, does not require cell culture, and can be applied directly on fresh or paraffin-embedded tissues for rapid evaluation of interphase nuclei...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910015/chromosome-recognition
#16
Thomas S K Wan, Eleanor K C Hui, Margaret H L Ng
Chromosomal analysis of human cells serves to characterize aberrations of chromosome number and structure. Individual chromosome can be identified precisely by recognition of its morphological characteristics and staining patterns according to specific landmarks, regions, and bands as described in the ideogram. Since the quality of metaphases obtained from malignant cells is generally poor for karyotyping, a practical and accurate chromosome recognition training guide is mandatory for a trainee or newly employed cytogenetic technologist in a cancer cytogenetics laboratory...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910013/cytogenetic-harvesting-of-cancer-cells-and-cell-lines
#17
Roderick A F MacLeod, Maren E Kaufmann, Hans G Drexler
We describe an evidence-based approach toward optimizing chromosome preparation from cancer cells and cell lines. The procedures described here emphasize the utility of both cell culture-to maximize the yields of the dividing cells needed to harvest mitotic metaphase chromosome preparations and how an empirical evaluation of hypotonic treatments enables optimal conditions to be efficiently determined.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910012/chromosome-preparation-for-chronic-lymphoid-malignancies
#18
Dorota Koczkodaj, Agata A Filip
Conventional cytogenetics is invariably one of the most important methods used in diagnostics of chronic lymphoproliferations. It complements fluorescence in situ hybridization (FISH) and molecular analysis. Presence of particular chromosomal alterations in chronic lymphocytic leukemia enables patients' stratification into appropriate cytogenetic risk groups and influences treatment decisions. In other non-Hodgkin lymphomas cytogenetic analyses are employed also in minimal residual disease assessment.As lymphocytes in chronic lymphoid malignancies are characterized by low proliferation rate in vitro, it is critical to induce their division in the culture properly...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910010/chromosome-preparation-for-myeloid-malignancies
#19
Eleanor K C Hui, Thomas S K Wan, Margaret H L Ng
Many cases of myeloid malignancies are associated with recurring cytogenetic aberrations. Chromosomal analysis can aid in diagnosis, predict prognosis, and disclose subsequent clonal evolution. Three different cell culture methods: direct harvest, nonsynchronized culture, and synchronized culture are usually prepared if the nucleated cell counts in marrow blood are sufficient. Synchronized culture is the first choice of method in myeloid malignancies, whereas the direct method can be omitted if the cell count is low...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#20
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
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