Spectral Karyotyping: The simultaneous identification of all chromosomes from a cell by fluorescence in situ hybridization (IN SITU HYBRIDIZATION, FLUORESCENCE) with chromosome-specific florescent probes that are discerned by their different emission spectra.Karyotyping: Mapping of the KARYOTYPE of a cell.Chromosome Aberrations: Abnormal number or structure of chromosomes. Chromosome aberrations may result in CHROMOSOME DISORDERS.Chromosome Painting: A technique for visualizing CHROMOSOME ABERRATIONS using fluorescently labeled DNA probes which are hybridized to chromosomal DNA. Multiple fluorochromes may be attached to the probes. Upon hybridization, this produces a multicolored, or painted, effect with a unique color at each site of hybridization. This technique may also be used to identify cross-species homology by labeling probes from one species for hybridization with chromosomes from another species.Chromosome Banding: Staining of bands, or chromosome segments, allowing the precise identification of individual chromosomes or parts of chromosomes. Applications include the determination of chromosome rearrangements in malformation syndromes and cancer, the chemistry of chromosome segments, chromosome changes during evolution, and, in conjunction with cell hybridization studies, chromosome mapping.Neoplasms, Adipose Tissue: Neoplasms composed of fatty tissue or connective tissue made up of fat cells in a meshwork of areolar tissue. The concept does not refer to neoplasms located in adipose tissue.Translocation, Genetic: A type of chromosome aberration characterized by CHROMOSOME BREAKAGE and transfer of the broken-off portion to another location, often to a different chromosome.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Chromosomes, Human, Pair 13: A specific pair of GROUP D CHROMOSOMES of the human chromosome classification.Aneuploidy: The chromosomal constitution of cells which deviate from the normal by the addition or subtraction of CHROMOSOMES, chromosome pairs, or chromosome fragments. In a normally diploid cell (DIPLOIDY) the loss of a chromosome pair is termed nullisomy (symbol: 2N-2), the loss of a single chromosome is MONOSOMY (symbol: 2N-1), the addition of a chromosome pair is tetrasomy (symbol: 2N+2), the addition of a single chromosome is TRISOMY (symbol: 2N+1).Chromosome Breakage: A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.Gene Rearrangement: The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.Chromosome Disorders: Clinical conditions caused by an abnormal chromosome constitution in which there is extra or missing chromosome material (either a whole chromosome or a chromosome segment). (from Thompson et al., Genetics in Medicine, 5th ed, p429)Karyotype: The full set of CHROMOSOMES presented as a systematized array of METAPHASE chromosomes from a photomicrograph of a single CELL NUCLEUS arranged in pairs in descending order of size and according to the position of the CENTROMERE. (From Stedman, 25th ed)

*  'cytogenetic analysis' Protocols and Video...

Spectral Karyotyping to Study Chromosome Abnormalities in Humans and Mice with Polycystic Kidney Disease', 'Generation of ... and Spectral Karyotyping (SKY) in Irradiated Mice', 'Chromosome Preparation From Cultured Cells', 'An Efficient Method for ... Spectral Karyotyping to Study Chromosome Abnormalities in Humans and Mice with Polycystic Kidney Disease. Wissam A. AbouAlaiwi1 ... and Spectral Karyotyping (SKY) in Irradiated Mice. Rupak Pathak1, Igor Koturbash2, Martin Hauer-Jensen1,3 ...

*  Hepatitis C Virus Inhibits DNA Damage Repair through Reactive Oxygen and Nitrogen Species and by Interfering with the ATM-NBS1...

Spectral karyotyping. Multicolor spectral karyotyping (SKY) was done, as previously described (4). In situ hybridization was ... Multicolor spectral karyotyping identifies new recurring breakpoints and translocations in multiple myeloma. Blood 92: 1743- ... We further karyotyped metaphases of primary splenocytes from 50-wk-old core-transgenic mice. Cytogenetic studies revealed that ... Karyotype analysis. Metaphase chromosomes were prepared using standard procedures (4). Cells were partially synchronized by ...

*  Patent US5991028 - Spectral bio-imaging methods for cell classification - Google Patents

According to the present invention there is provided a spectral bio-imaging methods which can be used for automatic and/or ... 1996) Multicolor spectral karyotyping of human chromosomes. Science, 273, 494-497; Garini et al. (1996) Spectral Karyotyping, ... The basic data set, i.e., the spectral cube, is composed of k spectral slices of the same object, where each spectral slice is ... One possible type of analysis of a spectral cube is to use spectral and spatial data separately, i.e., to apply spectral ...

*  Plus it

G-banding and spectral karyotyping. G-banding karyotyping was done according to the standard procedure. Spectral karyotyping ... subjected to G-banding/spectral karyotyping, and the composite G-banding/spectral karyotyping karyotypes were constructed based ... Composite karyotypes based on 12 to 25 G-banding/spectral karyotyping karyotypes were constructed. ... Combined G-banding/spectral karyotyping and FISH analyses of gene dosages. The composite karyotypes presented in Table 1 did ...

*  Plus it

Cytogenetic analyses and NOR staining. Spectral karyotyping (SKY) analyses were done as described ( 17). For NOR staining ( 18 ... Thirty-two metaphases each from HCT116-siTop1 and HCT-siCtrl were randomly selected and submitted to spectral karyotyping. The ... Detailed spectral karyotype analysis, however, revealed increased numerical aberrations in HCT116-siTop1. Thirty-two metaphases ... Representative karyotypes detected by SKY are shown. Chromosomal aberrations were computed from 32 metaphases for each cell ...

*  Overview of Fluorescence In Situ Hybridization Techniques for Molecular Cytogenetics - Current Protocols

Multicolor spectral karyotyping of human chromosomes. Science 273:494‐497.. Selig, S., Okumura, K., Ward, D.C., and Cedar, H. ... Multiple colors by fluorescence in situ hybridization using ratio‐labelled DNA probes create a molecular karyotype. Hum. Mol. ... Karyotyping human chromosomes by combinatorial multi‐fluor FISH. Nature Genet. 12:368‐375. ...

*  Case Reports r8p23q24AshokID100089

Subsequent Spectral Karyotyping confirmed the cytogenetic findings. The final karyotype was reported as: 47,XX,r(8)(p23q24)[30 ... Karyotype. Methods. Prognosis. Fugazza G et al, 1996. 65 year old male with Parkinson's Disease referred for hemorragic ... Figure 2: GTG banded karyotype showing Ring chromosome 8.. Comments. A 70-year-old female with AML-M2 was referred for ... Karyotype. Sample : Bone marrow aspirate. ; culture time : Overnight and 24 hours without stimulating agents. ; banding : GTG. ...

*  Cracking the Cancer Code | Sigma-Aldrich

Spectral karyotype analysis of colon cancer cell lines of the tumor suppressor and mutator pathway. Cytogenet Genome Res. 2002; ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Spectral karyotyping (SKY) allows visualization of the whole genome simultaneously, but the requirement for special software ... Spectral Karyotyping to Study Chromosome Abnormalities in Humans and Mice with Polycystic Kidney Disease ... To overcome the limitations of the banding technique, Spectral Karyotyping (SKY) is introduced to provide much reliable ... Medicine, Issue 60, Chromosome, Polycystic Kidney Disease, Primary Cilia, Spectral Karyotyping, Cytogenetics ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Spectral Karyotyping to Study Chromosome Abnormalities in Humans and Mice with Polycystic Kidney Disease ... To overcome the limitations of the banding technique, Spectral Karyotyping (SKY) is introduced to provide much reliable ... Medicine, Issue 60, Chromosome, Polycystic Kidney Disease, Primary Cilia, Spectral Karyotyping, Cytogenetics ... The end result is a metaphase and a karyotype classification image, in which each pair of chromosomes has a distinct color ( ...

*  Plus it

... we sought to conduct spectral karyotyping of freshly and precultured mammosphere-forming cells. Due to the very small numbers ... Chromosome hybridization and analysis for spectral karyotyping (SKY) were conducted according to a standard protocol with minor ... Applied Spectral Imaging, Inc.), respectively, using SpectraCube SD200 (Applied Spectral Imaging) and a Zeiss Axioscope II ... None of the karyotypes from freshly isolated cells (Supplementary Fig. S2A and B), regardless of their ploidy status, contained ...

*  Genetics and Cytogenetics of Multiple Myeloma | Cancer Research

Metaphase Spectral Karyotype Imaging/Multicolor-FISH (SKY/M-FISH) and CGH.. In an effort to improve on the accuracy of ... Multicolor spectral karyotyping identifies new recurring breakpoints and translocations in multiple myeloma. Blood, 92: 1743- ... Multicolour spectral karyotyping identifies new translocations and a recurring pathway for chromosome loss in multiple myeloma ... Identification of new nonrandom translocations in multiple myeloma with multicolor spectral karyotyping. Blood, 92: 4269-4278, ...

*  Truncating APC mutations have dominant effects on proliferation, spindle checkpoint control, survival and chromosome stability ...

Spectral karyotyping suggests additional subsets of colorectal cancers characterized by pattern of chromosome rearrangement. ... 6A). In stark contrast, the cells in the N750 culture displayed a wide range of karyotypes. Not only is the distribution ... a near diploid karyotype, a functional mitotic checkpoint and do not display chromosome instability (Abdel-Rahman et al., 2001 ... cells harbouring homozygous truncating APC mutations exhibit near-tetraploid karyotypes (Fodde et al., 2001; Kaplan et al., ...

*  Variant Philadelphia translocations with different breakpoints in six chronic myeloid leukemia patients / Alti kronik miyeloid...

... a use of double fusion signal FISH and spectral karyotyping. Leukemia 2000;14:1157-60.. (16.) Babicka L, Pavlistova L, ... Table 2. G-Banding and FISH results in the patients Patient Karyotype 1 46,XX,t(7;22)(p22;q11) 2 46, XY, t(9;22;15)(q34;q11;q22 ... The GTL (G-bands via trypsin using Leishman) banding technique (6) was applied to the slides, karyotypes were described ... Partial G-banding karyotypes are presented in Figure 1.. [FIGURE 1 OMITTED]. FISH analysis. In 5 patients (1, 3, 4, 5, and 6) ...

*  Transcriptomic profiling and quantitative high-throughput (qHTS) drug screening of CDH1 deficient hereditary diffuse gastric...

Spectral karyotyping. Metaphases of SB.mhdgc-1 cells were arrested by incubation with Colcemid (KaryoMax ® Colcemid Solution, ... Multiple SKY karyotyping shows a diploid karyotype with frequent chromosomal aberrations including losses, duplications, and ... c Karyotype and SKY images of SB.mhdgc-1 cells show features consistent with human cancer cells including aneuploidy (such as ... Spectral images of the hybridized metaphases were acquired using a SD301 SpectraCubeTM system (ASI, Carlsbad, CA) mounted on ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Spectral karyotyping (SKY) allows visualization of the whole genome simultaneously, but the requirement for special software ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

... and spectral karyotyping (SKY)14,15.. Basic Protocol, Issue 83, chromosome, cytogenetic, harvesting, karyotype, fluorescence in ... Spectral karyotyping (SKY) allows visualization of the whole genome simultaneously, but the requirement for special software ... Although human embryonic stem cells (hESC) have been shown to present a stable diploid karyotype 1, many studies have reported ... Chromosomal Spread Preparation of Human Embryonic Stem Cells for Karyotyping. Authors: Priscila B. Campos, Rafaela C. Sartore, ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

... and spectral karyotyping (SKY)14,15.. Basic Protocol, Issue 83, chromosome, cytogenetic, harvesting, karyotype, fluorescence in ...

*  Protocols and Video Articles Authored by D. Gary Gilliland (Translated to Turkish)

... spectral karyotyping, comparative genomic hybridization, loss of heterozygosity analysis, and characterization of point ... Analysis of patient karyotypes reveals that nonrandom, somatically acquired translocations and inversions occur in most acute ... A variety of prognostic factors can predict outcome and include the karyotype of the leukemic cells and the presence of ... In agreement with this, most patients with HES/CEL present with a normal karyotype. Here we describe three different techniques ...

*  Books - Lane Medical Library - Stanford University School of Medicine

Spectral karyotyping and fluorescence in situ hybridization of murine cells / Cornelia Rudolph and Brigitte Schlegelberger -- ... Characterization of chromosomal translocations in mouse models of hematological malignancies using spectral karyotyping, FISH, ... Human karyotypes and chromosome behavior -- Genetics of bacteria and their viruses -- Molecular biology of gene expression -- ...

*  Lineage analysis of early and advanced tubular adenocarcinomas of the stomach: continuous or discontinuous?

SNP-Array genotyping and spectral karyotyping reveal uniparental disomy as early mutational event in MSS- and MSI-colorectal ...

*  Transformation of human bronchial epithelial cells alters responsiveness to inflammatory cytokines | BMC Cancer | Full Text

Cells from the third passage were used for confirming consistency of cytokine response profile and spectral karyotyping (SKY) [ ... Rapid localization of transgenes in mouse chromosomes using a combined Spectral Karyotyping/FISH technique. Mammalian Genome. ... With the exception of one carcinoma, the cells showed normal karyotypes. The carcinoma cell culture carried a chromosome 10 ...

*  Defined genetic events associated with the spontaneous in vitro transformation of ElA/Ras-expressing human IMR90 fibroblasts :...

Spectral karyotyping; scid mice, severe combined immunodeficient mice ...

*  Errors in chromosome segregation during oogenesis and early embryogenesis - WRAP: Warwick Research Archive Portal

Sandalinas M, Marquez C, Munné S. Spectral karyotyping of fresh, non-inseminated oocytes. Mol Hum Reprod 2002;8(6):580-5.. 26. ... Oocyte karyotyping by comparative genomic hybridization provides a highly reliable method for selecting "competent" embryos, ... the co-existence of two modes of malsegregation evidenced by the karyotyping of 1397 in-vitro unfertilized oocytes. Hum Reprod ...

*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols

Array CGH for the detection of genomic copy number variants has replaced G-banded karyotype analysis. This paper describes the ... Integrated Photoacoustic Ophthalmoscopy and Spectral-domain Optical Coherence Tomography. Authors: Wei Song, Qing Wei, Shuliang ... we integrate PAOM and spectral-domain OCT (SD-OCT) for simultaneously in vivo retinal imaging of rat, where both optical ... spectral-domain, tomography, rat, animal model, imaging ...

(1/62) The utility of spectral karyotyping in the cytogenetic analysis of newly diagnosed pediatric acute lymphoblastic leukemia.

We applied multicolor spectral karyotyping (SKY) to a panel of 29 newly diagnosed pediatric pre B-cell ALLs with normal and abnormal G-banded karyotypes to identify cryptic translocations and define complex chromosomal rearrangements. By this method, it was possible to define all add chromosomes in six cases, a cryptic t(12;21)(p13;q11) translocation in six cases, marker chromosomes in two cases and refine the misidentified aberrations by G-banding in two cases. In addition, we identified five novel non-recurrent translocations - t(2;9)(p11.2;p13), t(2;22) (p11.2;q11.2), t(6;8)(p12;p11), t(12;14)(p13;q32) and t(X;8)(p22.3;q?). Of these translocations, t(2;9), t(2;22) and t(12;14) were identified by G-banding analysis and confirmed by SKY. We characterized a t(12;14)( p13;q32) translocation by FISH, and identified a fusion of TEL with IGH for the first time in ALL. We identified a rearrangement of PAX5 locus in a case with t(2;9)(p11.2;p13) by FISH and defined the breakpoint telomeric to PAX5 in der(9)t(3;9)(?;p13). These studies demonstrate the utility of using SKY in combination with G-banding and FISH to augment the precision with which chromosomal aberrations may be identified in tumor cells.  (+info)

(2/62) Multicolor karyotyping and clinicopathological analysis of three intravascular lymphoma cases.

Intravascular lymphoma (IVL) is a rare neoplastic disease characterized by the presence of large malignant lymphoid cells in small vessels. It is often diagnosed at autopsy. Clinical manifestations are typically neurologic and dermatologic. Karyotypic abnormalities have been described in a small number of cases and have revealed complex alterations in the majority of cases. We have identified three cases of IVL with varied clinicopathological findings. Karyotypic analysis was undertaken by standard G-banding and supplemented by multi-colored karyotyping (M-FISH) to decipher the chromosomal content of marker chromosomes and undefined additions. M-FISH clarified the chromosomal abnormalities in two cases and unveiled cryptic translocations der(10)t(10;22), der(17)t(17;22), and balanced t(11;14). Comparison with previously published karyotypes revealed prominent involvement of chromosomes 1, 3, 6, 11, 14, and 18, similar to the pattern of clonal evolution in other B-cell lymphomas. The most frequent alterations seen were -6 or 6q- and +18 or dup(18q), with a minimally deleted region located at 6q21-q23 and a commonly amplified region located at 18q13-q23, respectively. Few differences between the classical and Asian variant of this disease were apparent at the karyotypic level. Cytogenetic analysis of additional cases supplemented by multicolor karyotyping may help identify the full spectrum of genetic alterations associated with IVL and assist in the delineation of the critical mutations associated with initiation and progression of this disease.  (+info)

(3/62) ALK+, CD30-, CD20- large B-cell lymphoma containing anaplastic lymphoma kinase (ALK) fused to clathrin heavy chain gene (CLTC).

Pathological features and genomic basis of a rare case of ALK(+), CD30(-), CD20(-) large B-cell lymphoma were analyzed. A 36-year-old Japanese female was admitted because of lumbago and constitutional symptoms. Physical examination and laboratory tests showed anemia (hemoglobin, 7.5 g/dL), mild hepatosplenomegaly, and immunoglobin G (IgG) lambda-type monoclonal gammopathy (IgG, 2782 mg/dL). The lymphoma spread exclusively in extranodal sites such as bone marrow, liver, spleen, ovary, and muscle. Biopsy specimens obtained from the ovary showed monomorphic proliferation of large immunoblastic cells with basophilic cytoplasm, round-shaped nuclei with a high nuclear to cytoplasmic ratio, and prominent single nucleolus. Immunostaining with anti-anaplastic lymphoma kinase (ALK) antibody, ALK1, showed finely granular cytoplasmic staining pattern. These cells were also positive for epithelial membrane antigen, CD4, CD19, CD38, CD138, cytoplasmic IgG, and lambda chain, but negative for CD30 (Ber-H2), CD56, CD57, and other T- and B-cell markers. Southern blot analyses revealed that Ig heavy and lambda light chain genes, but not T-cell receptor (TCR) beta gene, were clonally rearranged. Chromosomal analyses by conventional G-banding, spectral karyotyping, and fluorescence in situ hybridization showed complex abnormality involving 2p23, and chromosome 2 was translocated to chromosome 17. As 2;17 translocation resulting in the fusion of clathrin heavy chain (CLTC) gene with ALK was previously reported in inflammatory myofibroblastic tumor, we performed reverse transcriptase-polymerase chain reaction and demonstrated that the lymphoma cells contained CLTC-ALK fusion transcript. Under the diagnosis of ALK(+), CD30(-), CD20(-) large B-cell lymphoma, she was treated with conventional combination chemotherapies. However, the lymphoma was primarily chemotherapy resistant, and the patient died 11 months after admission. We consider that this case confirms the existence of ALK(+), CD30(-), CD20(-) large B-cell lymphomas proposed by Delsol et al. (16) and further provides relevant information regarding their clinicopathological features and cytogenetics.  (+info)

(4/62) Karyotypic complexity of the NCI-60 drug-screening panel.

We used spectral karyotyping to provide a detailed analysis of karyotypic aberrations in the diverse group of cancer cell lines established by the National Cancer Institute for the purpose of anticancer drug discovery. Along with the karyotypic description of these cell lines we defined and studied karyotypic complexity and heterogeneity (metaphase-to-metaphase variations) based on three separate components of genomic anatomy: (a) ploidy; (b) numerical changes; and (c) structural rearrangements. A wide variation in these parameters was evident in these cell lines, and different association patterns between them were revealed. Analysis of the breakpoints and other specific features of chromosomal changes across the entire set of cell lines or within particular lineages pointed to a striking lability of centromeric regions that distinguishes the epithelial tumor cell lines. We have also found that balanced translocations are as frequent in absolute number within the cell lines derived from solid as from hematopoietic tumors. Important similarities were noticed between karyotypic changes in cancer cell lines and that seen in primary tumors. This dataset offers insights into the causes and consequences of the destabilizing events and chromosomal instability that may occur during tumor development and progression. It also provides a foundation for investigating associations between structural genome anatomy and cancer molecular markers and targets, gene expression, gene dosage, and resistance or sensitivity to tens of thousands of molecular compounds.  (+info)

(5/62) Features of chromosomal abnormalities in spontaneous abortion cell culture failures detected by interphase FISH analysis.

Cytogenetic analysis of reproductive wastage is an important stage in understanding the genetic background of early embryogenesis. The results of conventional cytogenetic studies of spontaneous abortions depend on tissue culturing and are associated with a significant cell culture failure rate. We performed interphase dual-colour FISH analysis to detect chromosomal abnormalities in noncultured cells from two different tissues-cytotrophoblast and extraembryonic mesoderm-of 60 first-trimester spontaneous abortions from which cells had failed to grow in culture. An original algorithm was proposed to optimize the interphase karyotype screening with a panel of centromere-specific DNA probes for all human chromosomes. The overall rate of numerical chromosomal abnormalities in these cells was 53%. Both typical and rare forms of karyotype imbalance were found. The observation of six cases (19%) of monosomy 7, 15, 21 and 22 in mosaic form, with a predominant normal cell line, was the most unexpected finding. Cell lines with monosomies 21 and 22 were found both in cytotrophoblast and mesoderm, while cells with monosomy 7 and 15 were confined to the cytotrophoblast. The tissue-specific compartmentalization of cell lines with autosomal monosomies provides evidence that the aneuploidy of different human chromosomes may arise during different stages of intrauterine development. The effect of aneuploidy on selection may differ, however, depending on the specific chromosome. The abortions also revealed a high frequency of intratissue chromosomal mosaicism (94%), in comparison with that detected by conventional cytogenetic analysis (29%; P<0.001). Confined placental mosaicism was found in 25% of the embryos. The results of molecular cytogenetic analysis of these cell culture failures illustrate that the diversity and phenotypic effects of chromosomal abnormalities during the early stages of human development are underestimated.  (+info)

(6/62) A novel FISH assay for SS18-SSX fusion type in synovial sarcoma.

Synovial sarcoma is a morphologically, clinically and genetically distinct entity that accounts for 5-10% of all soft tissue sarcomas. The t(X;18)(p11.2;q11.2) is the cytogenetic hallmark of synovial sarcoma and is present in more than 90% of the cases. It produces three types of fusion gene formed in part by SS18 from chromosome 18 and by SSX1, SSX2 or, rarely, SSX4 from the X chromosome. The SS18-SSX fusions do not seem to occur in other tumor types, and it has been shown that in synovial sarcoma a clear correlation exists between the type of fusion gene and histologic subtype and, more importantly, clinical outcome. Previous analyses regarding the type of fusion genes have been based on PCR amplification of the fusion transcript, requiring access to good-quality RNA. In order to obtain an alternative tool to diagnose and follow this malignancy, we developed a fluorescence in situ hybridization (FISH) assay that could distinguish between the two most common fusion genes, that is, SS18-SSX1 and SS18-SSX2. The specificity of the selected bacterial artificial chromosome clones used in the detection of these fusion genes, as well as the sensitivity of the analysis in metaphase and interphase cells, was examined in a series of 28 synovial sarcoma samples with known fusion gene status. In all samples, the type of fusion was correctly identified by FISH. Thus, the assay described here should be useful for clarifying unresolved chromosome markers and for identifying fusion gene status in samples from which RNA of sufficient quality for PCR could not be extracted.  (+info)

(7/62) Combined genetic and transcriptional profiling of acute myeloid leukemia with normal and complex karyotypes.

BACKGROUND AND OBJECTIVES: Acute myeloid leukemia (AML) is a heterogeneous group of diseases. Patients with a normal karyotype constitute the largest single group; multiple chromosome rearrangements involving three or more chromosomes occur in 5 10% of AML patients. The pathophysiologic mechanisms underlying both groups are largely unknown. In the current study, we have systematically combined transcriptional profiles with cytogenetic data from 15 AML patients with either normal or complex karyotypes. DESIGN AND METHODS: The expression profiles were investigated by unsupervised hierarchical clustering, supervised cluster analysis, and comparative genomic microarray analysis. In addition, the samples were analyzed by G-banding and/or spectral karyotyping and comparative genomic hybridization. RESULTS: Our results show that AML with complex karyotypes exhibit a gene expression profile that is specific to this group of patients. The differentially expressed genes included several located on 5q and 7q, as well as genes involved in controlling cell division. We also found that DNA gains and losses caused by multiple chromosome rearrangements result in altered gene expression in a gene-dosage-dependent manner. INTERPRETATION AND CONCLUSIONS: These data provide insight into the mechanisms of multiple chromosome rearrangements and further demonstrate that the expression patterns of AML are strongly linked to the karyotypic status, even for the relatively undefined cytogenetic subgroup AML with complex karyotype.  (+info)

(8/62) Genetic and expression profiles of squamous cell carcinoma of the head and neck correlate with cisplatin sensitivity and resistance in cell lines and patients.

PURPOSE: The choice of treatment for squamous cell carcinoma of the head and neck (SCCHN) is still primarily based on the tumor-node-metastasis classification. However, it is reasonable to believe that biological profiles of SCCHN may be independently associated with response to therapy. The aim of the present study was to examine genetic changes and gene expression profiles that might correlate with sensitivity to cisplatin [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay] in 10 SCCHN cell lines. EXPERIMENTAL DESIGN: Five cisplatin-sensitive and five cisplatin-resistant cell lines [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay] were studied by comparative genomic hybridization, spectral karyotyping, and cDNA microarray analysis (21,632 sequence-validated human cDNA; confirmation by reverse transcriptase-PCR for selected genes). For the MET proto-oncogene, which showed low expression in the chemosensitive cell lines, we did immunohistochemical staining on SCCHN of 29 patients who received induction chemotherapy. RESULTS: The five cisplatin-resistant cell lines showed significantly more genetic imbalances (regions of loss and amplification) and chromosomal abnormalities by comparative genomic hybridization and spectral karyotyping, respectively, than did the five cisplatin-sensitive cell lines. Microarray studies identified approximately 60 genes that clearly distinguish between the two groups of cell lines. Some of these genes are known to be involved in tumor progression, metastasis, and drug resistance. We identified low expression of c-met (immunohistochemistry) as a predictive factor for complete response in nondiploid tumors (P = 0.026). CONCLUSIONS: We conclude that cisplatin sensitivity and resistance are related to distinctive differences in the genetic and expression profiles in individual SCCHN tumor cell lines and in SCCHN patients. The genes we have identified may serve as potential targets for novel treatment strategies.  (+info)



chromosomal

  • Spectral karyotyping showed numerical and structural aberrations involving the chromosomal regions harboring these genes. (aacrjournals.org)
  • Presence of a ring chromosome either as part of a complex karyotype or as a sole chromosomal aberration is always in an unbalanced state. (atlasgeneticsoncology.org)

classification

  • According to the present invention there is provided a spectral bio-imaging methods which can be used for automatic and/or semiautomatic spectrally resolved morphometric classification of cells, the method comprising the steps of (a) preparing a sample to be spectrally imaged, the sample including at. (google.com)

molecular

  • Multiple colors by fluorescence in situ hybridization using ratio‐labelled DNA probes create a molecular karyotype. (currentprotocols.com)
  • Other molecular cytogenetics technics : Fluorescence in situ hybridization (FISH) using SKYPaint® Probe from Applied Spectral Imaging (Israel), was performed on metaphase chromosomes from cultured Bone marrow sample of this patient and analysed using GenASIs Spectral Karyotyping (HiSKY®) software. (atlasgeneticsoncology.org)

chromosomes

  • Following preparation of the sample, Karyotyping is performed and/or the specific chromosomes are analyzed. (jove.com)

hybridization

  • Seven glioma cell lines and two primary cultures were first analyzed for their sensitivity to TRAIL and chemotherapy and then examined for the genomic alterations in key TRAIL apoptotic genes by comparative genomic hybridization (CGH), G-banding/spectral karyotyping, and fluorescence in situ hybridization (FISH). (aacrjournals.org)

cell

  • A combination of G-banding/spectral karyotyping and FISH further defined the loss or gain of gene copy of these genes and further showed the simultaneous loss of one copy of DR4 / DR5, caspase-8, Bid , and Smac in two near-triploid cell lines that were resistant to the combination treatment with TRAIL and chemotherapy. (aacrjournals.org)

time

  • v) recording signals of each of said detector elements as function of time using a recording device to form a spectral cube of data. (google.com)