Advances in fluorescent in situ hybridisation

Current Opinion in Biotechnology

Volumn 9, Issue 1, 1998, Pages 19-24

  Ekong, Rosemary ^a   Wolfe, Jonathan ^b  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; CELL NUCLEUS; CHROMOSOME ANALYSIS; DNA PROBE; FLUORESCENCE IN SITU HYBRIDIZATION; HUMAN CELL; PRIORITY JOURNAL; REVIEW;

EID: 0031908142     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(98)80079-7     Document Type: Article

References (48)

1. Thein ATA, Han X, Heyderman E, Fox M, Steele SJ, Parrington JM. Molecular cytogenetic analysis of five newly established cervical cancer cell lines using G-banding and fluorescence in situ hybridization. Cancer Genet Cytogenet. 81:1996;1-9.
2. Delhanty JDA, Harper JC, Ao A, Handyside AH, Winston RML. Multicolour FISH detects frequent chromosomal mosaicism and chaotic division in normal preimplantation embryos from fertile patients. of special interest Hum Genet. 99:1997;755-760 Three satellite DNA probes specific for chromosomes 1, X and Y were used to examine interphase nuclei of 6-10 cell stage human embryos by three colour FISH. The embryos were spare embryos resulting form in vitro fertilisation. The study revealed a surprisingly high level of aneuploidy.
3. Bass HW, Marshall WF, Sedat JW, Agard DA, Cande WZ. Telomeres cluster de novo before the initiation of synapsis: a three-dimensional spatial analysis of telomere positions before and during meiotic prophase. of special interest J Cell Biol. 137:1997;5-18 A novel technique for the preservation of the three dimensional structure of nuclei and chromosomes: meiocytes were embedded in acrylamide before hybridisation to a telomere oligonucleotide probe.
4. Eils R, Dietzel S, Bertin E, Schrock E, Speicher MR, Reid T, Robert-Nicoud M, Cremer C, Cremer T. Three-dimensional reconstruction of painted human interphase chromosomes: active and inactive X chromosome territories have similar volumes but differ in shape and surface structure. of special interest J Cell Biol. 135:1996;1427-1440 Serial optical sections allow the reconstruction of the volume occupied by X chromosomes and chromosomes 7. The volumes occupied by active and inactive X chromosomes are similar but the surface area of the active X is much greater. The active X has a similar 'roundness factor' to that of chromosome 7.
5. Kurz A, Lampel S, Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P. Active and inactive genes localize preferentially in the periphery of chromosome territories. of special interest J Cell Biol. 135:1996;1195-1205 Using similar techniques as described by Eils et al. 1996 [4], the spacial localizations of three X-linked genes and two noncoding X-linked sequences were examined with respect to the territory occupied by the whole X chromosome. The genes are preferentially localised on the periphery of the chromosome.
6. Frengen E, Thomsen PD, Brede G, Solheim J, de Jong PJ, Prydz H. The gene cluster containing the LCAT gene is conserved between human and pig. Cytogenet Cell Genet. 76:1997;53-57.
7. Yang F, Muller S, Just R, Ferguson-Smith MA, Wienberg J. Comparative chromosome painting in mammals: human and the Indian muntjac (Muntiacus muntjak vaginalis). of special interest Genomics. 39:1997;396-401 Human chromosome specific paints used to paint muntjack chromosomes show some regions of conservation but an enormous amount of genome reshuffling.
8. Woodward K, Nahmias J, Hornigold N, West L, Pilz A, Benham F, Kwiatkowski D, Fitzgibbon J, Wolfe J, Povey S. Regional localization of 64 cosmid contigs including 18 genes and 14 markers to intervals on human chromosome 9q34. Genomics. 29:1995;257-260.
9. Yamamoto K, Kobayashi H, Miura O, Hirosawa S, Miyasaka N. Assignment of IL12RB1 and IL12RB2, interleukin-12 receptor β1 and β2 chains, to human chromosome 19 band p13.1 and chromosome 1 band p31.2, respectively, by in situ hybridization. Cytogenet Cell Genet. 77:1997;257-258.
10. Sebastian S, Hoebee B, Hande MP, Kenkare UW, Natarajan AT. Assignment of hexokinase types 1, 2, 3 (Hk1,2,3) and glucokinase (Gck) to rat chromosome band 20q11, 4q34, 17q12 and 14q21 respectively, by in situ hybridization. Cytogenet Cell Genet. 77:1997;266-267.
11. Elduque C, Laurent P, Hayes H, Rodellar C, Leveziel H, Zaragoza P. Assignment of the beta-nerve growth factor (NGFB) to bovine chromosome 3 band q23 by in situ hybridization. Cytogenet Cell Genet. 77:1997;306-307.
12. Guttenbach M, Engel W, Schmid M. Analysis of structural and numerical chromosome abnormalities in sperm of normal men and carriers of constitutional chromosome aberrations. A review. Hum Genet. 100:1997;1-21.
13. Michalet X, Ekong R, Fougerousse F, Rousseaux S, Schurra C, Hornigold N, van Slegtenhorst M, Wolfe J, Povey S, Beckmann JS, Bensimon A. Dynamic molecular combing: stretching the whole human genome for high-resolution studies. of outstanding interest Science. 277:1997;1518-1523 Uses purified high molecular weight DNA stretched onto a coverslip by a receding meniscus to achieve such uniform tension of the DNA strands that no normalisation is required. Both yeast artificial chromosome and total human genomic DNA are assayed. Deletion mutations (38-135 kb) are visualised and accurately measured, as well as the genomic distance between several pairs of cosmid clones.
14. Weier H-UG, Mang M, Mullikin JC, Zhu Y, Cheng J-F, Greulich KM, Bensimon A, Gray JW. Quantitative DNA fiber mapping. Hum Mol Genet. 4:1995;1903-1910.
15. Kraus J, Weber RG, Cremer M, Seebacher T, Fischer C, Schurra C, Jauch A, Lichter P, Bensimon A, Cremer T. High-resolution comparative hybridization to combed DNA fibers. Hum Genet. 99:1997;374-380.
16. Dreyling MH, Olopade OI, Bohlander SK. Generation of small insert genomic FISH probes with high signal intensity suitable for deletion mapping. of special interest Cytogenet Cell Genet. 76:1997;202-205 Repeat free fragments (2-4 kb) of cosmid clones were amplified by sequence-independent PCR and used as FISH probes. They gave good metaphase signals but were said to be no good on interphase nuclei. Their principle use may be in detecting small deletions.
17. Florijn RJ, van de Rijke FM, Vrolijk H, Blonden LAJ, Hofker MH, den Dunnen JT, Tanke HJ, van Ommen G-JB, Raap AK. Exon mapping by fibre-FISH or LR-PCR. of special interest Genomics. 38:1996;277-282 Hybridisations with 400bp PCR products of exons onto extended cosmids are shown as intensity profiles along the length of the cosmid. Hybridisation efficiencies drop from 70-90% to only 30% when fragments less than 300 bp were mapped. When mapping cDNAs (3.3 kb, 3.6 kb, 4.6 kb) with exon sizes varying from 25 bp to 860 bp onto their respective cosmids the exons could not be distinguished as each cDNA was seen as a single hybridisation spot. The inability to distinguish individual exons of each cDNA was attributed to the limited spatial separation between the exons.
18. Nilsson M, Krejci K, Koch J, Kwiatkowski M, Gustavsson P, Landegren U. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. of outstanding interest Nat Genet. 16:1997;252-255 The authors uses DNA ligase to concatenate a 'padlock probe' to a target sequence, having the astonishing ability to discriminate DNA sequences which differ by only a single basepair. Demonstrated here with the tandemly repeated α-satellite but with potential to view polymorphism directly on the chromosome. Using this technique we might one day be able to see a haplotype directly without needing to infer it.
19. Blough RI, Smolarek TA, Ulbright TM, Heerema NA. Bicolor fluorescence in situ hybridization on nuclei from formalin-fixed, paraffin-embedded testicular germ cell tumors: comparison with standard metaphase analysis. Cancer Genet Cytogenet. 94:1997;79-84.
20. Ghazvini S, Char DH, Kroll S, Waldman FM, Pinkel D. Comparative genomic hybridization analysis of archival formalin-fixed paraffin-embedded uveal melanomas. Cancer Genet Cytogenet. 90:1996;95-101.
21. Nahmias J, Hornigold N, Fitzgibbon J, Woodward K, Pilz A, Griffin D, Henske EP, Nakamura Y, Graw S, Florian F, et al. Cosmid contigs spanning 9q34 including the candidate region for TSC1. Eur J Hum Genet. 3:1995;65-77.
22. Identification of the tuberous sclerosis gene TSC1 on chromosome 9q34. Science. 277:1997;805-808.
23. Fidlerova H, Senger G, Kost M, Sanseau P, Sheer D. Two simple procedures for releasing chromatin from routinely fixed cells for fluorescence in situ hybridization. Cytogenet Cell Genet. 65:1994;203-205.
24. Haaf T, Ward DC. Structural analysis of α-satellite DNA and centromere proteins using extended chromatin and chromosomes. Hum Mol Genet. 3:1994;697-709.
25. Heng HHQ, Squire J, Tsui L-C. High-resolution mapping of mammalian genes by in situ hybridization to free chromatin. Proc Natl Acad Sci USA. 89:1992;9509-9513.
26. Parra I, Windle B. High resolution visual mapping of stretched DNA by fluorescent hybridization. Nat Genet. 5:1993;17-21.
27. Weigant J, Kalle W, Mullenders L, Brookes S, Hoovers JMN, Dauwerse JG, van Ommen GJB, Raap AK. High-resolution in situ hybridization using DNA halo preparations. Hum Mol Genet. 1:1992;587-591.
28. Heiskanen M, Karhu R, Hellsten E, Peltonen L, Kallioniemi OP, Palotie A. High resolution mapping using fluorescence in situ hybridization to extended DNA fibers prepared from agarose-embedded cells. Biotechniques. 17:1994;928-934.
29. Yokota H, Johnson F, Lu H, Robinson RM, Belu AM, Garrison MD, Ratner BD, Trask BJ, Miller DL. A new method for straightening DNA molecules for optical restriction mapping. Nucleic Acids Res. 25:1997;1064-1070.
30. Bensimon A, Simon A, Chifaudel A, Croquette V, Heslot F, Bensimon. Alignment and sensitive detection of DNA by a moving interface. Science. 265:1994;2096-2098.
31. Suto Y, Tokunaga K, Watanabe Y, Hirai M. Visual demonstration of the organisation of the human complement C4 and 21-hydroxylase genes by high-resolution fluorescence in situ hybridization. Genomics. 33:1996;321-324.
32. Shiels C, Coutelle C, Huxley C. Analysis of ribosomal and alphoid repetitive DNA by fibre-FISH. of special interest Cytogenet Cell Genet. 76:1997;20-22 DNA arrays up to 2.6 Mb measured.
33. Florijn RJ, Bonden LAJ, Vrolijk H, Weigant J, Vaandrager J-W, Baas F, den Dunnen JT, Tanke HJ, Van Ommen G-JB, Raap AK. High-resolution DNA fiber-FISH for genomic DNA mapping and colour bar-coding of large genes. Hum Mol Genet. 4:1995;831-836.
34. Lengauer C, Speicher MR, Popp S, Jauch A, Taniwaki M, Nagaraja R, Reithman H, Donis-Keller H, D'Urso M, Schlessinger D, Cremer T. Chromosomal bar codes produced by multicolor fluorescence in situ hybridization with multiple YAC clones and whole chromosome painting probes. Hum Mol Genet. 2:1993;505-512.
35. Muller S, Rocchi M, Ferguson-Smith MA, Weinberg J. Towards a multicolor chromosome bar code for the entire human karyotype by fluorescence in situ hybridization. of outstanding interest Hum Genet. 100:1997;271-278 A pretty paper. Irradiation fragment hybrid cell lines containing between them subregions of each human chromosome were amplified by Alu primed PCR. The resulting PCR products were placed into one of two pools which were labelled either with biotin or digoxigenin. The mixed probe was then used in a single hybridisation. Each human chromosome is identified by a unique set of signals and a coloured idiogram of all human chromosomes produced.
36. Shin J-C, Ross HL, Elias S, Nguyen DD, Mitchell-Leef D, Simpson JL, Bischoff FZ. Detection of chromosomal aneuploidy in endometriosis by multi-color fluorescence in situ hybridization (FISH). Hum Genet. 100:1997;401-406.
37. Guttenbach M, Michelmann HW, Hinney B, Engel W, Schmid M. Segregation of sex chromosomes into sperm nuclei in a man with 47, XXY Klinefelter's karyotype: a FISH analysis. Hum Genet. 99:1997;474-477.
38. Sherlock J, Halder A, Tutschek B, Delhanty J, Rodeck C, Adinolfi M. Prenatal detection of foetal aneuploidies using transcervical cell samples. J Med Genet. 34:1997;302-305.
39. Wegner RD, Schrock E, Obladen M, Becker R, Stumm M, Sperling K. Partial trisomy/monosomy 6q in foetal cells and CVS long-term culture not present in CVS short-term culture. Prenat Diagn. 16:1996;741-748.
40. Monteil M, Rousseaux S, Chevret E, Pelletier R, Cozzi J, Sele B. Increased aneuploid frequency in spermatozoa from a Hodgkin's disease patient after chemotherapy and radiotherapy. Cytogenet Cell Genet. 76:1997;134-138.
41. Robbins WA, Meistrich ML, Moore D, Hagemeister FB, Weier H-U, Cassel MJ, Wilson G, Eskenazi B, Wyrobek AJ. Chemotherapy induces transient sex chromosomal and autosomal aneuploidy in human sperm. Nat Genet. 16:1997;74-78.
42. Knight SJL, Horsley SW, Regan R, Lawrie NM, Maher EJ, Cardy DLN, Flint J, Kearney L. Development and clinical application of an innovative fluorescence in situ hybridization technique which detects submicroscopic rearrangements involving telomeres. of special interest Eur J Hum Gene. 5:1997;1-8 Cleverly uses a single slide with 24 separate hybridisations.
43. Ligon AH, Beaudet AL, Shaffer LG. Simultaneous, multilocus FISH analysis for detection of microdeletions in the diagnostic evaluation of developmental delay and mental retardation. of special interest Am J Hum Genet. 61:1997;51-59 Probing for many syndromes simultaneously can reduce the risk of misdiagnosis.
44. Fischer K, Scholl C, Salat J, Frohling S, Schlenk R, Bentz M, Stilgenbauer S, Lichter P, Dohner H. Design and validation of DNA probe sets for a comprehensive analysis of acute myeloid leukaemia. Blood. 88:1996;3962-3971.
45. Gersh M, Grady D, Rojas K, Lovett M, Moyzis R, Overhauser J. Development of diagnostic tools for the analysis of 5p deletions using interphase FISH. Cytogenet Cell Genet. 77:1997;246-251.
46. Santos SJ, Singh NP, Natarajan AT. Fluorescence in situ hybridization with comets. of special interest Exp Cell Res. 232:1997;407-411 Cells embedded in agarose before lysis and DNA stretched by electrophoresis prior to FISH.
47. Iwabuchi S, Muramatsu H, Chiba N, Kinjo Y, Murakami Y, Sakaguchi T, Yokoyama K, Tamiya E. Simultaneous detection of near-field topographic and fluorescence images of human chromosomes via scanning near-field optical/atomic force microscopy (SNOAM). of special interest Nucleic Acids Res. 25:1997;1662-1663 A new microscopy method. Has it a future in this field?
48. Craig JM, Kraus J, Cremer T. Removal of repetitive sequences from FISH probes using PCR-assisted affinity chromatography. Hum Genet. 100:1997;472-476.