Molecular pathology and future developments

European Journal of Cancer

Volumn 35, Issue 14, 1999, Pages 1895-1904

  Going, J J ^a   Gusterson, B A ^b  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

Bioinformatics; cDNA arrays; Comparative genomic hybridisation (CGH); Laser microdissection; Molecular pathology; Multiplex FISH; Proteomics; Real time PCR; Serial analysis of gene expression (SAGE); Tissue arrays

Indexed keywords

CANCER; CHROMOSOME PAINTING; CYTOGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENETIC TRANSCRIPTION; HISTOLOGY; HUMAN; MOUSE; NONHUMAN; PATHOLOGY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RAT; REVIEW; RNA TRANSLATION; TRANSGENIC ANIMAL;

EID: 0033388957     PISSN: 09598049     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-8049(99)00253-1     Document Type: Article

References (76)

1. Feulgen R., Rossenbeck H. Mikroskopic-chemischer Nachweis einen Nucleinsaure von Typus der Thymonucleinsaure und die darauf berhende elektive Färbung von Zellkernen in mikroskopischen Preparäten. Zeitschrift. Physiol. Chem. 135:1924;203-248.
2. Kohler G., Milstein C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature. 296:1975;495-497.
3. Kallioniemi O.P., Kallioniemi A., Sudar D.et al. Comparative genomic hybridisation - a rapid new method for detecting and mapping DNA amplifications in tumours. Semin. Cancer Biol. 4:1993;41-46.
4. Reid T., Just K.E., Holtgrevegrez H.et al. Comparative genomic hybridisation of formalin-fixed, paraffin-embedded breast tumours reveals different patterns of chromosomal gains and losses in fibroadenomas and diploid and aneuploid carcinomas. Cancer Res. 55:1995;5415-5423.
5. James L.A., Mitchell E.L.D., Menasce L., Varley J.M. Comparative genomic hybridisation of ductal carcinoma in situ of the breast. identification of regions of DNA amplification and deletion in common with invasive breast carcinoma Oncogene. 14:1997;1059-1065.
6. Zitzelsberger H., Lehmann L., Werner M., Bauchinger M. Comparative genomic hybridisation for the analysis of chromosomal imbalances in solid tumours and haematological malignancies. Histochem. Cell Biol. 108:1997;403-417.
7. Wells D., Sherlock J.K., Handyside A.H., Delhanty J.D.A. Detailed chromosomal and molecular genetic analysis of single cells by whole genome amplification and comparative genomic hybridisation. Nucl. Acids Res. 27:1999;1214-1218.
8. Bao Y.P., Muller U., Che D.et al. A novel microchip array for detecting gene amplification in cancer cells. Cytogenet. Cell Genet. 82:1998;140.
9. Ried T., Schrock E., Ning Y., Wienberg J. Chromosome painting. a useful art Hum. Mol. Genet. 7:1998;1619-1626.
10. Blough R.I., Heerema N.A., Ulbricht T.M., Smolarek T.A., Roth L.M., Einhorn L.H. Interphase chromosome painting of paraffin-embedded tissue in the differential diagnosis of possible germ-cell tumours. Modern Pathol. 11:1998;634-641.
11. Carter N.P., Ferguson-Smith M.A., Perryman M.T.et al. Reverse chromosome painting. a method for the rapid analysis of aberrant chromosomes in clinical cytogenetics J. Med. Genet. 29:1992;299-307.
12. Morris J.S., Carter N.P., Ferguson-Smith M.A., Edwards P.A.W. Cytogenetic analysis of three breast carcinoma cell lines using reverse chromosome painting. Genes Chromosomes Cancer. 20:1997;120-139.
13. Arkesteijn G., Jumelet E., Hagenbeek A., Smit E., Slater R., Martens A. Reverse chromosome painting for the identification of marker chromosomes and complex translocations in leukaemia. Cytometry. 35:1999;117-124.
14. Speicher M.R., Ballard S.G., Ward D.C. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nature Genet. 12:1996;368-375.
15. Schrock E., Veldman T., Padilla-Nash H.et al. Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities. Hum. Genet. 101:1997;255-262.
16. Macville M., Schrock E., Padilla-Nash H., Keck C., Ghadimi B.M., Zimonjic D., Popescu N., Ried T. Comprehensive and definitive molecular cytogenetic characterisation of HeLa cells by spectral karyotyping. Cancer Res. 59:1999;141-150.
17. Fox J.L. Complaints raised over restricted microarray access. Nat. Biotechnol. 17:1999;325-326.
18. Duggan D.J., Bittner M., Chen Y., Meltzer P., Trent J.M. Expression profiling using cDNA microarrays. Nature Genet. 21:1999;S10-S14.
19. Cheung V.G., Morley M., Aguilar F., Massimi A., Kucherlapati R., Childs G. Making and reading microarrays. Nature Genet. 21:1999;S15-S19.
20. Lipshutz R.J., Fodor S.P.A., Gingeras T.R., Lockhart D.J. High density synthetic oligonucleotide arrays. Nature Genet. 21:1999;S20-S24.
21. Southern E., Mir K., Shchepinov M. Molecular interactions on microarrays. Nature Genet. 21:1999;S5-S9.
22. Carulli J.P., Artinger M., Swain P.M.et al. High throughput analysis of differential gene expression. J. Cell Biochem. Suppl. 31:1998;286-296.
23. Velculescu V.E., Zhang L., Vogelstein B., Kinzler K.W. Serial analysis of gene expression. Science. 270:1995;484-487.
24. Datson N.A., van der Perk-de Jong J., van den Berg M.P., de Kloet E.R., Vreugdenhil E. MicroSAGE. a modified procedure for serial analysis of gene expression in limited amounts of tissue Nucleic Acids Res. 27:1999;1300-1307.
25. Powell J. Enhanced concatemer cloning - a modification to the SAGE (Serial Analysis of Gene Expression) technique. Nucl. Acids Res. 26:1998;3445-3446.
26. Bertelsen A.H., Velculescu V.E. High-throughput gene expression analysis using SAGE. Drug Discovery Today. 3:1998;152-159.
27. Hibi K., Liu Q., Beaudry G.A.et al. Serial analysis of gene expression in non-small cell lung cancer. Cancer Res. 58:1998;5690-5694.
28. Hacia J.G. Resequencing and mutational analysis using oligonucleotide microarrays. Nat. Genet. 21:1999;42-47.
29. Liang P., Pardee A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science. 257:1992;967-971.
30. Welsh J., Chada K., Dalal D., Cheng R., Ralph D., McLelland M. Arbitrarily primed PCR fingerprinting of RNA. Nucl. Acids Res. 20:1992;4965-4970.
31. Tortola S., Capella G., Marcuello E.et al. Analysis of differential gene expression in human colorectal tumor tissues by RNA arbitrarily primed-PCR. a technical assessment Lab. Invest. 78:1998;309-317.
32. Lisitsyn N., Lisitsyna N., Wigler M. Cloning the differences between two complex genomes. Science. 259:1993;946-951.
33. Hubank M., Schatz D.G. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucl. Acids Res. 22:1994;5640-5648.
34. Packer N.H., Harrison M.J. Glycobiology and proteomics. is mass spectroscopy the holy grail? Electrophoresis. 19:1998;1872-1882.
35. Smoluch M.T., Sallberg M., Silberring J. Nanospray mass spectrometry for identification of peptides. Acta Biochim. Pol. 46:1999;475-481.
36. Jespersen S., Chaurand P., Strien F.J.Cv, Spengler B., Greef Jvd. Direct sequencing of neuropeptides in biological tissues by MALDI-PSD mass spectrometry. Anal. Chem. 71:1999;660-666.
37. Celis J.E., Celis P., Ostergaard M.et al. Proteomics and immunohistochemistry define some of the steps involved in the squamous differentiation of the bladder transitional epithelium. a novel strategy for identifying metaplastic lesions Cancer Res. 59:1999;3003-3009.
38. Fu D.J., Tang K., Braun A.et al. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nature Biotechnol. 16:1998;381-384.
39. Kononen J., Bubendorf L., Kallioniemi A.et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nature Med. 4:1998;844-847.
40. Bubendorf L., Kononen J., Koivisto P.et al. Survey of gene amplifications during prostate cancer progression by high-throughout fluorescence in situ hybridization on tissue microarrays. Cancer Res. 59:1999;803-806. (Published erratum appears in Cancer Res 1999, 59(6), 1388).
41. Moch H., Schraml P., Bubendorf L.et al. High-throughput tissue microarray analysis to evaluate genes uncovered by cDNA microarray screening in renal cell carcinoma. Am. J. Pathol. 154:1999;981-986.
42. Emmert-Buck M.R., Bonner R.F., Smith P.D.et al. Laser capture microdissection. Science. 274:1996;998-1001.
43. Banks R.E., Dunn M.J., Forbes M.A.et al. The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - preliminary findings. Electrophoresis. 20:1999;689-700.
44. Bohm M., Wieland I., Schutze K., Rubben H., Microbeam M.O. MeNT. non-contact laser microdissection of membrane-mounted native tissue Am. J. Pathol. 151:1997;63-67.
45. Srinivasan R. Ablation of polymers and biological tissue by ultraviolet light. Science. 234:1986;559-565.
46. Fire A., Xu S.Q., Montgomery M.K., Kostas S.A., Driver S.E., Mello C.C. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 391:1998;806-811.
47. Montgomery M.K., Xu S.Q., Fire A. RNA as a target of double-stranded RNA mediated genetic interference in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA. 95:1998;15502-15507.
48. Ngo H., Tschudi C., Gull K., Ullu E. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc. Natl. Acad. Sci. USA. 95:1998;14687-14692.
49. Tabara H., Grishok A., Mello C.C. RNA in C. elegans. soaking in the genome sequence Science. 282:1998;430-431.
50. Hodgkin J., Herman R.K. Changing styles in C. elegans genetics. Trends Genet. 14:1998;352-357.
51. Lipschutz J.H. Molecular development of the kidney. a review of the results of gene disruption studies Am. J. Kidney Dis. 31:1998;383-397.
52. Takahashi N., Smithies O. Gene targeting approaches to analysing hypertension. J. Am. Soc. Nephrol. 10:1999;1598-1605.
53. Muller U. Ten years of gene targeting. targeted mouse mutants, from vector design to phenotype analysis Mechanisms Dev. 82:1999;3-21.
54. Boer Jd., Hoeijmakers J. Cancer from the outside, aging from the inside. mouse models to study the consequences of defective nucleotide excision repair Biochimie. 81:1999;127-137.
55. Ghebranious N., Donehower L.A. Mouse models in tumour suppression. Oncogene. 17:1998;3385-3400.
56. Banerjee A., Quirke P. Experimental models of colorectal cancer. Dis. Colon Rectum. 41:1998;490-505.
57. Cardiff R.D., Munn R.J. The histopathology of transgenes and knockouts in the mammary gland. Adv. Oncobiol. 2:1998;177-202.
58. Stewart T.A., Pattengale P.K., Leder P. Spontaneous mammary adenocarcinomas in transgenic mice that carry and express MTV/myc fusion genes. Cell. 38:1984;627-637.
59. Webster M.A., Hutchinson J.N., Rauh M.J.et al. Requirement for both Shc and phosphatidylinositol 3′ kinase signaling pathways in polyomavirus middle T-mediated mammary tumorigenesis. Mol. Cell Biol. 18:1998;2344-2359.
60. Kuhn R., Schwenk F., Aguet M., Rajewsky K. Inducible gene targeting in mice. Science. 269:1995;1427-1429.
61. Orlando C., Pinzani P., Pazzagli M. Developments in quantitative PCR. Clin. Chem. and Lab. Med. 36:1998;255-269.
62. Lie Y.S., Petropoulos C.J. Advances in quantitative PCR technology. 5′ nuclease assays Curr. Opinion Biotechnol. 9:1998;43-48.
63. Luthra R., McBride J.A., Cabanillas F., Sarris A. Novel 5′ exonuclease-based real-time PCR assay for the detection of t(14;18)(q32;q21) in patients with follicular lymphoma. Am. J. Pathol. 153:1998;63-68.
64. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868.
65. Törönen P., Kolehmainen M., Wong G., Castren E. Analysis of gene expression data using self-organizing maps. FEBS Lett. 451:1999;142-146.
66. Wittes J., Friedman H.P. Searching for evidence of altered gene expression. a comment on statistical analysis of microarray data J. Natl. Cancer Inst. 91:1999;400-401.
67. Michels K.B., Rosner B.A. Data trawling. to fish or not to fish Lancet. 348:1996;1152-1153.
68. Bassett D.E., Eisen M.B., Boguski M.S. Gene expression informatics - it's all in your mine. Nature Genetics. 21s:1999;51-55.
69. Ermolaeva O., Rastogi M., Pruitt K.D.et al. Data management and analysis for gene expression arrays. Nat. Genet. 20:1998;19-23.
70. Griffiths A.D., Duncan A.R. Strategies for selection of antibodies by phage display. Curr. Opin. Biotechnol. 9:1998;102-108.
71. Henn W. Genetic screening with the DNA chip. a new Pandora's box? J. Med. Ethics. 25:1999;200-203.
72. Cole K.A., Krizman D.B., Emmert-Buck M.R. The genetics of cancer - a 3D model. Nature Genet. 21:1999;38-41.
73. Goldenberg M.M. Trastuzumab, a recombinant DNA derived humanized monoclonal antibody, a novel agent for the treatment of metastatic breast cancer. Clin. Therw. 21:1999;309-318.
74. Jacobs T.W., Gown A.M., Yaziji H., Barnes M.J., Schnitt S.J. Specificity of HercepTest in determining HER-2/new status of breast cancers using the United States Food and Drug Administration approved scoring system. J. Clin. Oncol. 17:1999;1983-1987.
75. Quirke P., Mapstone N. The new biology. histopathology Lancet. 354:1999;S26-S31.
76. Jones D., Fletcher C.D.M. How shall we apply the new biology to diagnostics in surgical pathology? J. Pathol. 187:1999;147-154.