New developments in the analysis of gene expression

REFERENCES

• Alwine JC, Kemp DJ, Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Nail Acad Sci USA 1977; 74: 5350–5354.
   PubMed Web of Science ®Google Scholar
• Liang P, Pardee AB. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 1992; 257: 967–971.
   PubMed Web of Science ®Google Scholar
• Kuang WW, Thompson DA, Hoch RV, Weigel RJ. Differential screening and suppression subtractive hybridization identified genes differentially expressed in an estrogen receptor-positive breast carcinoma cell line. Nucleic Acids Res 1998; 26: 1116–1123.
   PubMed Web of Science ®Google Scholar
• Lisitsyn N, Wigler M. Cloning the differences between two complex genomes. Science 1993; 259: 946–951.
   PubMed Web of Science ®Google Scholar
• Bonner RF, Emmert-Buck M, Cole K et al. Laser capture microdissection: molecular analysis of tissue. Science 1997; 278: 1481–1483.
   PubMed Web of Science ®Google Scholar
• Gupta SK, Douglas-Jones AG, Morgan JM. Microdissection of stained archival tissue. Mol Pathol 1997; 50: 218–220.
   PubMedGoogle Scholar
• Lee JY, Dong SM, Kim SY, Yoo NJ, Lee SH, Park WS. A simple, precise and economical microdissection technique for analysis of genomic DNA from archival tissue sections. Virchows Arch 1998; 433: 305–309.
   PubMed Web of Science ®Google Scholar
• Berns M, Wright W, Wiegand-Steubing R. Laser microbeam as a tool in cell biology. Int Rev Cytol 1992; 129: 1–44.
   Google Scholar
• Bernsen MR, Dijkman HB, de Vries E et al. Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection. Lab Invest 1998; 78: 1267–1273.
   PubMed Web of Science ®Google Scholar
• Emmert-Buck MR, Bonner RF, Smith PD et al. Laser capture microdissection. Science 1996; 274: 998–1001.
   PubMed Web of Science ®Google Scholar
• Suarez-Quian CA, Goldstein SR, Pohida T et al. Laser capture microdissection of single cells from complex tissues. Biotechniques 1999; 26: 328–335.
   PubMed Web of Science ®Google Scholar
• Berthon P, Dimitrov T, Stower M, Cussenot O, Maitland NJ. A microdissection approach to detect molecular markers during progression of prostate cancer. Br J Cancer 1995; 72: 946–951.
   PubMed Web of Science ®Google Scholar
• Becker I, Becker KF, Rohrl MH, Minkus G, Schutze K, Hofler H. Single-cell mutation analysis of tumors from stained histologic slides. Lab Invest 1996; 75: 801–807.
   PubMed Web of Science ®Google Scholar
• Chen T, Dhingra K, Sahin A, Sneige N, Hortobagyi G, Aldaz CM. Technical approach for the study of the genetic evolution of breast cancer from paraffin-embedded tissue sections. Diagn Mol Pathol 1996; 39: 177–185.
   Google Scholar
• Lichy JH, Zavar M, Tsai MM, O'Leary TJ, Taubenberger JK. Loss of heterozygosity on chromosome 11p15 during histological progression in microdissected ductal carcinoma of the breast. Am J Pathol 1998; 153: 271–278.
   PubMed Web of Science ®Google Scholar
• Goldsworthy SM, Stockton PS, Trempus CS, Foley JF, Maronpot RR Effects of fixation on RNA extraction and amplification from laser capture microdissected tissue. Mol Carcinog 1999; 25: 86–91.
   PubMed Web of Science ®Google Scholar
• Abati A, Sanjuan X, Wilder A, Linehan WM, Hewitt SM, Merino MJ. Utilization of microdissection and the polymerase chain reaction for the diagnosis of adrenal cortical carcinoma in fine-needle aspiration cytology. Cancer 1999; 87: 231–237.
   PubMed Web of Science ®Google Scholar
• Chuaqui R, Cole K, Cuello M, Silva M, Quintana ME, Emmert-Buck MR. Analysis of mRNA quality in freshly prepared and archival Papanicolaou samples. Acta Cytol 1999; 43: 831–836.
   PubMedGoogle Scholar
• Fend F, Emmert-Buck MR, Chuaqui R et al. Immuno-LCM: laser capture microdissection of immunostained frozen sections for mRNA analysis. Am J Pathol 1999; 154: 61–66.
   PubMed Web of Science ®Google Scholar
• Jin L, Thompson CA, Qian X, Kuecker SJ, Kulig E, Lloyd RV. Analysis of anterior pituitary hormone mRNA expression in immunophenotypically characterized single cells after laser capture microdissection. Lab Invest 1999; 79: 511–512.
   PubMed Web of Science ®Google Scholar
• Cole KA, Krizman DB, Emmert-Buck MR. The genetics of cancer - a 3D model. Nat Genet 1999; 21: 38–41.
   PubMed Web of Science ®Google Scholar
• Boland CR, Thibodeau SN, Hamilton SR et al. A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 1998; 58: 5248–5257.
   PubMed Web of Science ®Google Scholar
• Nayar R, Zhuang Z, Merino MJ, Silverberg SG. Loss of heterozygosity on chromosome 11q13 in lobular lesions of the breast using tissue microdissection and polymerase chain reaction. Hum Pathol 1997; 28: 277–282.
   PubMed Web of Science ®Google Scholar
• Zhuang Z, Vortmeyer AO. Applications of tissue microdissection in cancer genetics. Cell Vision 1998; 5: 43–48.
   PubMedGoogle Scholar
• Dietmaier W, Hartmann A, Wallinger S et al. Multiple mutation analyses in single tumor cells with improved whole genome amplification. Am J Pathol 1999; 154: 83–95.
   PubMed Web of Science ®Google Scholar
• Kim SH, Godfrey T, Jensen RH. Whole genome amplification and molecular genetic analysis of DNA from paraffin-embedded prostate adenocarcinoma tumor tissue. J Urol 1999; 162: 1512–1518.
   PubMed Web of Science ®Google Scholar
• Muller-Navia J, Nebel A, Oehler D, Theile U, Zabel B, Schleiermacher E. Microdissection and DOP-PCR-based reverse chromosome painting as a fast and reliable strategy in the analysis of various structural chromosome abnormalities. Prenat Diagn 1996; 16: 915–922.
   PubMed Web of Science ®Google Scholar
• Zhang Z, Nakamura M, Taniguchi E, Shan L, Yokoi T, Kakudo K. A simple approach to single-cell microdissection and molecular analysis. Anal Quant Cytol Histol 1997; 19: 514–518.
   PubMed Web of Science ®Google Scholar
• Moskaluk CA, Kern SE. Microdissection and polymerase chain reaction amplification of genomic DNA from histological tissue sections. Am J Pathol 1997; 150: 1547–1552.
   PubMed Web of Science ®Google Scholar
• Jung V, Romeike BF, Henn W et al. Evidence of focal genetic microheterogeneity in glioblastoma multiforme by area-specific CGH on microdissected tumor cells. J Neuropathol Exp Neurol 1999; 58: 993–999.
   PubMed Web of Science ®Google Scholar
• Wolf NG, Abdul-Karim FW, Farver C, Schrock E, du Manoir S, Schwartz S. Analysis of ovarian borderline tumors using comparative genomic hybridization and fluorescence in situ hybridization. Genes Chromosomes Cancer 1999; 25: 307–315.
   PubMed Web of Science ®Google Scholar
• Ponten F, Williams C, Ling Get al. Genomic analysis of single cells from human basal cell cancer using laser-assisted capture microscopy. Mutat Res 1997; 382: 45–55.
   PubMed Web of Science ®Google Scholar
• Chandrasekharappa SC, Guru SC, Manickam P et al. Positional cloning of the gene for multiple endocrine neoplasia-type 1. Science 1997; 276: 404 407.
   PubMedGoogle Scholar
• Hiller T, Snell L, Watson PH. Microdissection RT-PCR analysis of gene expression in pathologically defined frozen tissue sections. Biotechniques 1996; 21: 38–40.
   PubMed Web of Science ®Google Scholar
• Fink L, Seeger W, Ermert Let al. Real-time quantitative RT-PCR after laser-assisted cell picking. Nat Med 1998; 4: 1329–1333.
   PubMed Web of Science ®Google Scholar
• Luo L, Salunga RC, Guo H et al. Gene expression profiles of laser-captured adjacent neuronal subtypes. Nat Med 1999; 5: 117–122.
   PubMed Web of Science ®Google Scholar
• Kuczyk M, Serth J, Bokemeyer C et al. The need for microdissectional tumor cell preparation during the molecular genetic analysis of prostate cancer. World J Urol 1999; 17: 115–122.
   PubMed Web of Science ®Google Scholar
• Banks RE, Dunn MJ, Forbes MA et al. The potential use of laser capture microdissection to selectively obtain distinct populations of cells for proteomic analysis - preliminary findings. Electrophoresis 1999; 20: 689–700.
   PubMed Web of Science ®Google Scholar
• Southern EM. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol 1975; 98: 503–517.
   PubMed Web of Science ®Google Scholar
• Lennon GG, Lehrach H. Hybridization analyses of arrayed cDNA libraries. Trends Genet 1991; 7: 314–317.
   PubMed Web of Science ®Google Scholar
• Kafatos FC, Jones CW, Efstratiadis A. Determination of nucleic acid sequence homologies and relative concentrations by a dot hybridization procedure. Nucleic Acids Res 1979; 7: 1541–1552.
   PubMed Web of Science ®Google Scholar
• Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995; 270: 467–470.
   PubMed Web of Science ®Google Scholar
• Southern E, Mir K, Shchepinov M. Molecular interactions on microarrays. Nat Genet 1999; 21: 5–9.
   PubMed Web of Science ®Google Scholar
• Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nat Genet 1999; 21: 10–14.
   PubMed Web of Science ®Google Scholar
• Cheung VG, Morley M, Aguilar F, Massimi A, Kucherlapati R, Childs G. Making and reading microarrays. Nat Genet 1999; 21: 15–19.
   PubMed Web of Science ®Google Scholar
• Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet 1999; 21: 20–24.
   PubMed Web of Science ®Google Scholar
• Lipshutz RJ, Morris D, Chee M et al. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 1995; 19: 442–447.
   PubMed Web of Science ®Google Scholar
• Singh-Gasson S, Green RD, Yue Y et al. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat Biotechnol 1999; 17: 974–978.
   PubMed Web of Science ®Google Scholar
• Adams MD, Kelley JM, Gocayne JD et al. Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991; 252: 1651–1656.
   PubMed Web of Science ®Google Scholar
• Bowtell DD. Options available - from start to finish - for obtaining expression data by microarray [published erratum appears in Nat Genet 1999; 21: 2411. Nat Genet 1999; 21: 25–32.
   PubMed Web of Science ®Google Scholar
• Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996; 93: 10614–10619.
   PubMed Web of Science ®Google Scholar
• Eberwine J, Yeh H, Miyashiro K et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci USA 1992; 89: 3010–3014.
   PubMed Web of Science ®Google Scholar
• Lockhart DJ, Dong H, Byrne MC et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996; 14: 1675–1680.
   PubMed Web of Science ®Google Scholar
• Lander ES. Array of hope. Nat Genet 1999; 21: 3–4.
   PubMed Web of Science ®Google Scholar
• Rajeevan MS, Dimulescu IM, Unger ER, Vernon SD. Chemiluminescent analysis of gene expression on high-density filter arrays. J Histochem Cytochem 1999; 47: 337–342.
   PubMed Web of Science ®Google Scholar
• Pieta G, Alibert O, Guichard V et al. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array. Genome Res 1996; 6: 492–503.
   PubMed Web of Science ®Google Scholar
• Zhao N, Hashida H, Takahashi N, Misumi Y, Sakaki Y. High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression. Gene 1995; 156: 207–213.
   PubMed Web of Science ®Google Scholar
• Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998; 95: 14863–14868.
   PubMed Web of Science ®Google Scholar
• DeRisi J, Penland L, Brown PO et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996; 14: 457–460.
   PubMed Web of Science ®Google Scholar
• Spellman PT, Sherlock G, Zhang MQ et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 1998; 9: 3273–3297.
   PubMed Web of Science ®Google Scholar
• Iyer VR, Eisen MB, Ross DT et al. The transcriptional program in the response of human fibroblasts to serum. Science 1999; 283: 83–87.
   PubMed Web of Science ®Google Scholar
• Heller RA, Schena M, Chai A et al. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA 1997; 94: 2150–2155.
   PubMed Web of Science ®Google Scholar
• Hayward R, Derisi J, Alfadhli S, Kaslow D, Brown P, Rathod P. Shotgun DNA microarrays and stage-specific gene expression in Plasmodium fakiparum malaria. Mol Microbiol 2000; 35: 6–14.
   PubMed Web of Science ®Google Scholar
• Dobrowolski SF, Banas RA, Naylor EW, Powdrill T, Thakkar D. DNA microarray technology for neonatal screening. Acta Paediatr Suppl 1999; 88: S61–S64.
   PubMedGoogle Scholar