Current and potential uses for DNA microarrays in transplantation medicine: Lessons from other disciplines

Tissue Antigens

Volumn 62, Issue 2, 2003, Pages 93-103

  Boussioutas, Alex ^a   Haviv, I ^a  

^a PETER MACCALLUM CANCER CENTRE   (Australia)

Author keywords

Expression profiling; Genotypic background; Microarray; Molecular classification; Molecular tissue typing; Single nucleotide polymorphism (SNP) profiling

Indexed keywords

COMPLEMENTARY DNA; DNA; MESSENGER RNA;

BIOINFORMATICS; CANCER RESEARCH; DNA MICROARRAY; DNA PROBE; EXPERIMENTAL DESIGN; GENE; GENE EXPRESSION; GENE LOCUS; GENOTYPE; INTERNET; MEDICAL RESEARCH; MOLECULAR BIOLOGY; PRIORITY JOURNAL; REVIEW; RNA ISOLATION; TRANSPLANTATION;

COMPUTATIONAL BIOLOGY; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN TRANSPLANTATION; PEDIGREE;

ARENA;

EID: 0042530276     PISSN: 00012815     EISSN: None     Source Type: Journal    
DOI: 10.1034/j.1399-0039.2003.00109.x     Document Type: Review

References (75)

1. Golub TR, Slonim DK, Tamayo P et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999: 286: 531-7.
2. Heller RA, Schena M, Chai A et al. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci U S A 1997: 94: 2150-5.
3. Shaffer AL, Rosenwald A, Hurt EM et al. Signatures of the immune response. Immunity 2001: 15: 375-85.
4. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell 2000: 100: 57-70.
5. Liotta LA, Kohn EC. The microenvironment of the tumour-host interface. Nature 2001: 411: 375-9.
6. Shou J, Soriano R, Hayward SW, Cunha GR, Williams PM, Gao WQ. Expression profiling of a human cell line model of prostatic cancer reveals a direct involvement of interferon signaling in prostate tumor progression. Proc Natl Acad Sci U S A 2002: 99: 2830-5.
7. Kannan K, Kaminski N, Rechavi G, Jakob-Hirsch J, Amariglio N, Givol D. DNA microarray analysis of genes involved in p53 mediated apoptosis: activation of Apaf-1. Oncogene 2001: 20: 3449-55.
8. Schubert CM. Microarray to be used as routine clinical screen. Nat Med 2003: 9: 9.
9. Kruglyak L, Nickerson DA. Variation is the spice of life. Nat Genet 2001: 27: 234-6.
10. Couzin J, Genomics. New mapping project splits the community. Science 2002: 296: 1391-3.
11. Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S. A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A 2000: 97: 14668-73.
12. Holloway AJ, van Laar RK, Tothill RW, Bowtell DD. Options available - from start to finish - for obtaining data from DNA microarrays II. Nat Genet 2002: 32: 481-9.
13. Eberwine J, Yeh H, Miyashiro K et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci U S A 1992: 89: 3010-4.
14. Yang YH, Dudoit S, Luu P et al. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002: 30: e15.
15. Yang YH, Speed T. Design issues for cDNA microarray experiments. Nat Rev Genet 2002: 3: 579-88.
16. Colantuoni C, Henry G, Zeger S, Pevsner J. SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. Bioinformatics 2002: 18: 1540-1.
17. Claverie JM. Computational methods for the identification of differential and coordinated gene expression. Hum Mol Genet 1999: 8: 1821-32.
18. Deutsch JM. Evolutionary algorithms for finding optimal gene sets in microarray prediction. Bioinformatics 2003: 19: 45-52.
19. Lee KE, Sha N, Dougherty ER, Vannucci M, Mallick BK. Gene selection: a Bayesian variable selection approach. Bioinformatics 2003: 19: 90-7.
20. Brazma A, Vilo J. Gene expression data analysis. FEBS Lett 2000: 480: 17-24.
21. Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 2000: 16: 906-14.
22. Selaru FM, Xu Y, Yin J, et al. Artificial neural networks distinguish among subtypes of neoplastic colorectal lesions. Gastroenterology 2002: 122: 606-13.
23. Hedenfalk IA, Ringner M, Trent JM, Borg A. Gene expression in inherited breast cancer. Adv Cancer Res 2002: 84: 1-34.
24. Lonnstedt I, Speed TP. Replicated microarray data. Statistical Sinica, 2003: in press.
25. DeMello AJ. Microfluidics: DNA amplification moves on. Nature 2003: 422: 28-9.
26. Kallioniemi OP, Wagner U, Kononen J, Sauter G. Tissue microarray technology for high-throughput molecular profiling of cancer. Hum Mol Genet 2001: 10: 657-62.
27. Brazma A, Hingamp P, Quackenbush J et al. Minimum information about a microarray experiment (MIAME) -toward standards for microarray data. Nat Genet 2001: 29: 365-71.
28. Brazma A, Parkinson H, Sarkans U et al. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucl Acids Res 2003: 31: 68-71.
29. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995: 270: 467-70.
30. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997: 278: 680-6.
31. Ross DT, Scherf U, Eisen MB et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000: 24: 227-35.
32. Su AI, Welsh JB, Sapinoso LM et al. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res 2001: 61: 7388-93.
33. Su AI, Cooke MP, Ching KA et al. Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci U S A 2002: 99: 4465-70.
34. Touloukian CE, Leitner WW, Schnur RE et al. Normal tissue depresses while tumor tissue enhances human T cell responses in vivo to a novel self/ tumor melanoma antigen, OA1. J Immunol 2003: 170: 1579-85.
35. Alizadeh AA, Staudt LM. Genomic-scale gene expression profiling of normal and malignant immune cells. Curr Opin Immunol 2000: 12: 219-25.
36. Staudt LM, Brown PO. Genomic views of the immune system. Annu Rev Immunol 2000: 18: 829-59.
37. Teague TK, Hildeman D, Kedl RM et al. Activation changes the spectrum but not the diversity of genes expressed by T cells. Proc Natl Acad Sci U S A 1999: 96: 12691-6.
38. Alizadeh AA, Eisen MB, Davis RE et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000: 403: 503-11.
39. St Croix B, Rago C, Velculescu V et al. Genes expressed in human tumor endothelium. Science 2000: 289: 1197-202.
40. Liotta L, Petricoin E. Molecular profiling of human cancer. Nat Rev Genet 2000: 1: 48-56.
41. Aoyagi K, Tatsuta T, Nishigaki M et al. A faithful method for PCR-mediated global mRNA amplification and its integration into microarray analysis on laser-captured cells. Biochem Biophys Res Commun 2003: 300: 915-20.
42. Boussioutas A, Li H, Liu J et al. Distinctive patterns of gene expression in premalignant gastric mucosa and gastric cancer. Cancer Research 2003: 63: 2569-77.
43. Saiura A, Mataki C, Murakami T et al. A comparison of gene expression in murine cardiac allografts and isografts by means DNA microarray analysis. Transplantation 2001: 72: 320-9.
44. Saiura A, Kohro T, Yamamoto T et al. Detection of an up-regulation of a group of chemokine genes in murine cardiac allograft in the absence of interferon-gamma by means of DNA microarray. Transplantation 2002: 73: 1480-6.
45. Hofmann WK, de Vos S, Elashoff D et al. Relation between resistance of Philadelphia-chromosome-positive acute lymphoblastic leukaemia to the tyrosine kinase inhibitor STI571 and gene-expression profiles: a gene-expression study. Lancet 2002: 359: 481-6.
46. Kudoh K, Ramanna M, Ravatn R et al. Monitoring the expression profiles of doxorubicin-induced and doxorubicin-resistant cancer cells by cDNA microarray. Cancer Res 2000: 60: 4161-6.
47. Ramaswamy S, Tamayo P, Rifkin R et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A 2001: 98: 15149-54.
48. Pomeroy SL, Tamayo P, Gaasenbeek M et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002: 415: 436-42.
49. van 't Veer LJ, Dai H, van de Vijver MJ et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002: 415: 530-6.
50. van de Vijver MJ, He YD, van't Veer LJ et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002: 347: 1999-2009.
51. Kallioniemi A. Molecular signatures of breast cancer - predicting the future. N Engl J Med 2002: 347: 2067-8.
52. Glynne R, Akkaraju S, Healy JI, Rayner J, Goodnow CC, Mack DH. How self-tolerance and the immunosuppressive drug FK506 prevent B-cell mitogenesis. Nature 2000: 403: 672-6.
53. Glynne RJ, Ghandour G, Goodnow CC. Genomic-scale gene expression analysis of lymphocyte growth, tolerance and malignancy. Current Opinion Immunol 2000: 12: 210-4.
54. Armstrong SA, Staunton JE, Silverman LB et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet 2002: 30: 41-7.
55. Armstrong SA, Kung AL, Mabon ME et al. Inhibition of FLT3 in MLL. Validation of a therapeutic target identified by gene expression based classification. Cancer Cell 2003: 3: 173-83.
56. Bernards R, Weinberg RA. A progression puzzle. Nature 2002: 418: 823.
57. Bittner M, Meltzer P, Chen Y et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 2000: 406: 536-40.
58. Webb T. Microarray studies challenge theories of metastasis. JNCI Cancer Spectrum 2003: 95: 350-1.
59. Shipp MA, Ross KN, Tamayo P et al. Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med 2002: 8: 68-74.
60. Dhanasekaran SM, Barrette TR, Ghosh D et al. Delineation of prognostic biomarkers in prostate cancer. Nature 2001: 412: 822-6.
61. Singh D, Febbo PG, Ross K et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002: 1: 203-9.
62. Beer DG, Kardia SL, Huang CC et al. Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Medical 2002: in press.
63. Kallioniemi A, Kallioniemi OP, Sudar D et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992: 258: 818-21.
64. Pinkel D, Segraves R, Sudar D et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998: 20: 207-11.
65. Pollack JR, Perou CM, Alizadeh AA et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999: 23: 41-6.
66. Pollack JR, Sorlie T, Perou CM et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 2002: 99: 12963-8.
67. Warrington JA, Shah NA, Chen X et al. New developments in high-throughput resequencing and variation detection using high density microarrays. Hum Mutat 2002: 19: 402-9.
68. Anzick SL, Trent JM. Role of genomics in identifying new targets for cancer therapy. Oncology 2002: 16: 7-13.
69. Stickney HL, Schmutz J, Woods IG et al. Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res 2002: 12: 1929-34.
70. Brookes AJ. The essence of SNPs. Gene 1999: 234: 177-86.
71. Pritchard JK. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 2001: 69: 124-37.
72. Primdahl H, Wikman FP, von der Maase H, Zhou XG, Wolf H, Orntoft TF. Allelic imbalances in human bladder cancer: genome-wide detection with high-density single-nucleotide polymorphism arrays. J Natl Cancer Inst 2002: 94: 216-23.
73. Wen WH, Bernstein L, Lescallett J et al. Comparison of TP53 mutations identified by oligonucleotide microarray and conventional DNA sequence analysis. Cancer Res 2000: 60: 2716-22.
74. Hedenfalk I, Ringner M, Ben-Dor A et al. Molecular classification of familial non-BRCA1/BRCA2 breast cancer. Proc Natl Acad Sci U S A 2003: 100: 2532-7.
75. Dong S, Wang E, Hsie L, Cao Y, Chen X, Gingeras TR. Flexible use of high-density oligonucleotide arrays for single-nucleotide polymorphism discovery and validation. Genome Res 2001: 11: 1418-24.