Genomic microarrays in the spotlight

Trends in Genetics

Volumn 20, Issue 2, 2004, Pages 87-94

  Mantripragada, Kiran K ^a   Buckley, Patrick G ^a   Diaz De Ståhl, Teresita ^a   Dumanski, Jan P ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; DNA;

CLONE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; EPIGENETICS; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENOMICS; HUMAN; MEDICAL RESEARCH; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW;

EID: 1642473037     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2003.12.008     Document Type: Review

References (72)

1. Kallioniemi A., et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 258:1992;818-821.
2. Solinas-Toldo S., et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 20:1997;399-407.
3. Pinkel D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20:1998;207-211.
4. Pollack J.R., et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23:1999;41-46.
5. Snijders A.M., et al. Assembly of microarrays for genome-wide measurement of DNA copy number. Nat. Genet. 29:2001;263-264.
6. Buckley P.G., et al. A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum. Mol. Genet. 11:2002;3221-3229.
7. Klein C.A., et al. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc. Natl. Acad. Sci. U. S. A. 96:1999;4494-4499.
8. Telenius H., et al. Cytogenetic analysis by chromosome painting using DOP-PCR amplified flow sorted chromosomes. Genes Chromosomes Cancer. 4:1992;257-263.
9. Telenius H., et al. Degenerate oligonucleotide-primed PCR: general amplification of target DNA by single degenerate primer. Genomics. 13:1992;718-725.
10. Veltman J.A., et al. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am. J. Hum. Genet. 70:2002;1269-1276.
11. Fiegler H., et al. DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer. 36:2003;361-374.
12. Dean F.B., et al. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U. S. A. 99:2002;5261-5266.
13. Lage J.M., et al. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res. 13:2003;294-307.
14. Hosono S., et al. Unbiased whole-genome amplification directly from clinical samples. Genome Res. 13:2003;954-964.
15. Dunham I., et al. The DNA sequence of human chromosome 22. Nature. 402:1999;489-495.
16. Mantripragada K.K., et al. Development of NF2 gene specific, strictly sequence defined diagnostic microarray for deletion detection. J. Mol. Med. 81:2003;443-451.
17. Schena M., et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
18. Pollack J.R., 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. 99:2002;12963-12968.
19. Kauraniemi P., et al. New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res. 61:2001;8235-8240.
20. Monni O., et al. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc. Natl. Acad. Sci. U. S. A. 98:2001;5711-5716.
21. Porkka K., et al. Amplification and overexpression of Elongin C gene discovered in prostate cancer by cDNA microarrays. Lab. Invest. 82:2002;629-637.
22. Beheshti B., et al. Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. Neoplasia. 5:2003;53-62.
23. Clark J., et al. Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene. 22:2003;1247-1252.
24. Kapranov P., et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science. 296:2002;916-919.
25. Rinn J.L., et al. The transcriptional activity of human Chromosome 22. Genes Dev. 17:2003;529-540.
26. Mantripragada, K.K. et al. DNA copy number analysis of the typically deleted region in DiGeorge syndrome using array-CGH with genomic and PCR-based targets. Int. J. Mol. Med. (in press).
27. Fritz B., et al. Microarray-based copy number and expression profiling in dedifferentiated and pleomorphic liposarcoma. Cancer Res. 62:2002;2993-2998.
28. Wilhelm M., et al. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 62:2002;957-960.
29. Zhao J., et al. Combined comparative genomic hybridization and genomic microarray for detection of gene amplifications in pulmonary artery intimal sarcomas and adrenocortical tumors. Genes Chromosomes Cancer. 34:2002;48-57.
30. Weiss M.M., et al. Genomic profiling of gastric cancer predicts lymph node status and survival. Oncogene. 22:2003;1872-1879.
31. Snijders A.M., et al. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 22:2003;4281-4286.
32. Sanchez-Izquierdo D., et al. MALT1 is deregulated by both chromosomal translocation and amplification in B-cell non-Hodgkin lymphoma. Blood. 101:2003;4539-4546.
33. Martinez-Climent J.A., et al. Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Blood. 101:2003;3109-3117.
34. Locke D.P., et al. Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res. 13:2003;347-357.
35. Geschwind D.H., et al. Klinefelter's syndrome as a model of anomalous cerebral laterality: testing gene dosage in the X chromosome pseudoautosomal region using a DNA microarray. Dev. Genet. 23:1998;215-229.
36. Yu W., et al. Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions. Hum. Mol. Genet. 12:2003;2145-2152.
37. Kinzler K.W., Vogelstein B. Lessons from hereditary colorectal cancer. Cell. 87:1996;159-170.
38. Bruder C.E., et al. High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Hum. Mol. Genet. 10:2001;271-282.
39. Redon R., et al. Amplicon mapping and transcriptional analysis pinpoint Cyclin L as a candidate oncogene in head and neck cancer. Cancer Res. 62:2002;6211-6217.
40. Mantripragada K.K., et al. High-resolution profiling of an 11 Mb segment of human chromosome 22 in sporadic schwannoma using array-CGH. Int. J. Oncol. 22:2003;615-622.
41. Wessendorf S., et al. Hidden gene amplifications in aggressive B-cell non-Hodgkin lymphomas detected by microarray-based comparative genomic hybridization. Oncogene. 22:2003;1425-1429.
42. Goldstein M., et al. Combined cytogenetic and array-based comparative genomic hybridization analyses of Wilms tumors: amplification and overexpression of the multidrug resistance associated protein 1 gene (MRP1) in a metachronous tumor. Cancer Genet. Cytogenet. 141:2003;120-127.
43. Fiegler H., et al. Array painting: a method for the rapid analysis of aberrant chromosomes using DNA microarrays. J. Med. Genet. 40:2003;664-670.
44. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
45. Venter J.C., et al. The sequence of the human genome. Science. 291:2001;1304-1351.
46. Armour J.A., et al. The detection of large deletions or duplications in genomic DNA. Hum. Mutat. 20:2002;325-337.
47. Lupski J.R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14:1998;417-422.
48. Lopez-Correa C., et al. Recombination hotspot in NF1 microdeletion patients. Hum. Mol. Genet. 10:2001;1387-1392.
49. Jenne D.E., et al. Complete physical map and gene content of the human NF1 tumor suppressor region in human and mouse. Genes Chromosomes Cancer. 37:2003;111-120.
50. Jones P.A., Laird P.W. Cancer epigenetics comes of age. Nat. Genet. 21:1999;163-167.
51. Post W.S., et al. Methylation of the estrogen receptor gene is associated with aging and atherosclerosis in the cardiovascular system. Cardiovasc. Res. 43:1999;985-991.
52. Jirtle R.L., et al. Genomic imprinting and environmental disease susceptibility. Environ. Health Perspect. 108:2000;271-278.
53. Tycko B., Ashkenas J. Epigenetics and its role in disease. J. Clin. Invest. 105:2000;245-246.
54. Robertson K.D., Wolffe A.P. DNA methylation in health and disease. Nat. Rev. Genet. 1:2000;11-19.
55. Laird P.W. The power and the promise of DNA methylation markers. Nat. Rev. Cancer. 3:2003;253-266.
56. Ehrlich M., et al. Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene. 21:2002;6694-6702.
57. Pollack J.R., Iyer V.R. Characterizing the physical genome. Nat. Genet. 32:(Suppl.):2002;515-521.
58. Zardo G., et al. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat. Genet. 32:2002;453-458.
59. Karpf A.R., et al. Inhibition of DNA methyltransferase stimulates the expression of signal transducer and activator of transcription 1, 2, and 3 genes in colon tumor cells. Proc. Natl. Acad. Sci. U. S. A. 96:1999;14007-14012.
60. Jackson-Grusby L., et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nat. Genet. 27:2001;31-39.
61. Liang G., et al. Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2′- deoxycytidine. Cancer Res. 62:2002;961-966.
62. Suzuki H., et al. A genomic screen for genes upregulated by demethylation and histone deacetylase inhibition in human colorectal cancer. Nat. Genet. 31:2002;141-149.
63. Huang T.H., et al. Methylation profiling of CpG islands in human breast cancer cells. Hum. Mol. Genet. 8:1999;459-470.
64. Yan P.S., et al. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res. 61:2001;8375-8380.
65. Yan P.S., et al. Applications of CpG island microarrays for high-throughput analysis of DNA methylation. J. Nutr. 132:2002;2430S-2434S.
66. Tompa R., et al. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12:2002;65-68.
67. Gitan R.S., et al. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12:2002;158-164.
68. Adorjan P., et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30:2002;e21.
69. Ren B., et al. Genome-wide location and function of DNA binding proteins. Science. 290:2000;2306-2309.
70. Iyer V.R., et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409:2001;533-538.
71. Lucito R., et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13:2003;2291-2305.
72. Liu R.H., et al. Hybridization enhancement using cavitation microstreaming. Anal. Chem. 75:2003;1911-1917.