Recent advances in array comparative genomic hybridization technologies and their applications in human genetics

European Journal of Human Genetics

Volumn 14, Issue 2, 2006, Pages 139-148

  Lockwood, William W ^a   Chari, Raj ^a   Chi, Bryan ^a   Lam, Wan L ^a  

^a BRITISH COLUMBIA CANCER RESEARCH CENTRE   (Canada)

Author keywords

Array CGH; Array CGH software; Cancer genetics; Cancer genome; Copy number alteration; Genetic disease; Matrix CGH

Indexed keywords

DNA;

CANCER CELL CULTURE; CANCER GENETICS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; DNA MICROARRAY; GENE DELETION; GENE DUPLICATION; GENE MUTATION; GENE TECHNOLOGY; GENETIC ANALYSIS; GENETIC DISORDER; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOME; HUMAN; METHODOLOGY; PRIORITY JOURNAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

GENE DOSAGE; GENETIC MARKERS; GENOMICS; HUMANS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 31344457934     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201531     Document Type: Review

References (77)

1. Solinas-Toldo S, Lampel S, Stilgenbauer S et al: Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997; 20: 399-407.
2. 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: 207-211.
3. Inazawa J, Inoue J, Imoto I: Comparative genomic hybridization (CGH)-arrays pave the way for identification of novel cancer-related genes. Cancer Sci 2004; 95: 559-563.
4. Oostlander AE, Meijer GA, Ylstra B: Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet 2004; 66: 488-495.
5. Pollack JR, Perou CM, Alizadeh AA et al: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999; 23: 41-46.
6. Ishkanian AS, Malloff CA, Watson SK et al: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004; 36: 299-303.
7. 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 USA 2002; 99: 12963-12968.
8. Dhami P, CDffey AJ, Abbs S et al: Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. Am J Hum Genet 2005; 76: 750-762.
9. Snijders AM, Nowak N, Segraves R et al: Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 2001; 29: 263-264.
10. Vissers LE, de Vries BB, Osoegawa K et al: Array-based comparative genomic hybridization for the genomewide detection of sub-microscopic chromosomal abnormalities. Am J Hum Genet 2003; 73: 1261-1270.
11. Fiegler H, Carr P, Douglas EJ et al: DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003; 36: 361-374.
12. Greshock J, Naylor TL, Margolin A et al: 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-187.
13. Snijders AM, Pinkel D, Albertson DG: Current status and future prospects of array-based comparative genomic hybridisation. Brief Funct Genomic Proteomic 2003; 2: 37-45.
14. Bignell GR, Huang J, Greshock J et al: High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004; 14: 287-295.
15. Kennedy GC, Matsuzaki H, Dong S et al: Large-scale genotyping of complex DNA. Nat Biotechnol 2003; 21: 1233-1237.
16. Zhao X, Li C, Paez JG et al: An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004; 64: 3060-3071.
17. Matsuzaki H, Dong S, Loi H et al: Genotyping over 100 000 SNPs on a pair of oligonucleotide arrays. Nat Meth 2004; 1: 109-111.
18. Brennan C, Zhang Y, Leo C et al: High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 2004; 64: 4744-4748.
19. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B: High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol 2004; 57: 644-646.
20. Barrett MT, Scheffer A, Ben-Dor A et al: Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci USA 2004; 101: 17765-17770.
21. Selzer RR, Richmond TA, Pofahl NJ et al: Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 2005; 44: 305-319.
22. Lucito R, Healy J, Alexander J et al: Representational oligonucleotide microarray analysis: A high-resolution method to detect genome copy number variation. Genome Res 2003; 13: 2291-2305.
23. Wang TL, Maierhofer C, Speicher MR et al: Digital karyotyping. Proc Natl Acad Sci USA 2002; 99: 16156-16161.
24. Tuzun E, Sharp AJ, Bailey JA et al: Fine-scale structural variation of the human genome. Nat Genet 2005; 37: 727-732.
25. Squire JA, Pei J, Marrano P et al: High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays. Genes Chromosomes Cancer 2003; 38: 215-225.
26. Pettus JA, Cowley BC, Maxwell T et al: Multiple abnormalities detected by dye reversal genomic microarrays in prostate cancer: A much greater sensitivity than conventional cytogenetics. Cancer Genet Cytogenet 2004; 154: 110-118.
27. Garnis C, Coe BP, Lam SL, Macaulay C, Lam WL: High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics 2005; 85: 790-793.
28. Coe BP, Henderson LJ, Garnis C et al: High-resolution chromosome arm 5p array CGH analysis of small cell lung carcinoma cell lines. Genes Chromosomes Cancer 2005; 42: 308-313.
29. Garnis C, Baldwin C, Zhang L, Rosin MP, Lam WL: Use of complete coverage array comparative genomic hybridization to define copy number alterations on chromosome 3p in oral squamous cell carcinomas. Cancer Res 2003; 63: 8582-8585.
30. Henderson LJ, Coe BP, Lee EH et al: Genomic and gene expression profiling of minute alterations of chromosome arm 1p in small-cell lung carcinoma cells. Br J Cancer 2005; 92: 1553-1560.
31. Garnis C, Davies JJ, Buys TP et al: Chromosome 5p aberrations are early events in lung cancer: Implication of glial cell line-derived neurotrophic factor in disease progression. Oncogene 2005; 24: 4806-4812.
32. Garnis C, Campbell J, Davies JJ, Macaulay C, Lam S, Lam WL: Involvement of multiple developmental genes on chromosome 1p in lung tumorigenesis. Hum Mol Genet 2005; 14: 475-482.
33. Seng TJ, Ichimura K, Liu L, Tingby O, Pearson DM, Collins VP: Complex chromosome 22 rearrangements in astrocytic tumors identified using microsatellite and chromosome 22 tile path array analysis. Genes Chromosomes Cancer 2005; 43: 181-193.
34. Buckley PG, Mantripragada KK, Benetkiewicz M et al: A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications. Hum Mol Genet 2002; 11: 3221-3229.
35. Holzmann K, Kohlhammer H, Schwaenen C et al: Genomic DNA-chip hybridization reveals a higher incidence of genomic amplifications in pancreatic cancer than conventional comparative genomic hybridization and leads to the identification of novel candidate genes. Cancer Res 2004; 64: 4428-4433.
36. Zielinski B, Gratias S, Toedt G et al: Detection of chromosomal imbalances in retinoblastoma by matrix-based comparative genomic hybridization. Genes Chromosomes Cancer 2005; 43: 294-301.
37. Takada H, Imoto I, Tsuda H et al: Screening of DNA copy-number aberrations in gastric cancer cell lines by array-based comparative genomic hybridization. Cancer Sci 2005; 96: 100-110.
38. Baldwin C, Garnis C, Zhang L, Rosin MP, Lam WL: Multiple microalterations detected at high frequency in oral cancer. Cancer Res 2005; 65: 7561-7567.
39. van Dekken H, Paris PL, Albertson DG; et al: Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis. Genes Chromosomes Cancer 2004; 39: 249-256.
40. Rubio-Moscardo F, Climent J, Siebert R et al: Mantle-cell lymphoma genotypes identified with CGH to BAC microarrays define a leukemic subgroup of disease and predict patient outcome. Blood 2005; 105: 4445-4454.
41. Pang E, Hu Y, Chan KY et al: Karyotypic imbalances and differential gene expressions in the acquired doxorubicin resistance of hepatocellular carcinoma cells. Lab Invest 2005; 85: 664-674.
42. Schwaenen C, Nessling M, Wessendorf S et al: Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci USA 2004; 101: 1039-1044.
43. Kohlhammer H, Schwaenen C, Wessendorf S et al: Genomic DNA-chip hybridization in t(11;14)-positive mantle cell lymphomas shows a high frequency of aberrations and allows a refined characterization of consensus regions. Blood 2004; 104: 795-801.
44. de Leeuw RJ, Davies JJ, Rosenwald A et al: Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet 2004; 13: 1827-1837.
45. Lim G, Karaskova J, Beheshti B et al: An integrated mBAND and submegabase resolution tiling set (SMRT) CGH array analysis of focal amplification, microdeletions, and ladder structures consistent with breakage-fusion-bridge cycle events in osteosarcoma. Genes Chromosomes Cancer 2005; 42: 392-403.
46. Coe BP, Lee EH, Chi B et al: Tiling genomic array profiling of small cell lung cancer cell lines identifies highly frequent copy number gains of MAD1L1. Genes Chromosomes Cancer 2005; 45: 11-19.
47. Garnis C, Lockwood WW, Vucic E et al: Comparing canonical non-small cell lung squamous and adenocarcinoma model genomes. Int J Cancer 2005; In Press.
48. Shaw-Smith C, Redon R, Rickman L et al: Microarray based comparative genomic hybridisation (array-CGH) detects submicroscopic chromosomal deletions and duplications in patients with learning disability/mental retardation and dysmorphic features. J Med Genet 2004; 41: 241-248.
49. Schaeffer AJ, Chung J, Heretis K, Wong A, Ledbetter DH, Lese Martin C: Comparative genomic hybridization-array analysis enhances the detection of aneuploidies and submicroscopic imbalances in spontaneous miscarriages. Am J Hum Genet 2004; 74: 1168-1174.
50. Klaassens M, van Dooren M, Eussen HJ et al: Congenital diaphragmatic hernia and chromosome 15q26: Determination of a candidate region by use of fluorescent in situ hybridization and array-based comparative genomic hybridization. Am J Hum Genet 2005; 76: 877-882.
51. Klein OD, Cotter PD, Albertson DG et al: Prader-Willi syndrome resulting from an unbalanced translocation: Characterization by array comparative genomic hybridization. Clin Genet 2004; 65: 477-482.
52. Zhang X, Snijders A, Segraves R et al: High-resolution mapping of genotype-phenotype relationships in cri-du-chat syndrome using array comparative genomic hybridization. Am J Hum Genet 2005; 76: 312-326.
53. Iafrate AJ, Feuk L, Rivera MN et al: Detection of large-scale variation in the human genome. Nat Genet 2004; 36: 949-951.
54. Sharp AJ, Locke DP, McGrath SD et al: Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005; 77: 78-88.
55. Sebat J, Lakshmi B, Troge J et al: Large-scale copy number polymorphism in the human genome. Science 2004; 305: 525-528.
56. Locke DP, Segraves R, Carbone L et al: Large-scale variation among human and great ape genomes determined by array comparative genomic hybridization. Genome Res 2003; 13: 347-357.
57. Fortna A, Kim Y, MacLaren E et al: Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol 2004; 2: E207.
58. Bejjani BA, Saleki R, Ballif BC et al: Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am J Med Genet A 2005; 134: 259-267.
59. Yu W, Ballif BC, Kashork CD et al: Development of a comparative genomic hybridization microarray and demonstration of its utility with 25 well-characterized 1p36 deletions. Hum Mol Genet 2003; 12: 2145-2152.
60. Cheung SW, Shaw CA, Yu W et al: Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet Med 2005; 7: 422-432.
61. Wilton L, Williamson R, McBain J, Edgar D, Voullaire L: Birth of a healthy infant after preimplantation confirmation of euploidy by comparative genomic hybridization. N Engl J Med 2001; 345: 1537-1541.
62. Larrabee PB, Johnson KL, Pestova E et al: Microarray analysis of cell-free fetal DNA in amniotic fluid: A prenatal molecular karyotype. Am J Hum Genet 2004; 75: 485-491.
63. Jong K, Marchiori E, Meijer G, Vaart AV, Ylstra B: Breakpoint identification and smoothing of array comparative genomic hybridization data. Bioinformatics 2004; 20: 3636-3637.
64. Kim SYA Nam SW, Lee SH et al: ArrayCyGHt: a web application for analysis and visualization of array-CGH data. Bioinformatics 2005; 21: 2554-2555.
65. Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G: Caryoscope: an Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004; 5: 151.
66. MargoliA AA, Greshock J, Naylor TL et al: CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics 2005; 21: 3308-3311.
67. Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R: CGHPRO - a comprehensive data analysis tool for array CGH. BMC Bioinformatics 2005; 6: 85.
68. Lingjaerde OC, Baumbusch LO, Liestol K, Glad IK, Borresen-Dale AL: CGH-Explorer: A program for analysis of array-CGH data. Bioinformatics 2005; 21: 821-822.
69. Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R: A method for calling gains and losses in array CGH data. Biostatistics 2005; 6: 45-58.
70. Autio R, Hautaniemi S, Kauraniemi P et al: CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics 2003; 19: 1714-1715.
71. Myers CL, Dunham MJ, Kung SY, Troyanskaya OG: Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 2004; 20: 3533-3543.
72. Yi Y, Mirosevich J, Shyr Y, Matusik R, George Jr AL: Coupled analysis of gene expression and chromosomal location. Genomics 2005; 85: 401-412.
73. WAng J, Meza-Zepeda LA, Kresse SH, Myklebost O: M-CGH: analysing microarray-based CGH experiments. BMC Bioinformatics 2004; 5: 74.
74. Beheshti B, Braude I, Marrano P, Thorner P, Zielenska M, Squire JA: Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. Neoplasia 2003; 5: 53-62.
75. Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH - a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004; 5: 13.
76. Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D: Fully automatic quantification of microarray image data. Genome Res 2002; 12: 325-332.
77. Weber M, Davies JJ, Wittig D et al: Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005; 37: 853-862.