Construction and application of a zebrafish array comparative genomic hybridization platform

Genes Chromosomes and Cancer

Volumn 48, Issue 2, 2009, Pages 155-170

  Freeman, Jennifer L ^a,b,e   Ceol, Craig ^b,c   Feng, Hui ^b,d   Langenau, David M ^b,c   Belair, Cassandra ^b,c,f   Stern, Howard M ^a,g   Song, Anhua ^b,c   Paw, Barry H ^a,b   Look, A Thomas ^b,d   Zhou, Yi ^b,c   Zon, Leonard I ^b,c   Lee, Charles ^a,b  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c BOSTON CHILDREN S HOSPITAL   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e PURDUE UNIVERSITY   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g GENENTECH INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CANCER MODEL; CARCINOGENESIS; COMPARATIVE GENOMIC HYBRIDIZATION; CYTOGENETICS; GENETIC MODEL; GENOME ANALYSIS; MICROARRAY ANALYSIS; MOLECULAR CLONING; NONHUMAN; ONCOGENE; PRIORITY JOURNAL; TUMOR SUPPRESSOR GENE; ZEBRA FISH;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CHROMOSOMES, ARTIFICIAL, BACTERIAL; COMPARATIVE GENOMIC HYBRIDIZATION; DISEASE MODELS, ANIMAL; GENES, TUMOR SUPPRESSOR; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MELANOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENES; PRECURSOR T-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; REPRODUCIBILITY OF RESULTS; RHABDOMYOSARCOMA; ZEBRAFISH;

BACTERIA (MICROORGANISMS); DANIO RERIO;

EID: 59949103492     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20623     Document Type: Article

References (52)

1. Adams DJ, Dermitzakis ET, Cox T, Smith J, Davies R, Banerjee R, Bonfield J, Mullikin JC, Chung YJ, Rogers J, Bradley A. 2005. Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains. Nat Genet 37:532-536.
2. Amillet JM, Ferbus D, Real FX, Antony C, Muleris M, Gress TM, Goubin G. 2006. Characterization of human Rab20 overexpressed in exocrine pancreatic carcinoma. Hum Pathol 37:256-263.
3. Berghmans S, Jette C, Langenau D, Hsu K, Stewart R, Look T, Kanki JP. 2005. Making waves in cancer research: New models in the zebrafish. Biotechniques 39:227-237.
4. Bodmer D, Eleveld M, Kater-Baats E, Janssen I, Janssen B, Weterman M, Schoenmakers E, Nickerson M, Linehan M, Zbar B, van Kessel AG. 2002. Disruption of a novel MFS transporter gene, DIRC2, by a familial renal cell carcinoma-associated t(2;3)(q35;q21). Hum Mol Genet 11:641-649.
5. Bodmer D, Schepens M, Eleveld MJ, Schoenmakers EF, Geurts van Kessel A. 2003. Disruption of a novel gene, DIRC3-HSPBAP1 fusion transcripts in a case of familial renal cell cancer and t(2;3)(q35;q21). Genes Chromosomes Cancer 38:107-116.
6. Cai W, Mao J, Chow C, Damani S, Balmain A, Bradley A. 2002. Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat Biotech 20:393-396.
7. Chiba S. 1998. Homeobox genes in normal hematopoiesis and leukemogenesis. Int J Hematol 68:343-353.
8. Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, Pinkel D, Bastian BC. 2005. Distinct sets of genetic alterations in melanoma. N Engl J Med 353:2135-2147.
9. Davies JJ, Wilson IM, Lam WL. 2005. Array CGH technologies and their applications to cancer genomes. Chromosome Res 13:237-248.
10. Feng H, Langenau DM, Madge JA, Quinkertz A, Gutierrez A, Neuberg DS, Kanki JP, Look AT. 2007. Heat-shock induction of T-cell lymphoma/leukemia in conditional Cre/lox-regulated transgenic zebrafish. Br J Haematol 138:169-175.
11. Fiegler H, Redon R, Carter NP. 2007. Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes. Nat Protocols 2:577-587.
12. FitzGerald KT, Diaz MO. 1999. MLL2: A new mammalian member of the trx/MLL family of genes. Genomics 59:187-192.
13. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, Altshuler DM, Aburatani H, Jones KW, Tyler-Smith C, Hurles ME, Carter NP, Scherer SW, Lee C. 2006. Copy number variation: New insights in genome diversity. Genome Res 16:949-961.
14. Freeman JL, Adeniyi A, Banerjee R, Dallaire S, Maguire SF, Chi J, Ng BL, Zepeda C, Humphray S, Rogers J, Zhou Y, Zon LI, Carter NP, Yang F, Lee C. 2007. Definition of the zebrafish genome using flow cytometry and cytogeneticmapping. BMC Genomics8:195.
15. Fujii C, Nakamoto Y, Lu P, Tsuneyama K, Popivanova BK, Kaneko S, Mukaida N. 2005. Aberrant expression of serine/threonine kinase Pim-3 in hepatocellular carcinoma development and its role in the proliferation of human hepatoma cell lines. Int J Cancer 114:209-218.
16. Fujiwara S, Yamashita Y, Choi YL, Watanabe H, Kurashina K, Soda M, Enomoto M, Hatanaka H, Takada S, Ozawa K, Mano H. 2007. Transforming activity of purinergic receptor P2Y, G protein coupled, 8 revealed by retroviral expression screening. Leuk Lymphoma 48:978-986.
17. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, Lee C, Wagner SN, Li C, Golub TR, Rimm DL, Meyerson ML, Fisher DE, Sellers WR. 2005. Integrative genomic analyses identify MITF as a lineage survival oncogenes amplified in malignant melanoma. Nature 436:117-122.
18. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud J, Ley JL. 2007. A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3:e3.
19. Hegde GV, Munger CM, Emanuel K, Joshi AD, Greiner TC, Weisenburger DD, Vose JM, Joshi SS. 2008. Targeting of sonic hedgehog-GLI signaling: A potential strategy to improve therapy for mantel cell lymphoma. Mol Cancer Ther 7:1450-1460.
20. Hodgson G, Hager JH, Volik S, Hariono S, Wernick M, Moore D, Albertson DG, Pinkel D, Collins C, Hanahan D, Gray JW. 2001. Genome scanning with array CGH delineates regional alterations in mouse islet carcinomas. Nat Genet 29:459-464.
21. Huang S, Qiu Y, Stein RW, Brandt SJ. 1999. p300 functions as a transcriptional coactivator for the TAL1/SCL oncoprotein. Oncogene 18:4958-4967.
22. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human genome. Nat Genet 36:949-951.
23. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D. 1992. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818-821.
24. Krause K, Karger S, Sheu SY, Aigner T, Kursawe R, Gimm O, Schmid KW, Dralle H, Fuhrer D. 2008. Evidence for a role of the amyloid precursor protein in thyroid carcinogenesis. J Endocrinol 198:291-9.
25. Lakshmi B, Hall IM, Egan C, Alexander J, Leotta A, Healy J, Zender L, Spector MS, Xue W, Lowe SW, Wigler M, Lucito R. 2006. Mouse genomic representational oligonucleotide microarray analysis: Detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci USA 103:11234-11239.
26. Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, Tong Y, Zhan H, Govindarajan KR, Lee S, Mathavan S, Murthy KR, Buhler DR, Liu ET, Gong Z. 2006. Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat Biotech 24:73-75.
27. Langenau DM, Traver D, Ferrando AA, Kutok JL, Aster JC, Kanki JP, Lin S, Prochownik E, Trede NS, Zon LI, Look TA. 2003. Mycinduced T cell leukemia in transgenic zebrafish. Science 299:887-890.
28. Langenau DM, Feng H, Berghmans S, Kanki JP, Kutok JL, Look AT. 2005. Cre/lox-regulated transgenic zebrafish model with conditional myc-induced T cell acute lymphoblastic leukemia. Proc Natl Acad Sci USA 102:6068-6073.
29. Langenau DM, Keefe MD, Storer NY, Guyon JR, Kutok JL, Le X, Goessling W, Neuberg DS, Kunkel LM, Zon LI. 2007. Effects of RAS on the genesis of embryonal rhabdomyosarcoma. Genes Dev 21:1382-1395.
30. Lawrence HJ, Sauvageau G, Humphries RK, Largman C. 1996. The role of HOX homeobox genes in normal and leukemic hematopoiesis. Stem Cells 14:281-291.
31. Lee C, Smith A. 2004. Molecular cytogenetic methodologies and bacterial artificial chromosome (BAC) probe panel resource for genomic analyses in zebrafish. Method Cell Biol 77:241-254.
32. Li J, Jiang T, Mao JH, Balmain A, Peterson L, Harris C, Rao PH, Havlak P, Gibbs R, Cai WW. 2004. Genomic segmental polymorphisms in inbred mouse strains. Nat Genet 36:952-954.
33. Li YY, Popivanova BK, Nagai Y, Ishikura H, Fujii C, Mukaida N. 2006. Pim-3, a proto-oncogene with serine/threonine kinase activity, is aberrantly expressed in human pancreatic cancer and phosphorylates bad to block bad-mediated apoptosis in human pancreatic cancer cell lines. Cancer Res 66:6741-6747.
34. Lieschke GJ, Currie PD. 2007. Animal models of human disease: Zebrafish swim into view. Nat Rev Genet 8:353-367.
35. Lin WM, Baker AC, Beroukhim R, Winckler W, Feng W, Marmion JM, Laine E, Greulich H, Tseng H, Gates C, Hodi FS, Dranoff G, Sellers WR, Thomas RK, Meyerson M, Golub TR,
36. Dummer R, Herlyn M, Getz G, Garraway LA. 2008. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res 68:664-673.
37. Maydan JS, Filbotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas JH, Moerman DG. 2007. Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res 17:337-347.
38. Nowak NJ, Gaile D, Conroy JM, McQuaid D, Cowell J, Carter R, Goggins MG, Hruban RH, Maitra A. 2005. Genome-wide aberrations in pancreatic adenocarcinoma. Cancer Genet Cytogen 161:36-50.
39. Patton EE, Widlund HR, Kutok JL, Kopani KR, Amatruda JF, Murphey RD, Berghmans S, Mayhall EA, Traver D, Fletcher CDM, Aster JC, Granter SR, Look AT, Lee C, Fisher DE, Zon LI. 2005. BRAF mutations are sufficient to promote nevi formation and cooperate with p53 in the genesis of melanoma. Curr Biol 15:249-254.
40. Perry GH, Tchinda J, McGrath SD, Zhang J, Picker SR, Caceres AM, Iafrate AJ, Tyler-Smith C, Scherer SW, Eichler EE, Stone AC, Lee C. 2006. Hotspots for copy number variation in chimpanzees and humans. Proc Natl Acad Sci USA 103:8006-8011.
41. Pinkel D, Albertson DG. 2005. Comparative genomic hybridization. Annu Rev Genomics Hum Genet 6:331-354.
42. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Dairkee SH, Ljung B, Gray JW. 1998. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207-211.
43. Prasad R, Zhadanov AB, Sedkov Y, Bullrich F, Druck T, Rallapalli R, Yano T, Alder H, Croce CM, Huebner K, Mazo A, Canaani E. 1997. Structure and expression pattern of human ALR, a novel gene with strong homology to ALL-1 involved in acute leukemia and to Drosophila trithorax. Oncogene 15:549-560.
44. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, Cho EK, Dallaire S, Freeman JL, Gonzalez JR, Gratacos M, Huang J, Kalaitzopoulos D, Komura D, MacDonald JR, Marshall CR, Mei R, Montgomery L, Nishimura K, Okamura K, Shen F, Somerville MJ, Tchinda J, Valsesia A, Woodwark C, Yang F, Zhang J, Zerjal T, Zhang J, Armengol L, Conrad DF, Estivill X, Tyler-Smith C, Carter NP, Aburatani H, Lee C, Jones KW, Scherer SW, Hurles M. 2006. Global variation in copy number in the human genome. Nature 444:444-454.
45. Ruano Y, Mollejo M, Ribalta T, Fiano C, Camacho FI, Gomez E, de Lope AR, Hernandez-Moneo JL, Martinez P, Melendez B. 2006. Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling. Mol Cancer 5:39.
46. Ryu B, Kim DS, Deluca AM, Alani RM. 2007. Comprehensive expression profiling of tumor cell lines identifies molecular signatures of melanoma progression. PLoS ONE 2:e594.
47. Sander S, Bullinger L, Karlsson A, Giuriato S, Hernandez-Boussard T, Felsher DW, Pollack JR. 2005. Comparative genomic hybridization on mouse cDNA microarrays and its application to a murine lymphoma model. Oncogene 24:6101-6107.
48. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M. 2004. Large-scale copy number polymorphism in the human genome. Science 305:525-528.
49. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P. 1997. Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399-407.
50. Thomas R, Duke SE, Bloom SK, Breen TE, Young AC, Feiste E, Seiser EL, Tsai PC, Langford CF, Ellis P, Karlsson EK, Lindblad-Toh K, Breen M. 2007. A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. J Hered 98:474-484.
51. van den Boom J, Wolter M, Kuick R, Misek DE, Youkilis AS, Wechsler DS, Sommer C, Reifenberger G, Hanash SM. 2003. Characterization of gene expression profiles associated with glioma progression using oligonucleotide-based microarray analysis and real-time reverse transcription-polymerase chain reaction. Am J Pathol 163:1033-1043.
52. Zheng HC, Tsuneyama K, Takahashi H, Miwa S, Sugiyama T, Popivanova BK, Fujii C, Nomoto K, Mukaida N, Takano Y. 2008. Aberrant Pim-3 expression is involved in gastric adenoma- adenocarcinoma sequence and cancer progression. J Cancer Res Clin Oncol 134:481-488.