Array comparative genomic hybridization detects chromosomal abnormalities in hematological cancers that are not detected by conventional cytogenetics

Journal of Molecular Diagnostics

Volumn 12, Issue 5, 2010, Pages 670-679

  Shao, Lina ^a   Kang, Sung Hae L ^a   Li, Jian ^a   Hixson, Patricia ^a   Taylor, Jesalyn ^b   Yatsenko, Svetlana A ^a   Shaw, Chad A ^a   Milosavljevic, Aleksandar ^a   Chang, Chung Che ^b,c   Cheung, Sau Wai ^a   Patel, Ankita ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b HOUSTON METHODIST RESEARCH INSTITUTE   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; BCL11A GENE; BLOOD SAMPLING; BURKITT LYMPHOMA; CHROMOSOME 10; CHROMOSOME 15; CHROMOSOME 19; CHROMOSOME 22; CHROMOSOME 8; CHROMOSOME ABERRATION; CHROMOSOME DELETION; CHROMOSOME REARRANGEMENT; CHROMOSOME TRANSLOCATION; CHRONIC LYMPHATIC LEUKEMIA; CHRONIC MYELOMONOCYTIC LEUKEMIA; COPY NUMBER VARIATION; CYTOGENETICS; FLUORESCENCE IN SITU HYBRIDIZATION; FOLLOW UP; GENE; GENOMIC IN SITU HYBRIDIZATION; HEMATOLOGIC MALIGNANCY; HUMAN; HUMAN CELL; HUMAN TISSUE; ISOCHROMOSOME; ISOCHROMOSOME 17Q; LARGE CELL LYMPHOMA; MULTIPLE MYELOMA; MYELODYSPLASTIC SYNDROME; MYELOPROLIFERATIVE DISORDER; NONHODGKIN LYMPHOMA; PARTIAL TRISOMY 10; PILOT STUDY; PROTO ONCOGENE; TETRASOMY; TETRASOMY 11; THROMBOCYTHEMIA; TRISOMY; TRISOMY 14; TRISOMY 15; TRISOMY 19; TRISOMY 22;

EID: 77956866811     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2010.090192     Document Type: Article

References (49)

1. Slavotinek AM: Novel microdeletion syndromes detected by chromosome microarrays. Hum Genet 2008, 124:1-17
2. Hastings PJ, Lupski JR, Rosenberg SM, Ira G: Mechanisms of change in gene copy number. Nat Rev Genet 2009, 10:551-564
3. Mefford HC, Eichler EE: Duplication hotsposts, rare genomic disorders, and common disease. Curr Opin Genet Dev 2009, 19:196-204
4. Kallioniemi A: CGH microarrays and cancer. Curr Opin Biotechnol 2008, 19:36-40
5. Costa JL, Meijer G, Ylstra B, Caldas C: Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies. Semin Radiat Oncol 2008, 18:98-104 (Pubitemid 351296452)
6. Watson SK, deLeeuw RJ, Horsman DE, Squire JA, Lam WL: Cytogenetically balanced translocations are associated with focal copy number alterations. Hum Genet 2007, 120:795-805
7. Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H, Thiele J, Vardiman JW (eds): WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, 4th ed. Lyon, IARC Press, 2008
8. van Vlierberghe P, Meijerink JP, Lee C, Ferrando AA, Look AT, van Wering ER, Beverloo HB, Aster JC, Pieters R: A new recurrent 9q34 duplication in pediatric T-cell acute lymphoblastic leukemia. Leukemia 2006, 20:1245-1253
9. Schwaenen C, Nessling M, Wessendorf S, Salvi T, Wrobel G, Radlwimmer B, Kestler HA, Haslinger C, Stilgenbauer S, Döhner H, Bentz M, Lichter P: 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
10. Patel A, Kang SH, Lennon PA, Li YF, Rao PN, Abruzzo L, Shaw C, Chinault AC, Cheung SW: Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia. Am J Hematol 2008, 83:540-546
11. Gunn SR, Mohammed MS, Gorre ME, Cotter PD, Kim J, Bahler DW, Preobrazhensky SN, Higgins RA, Bolla AR, Ismail SH, de Jong D, Eldering E, van Oers MH, Mellink CH, Keating MJ, Schlette EJ, Abruzzo LV, Robetorye RS: Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J Mol Diagn 2008, 10:442-451
12. Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572 (Pubitemid 41180205)
13. Lu X, Shaw CA, Patel A, Li J, Cooper ML, Wells WR, Sullivan CM, Sahoo T, Yatsenko SA, Bacino CA, Stankiewicz P, Ou Z, Chinault AC, Beaudet AL, Lupski JR, Cheung SW, Ward PA: Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One 2007, 2:e327
14. McClure RF, Dewald GW, Hoyer JD, Hanson CA: Isolated isochromosome 17q: a distinct type of mixed myeloproliferative disorder/myelodysplastic syndrome with an aggressive clinical course. Br J Haematol 1999, 106:445-454
15. Shashaty GG, Baumiller RC: Philadelphia chromosome-negative chronic myelogenous leukemia with trisomy D. Arch Pathol Lab Med 1980, 104:376-378
16. Zaccaria A, Valenti AM, Donti E, Gozzetti A, Ronconi S, Spedicato F: Persistence of chromosomal abnormalities additional to the Philadelphia chromosome after Philadelphia chromosome disappearance during imatinib therapy for chronic myeloid leukemia. Haematologica 2007, 92:564-565
17. Morgan R, Chen Z, Stone JF, Cohen J, Gustafson E, Jolly PC, Sandberg AA: Trisomy 10: age and leukemic lineage associations. Cancer Genet Cytogenet 1996, 89:173-174 (Pubitemid 26286759)
18. Tabernero D, San Miguel JF, Garcia-Sanz M, Nájera L, García-Isidoro M, Peréz-Simon JA, Gonzalez M, Wiegant J, Raap AK, Orfão A: Incidence of chromosome numerical changes in multiple myeloma: fluorescence in situ hybridization analysis using 15 chromosomespecific probes. Am J Pathol 1996, 149:153-161
19. Cremer FW, Kartal M, Hose D, Bila J, Buck I, Bellos F, Raab MS, Brough M, Moebus A, Hager HD, Goldschmidt H, Moos M, Bartram CR, Jauch A: High incidence and intraclonal heterogeneity of chromosome 11 aberrations in patients with newly diagnosed multiple myeloma detected by multiprobe interphase FISH. Cancer Genet Cytogenet 2005, 161:116-124
20. Di Bernardo MC, Crowther-Swanepoel D, Broderick P, Webb E, Sellick G, Wild R, Sullivan K, Vijayakrishnan J, Wang Y, Pittman AM, Sunter NJ, Hall AG, Dyer MJ, Matutes E, Dearden C, Mainou-Fowler T, Jackson GH, Summerfield G, Harris RJ, Pettitt AR, Hillmen P, Allsup DJ, Bailey JR, Pratt G, Pepper C, Fegan C, Allan JM, Catovsky D, Houlston RS: A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia. Nat Genet 2008, 40:1204-1210
21. Usvasalo A, Savola S, Räty R, Vettenranta K, Harila-Saari A, Koistinen P, Savolainen ER, Elonen E, Saarinen-Pihkala UM, Knuutila S: CDKN2A deletions in acute lymphoblastic leukemia of adolescents and young adults: an array CGH study. Leuk Res 2008, 32: 1228-1235
22. Tsirigotis P, Pappa V, Labropoulos S, Papageorgiou S, Kontsioti F, Dervenoulas J, Papageorgiou E, Panani A, Mantzios G, Economopoulos T, Raptis S: Mutational and methylation analysis of the cyclindependent kinase 4 inhibitor (p16INK4A) gene in chronic lymphocytic leukemia. Eur J Haematol 2006, 76:230-236
23. Cazzaniga G, Tosi S, Aloisi A, Giudici G, Daniotti M, Pioltelli P, Kearney L, Biondi A: The tyrosine kinase abl-related gene ARG is fused to ETV6 in an AML-M4Eo patient with a t(1;12)(q25;p13): molecular cloning of both reciprocal transcripts. Blood 1999, 94:4370-4373
24. Fan YS, Rizkalla K, Barr RM: A new complex variant Philadelphia chromosome, t(1;9:22)ins(17;22), characterized by fluorescence in situ hybridization in an adult ALL. Leuk Res 1999, 23:1001-1006 (Pubitemid 29488646)
25. Balgobind BV, Van Vlierberghe P, van den Ouweland AM, Beverloo HB, Terlouw-Kromosoeto JN, van Wering ER, Reinhardt D, Horstmann M, Kaspers GJ, Pieters R, Zwaan CM, Van den Heuvel-Eibrink MM, Meijerink JP: Leukemia-associated NF1 inactivation in patients with pediatric T-ALL and AML lacking evidence for neurofibromatosis. Blood 2008, 111:4322-4328
26. Gunn SR, Hibbard MK, Ismail SH, Lowery-Nordberg M, Mellink CH, Bahler DW, Abruzzo LV, Enriquez EL, Gorre ME, Mohammed MS, Robetorye RS: Atypical 11q deletions identified by array CGH may be missed by FISH panels for prognostic markers in chronic lymphocytic leukemia. Leukemia 2009, 23:1011-1017
27. Cui Y, Ying Y, van Hasselt A, Ng KM, Yu J, Zhang Q, Jin J, Liu D, Rhim JS, Rha SY, Loyo M, Chan AT, Srivastava G, Tsao GS, Sellar GC, Sung JJ, Sidransky D, Tao Q: OPCML is a broad tumor suppressor for multiple carcinomas and lymphomas with frequently epigenetic inactivation. PLoS One 2008, 3:e2990
28. Christacos NC, Sherman L, Roy A, DeAngelo DJ, Dal Cin P: Is the cryptic interstitial deletion of 8q24 surrounding MYC a common mechanism in the formation of double minute chromosome? Cancer Genet Cytogenet 2005, 161:90-92
29. Pfeifer D, Pantic M, Skatulla I, Rawluk J, Kreutz C, Martens UM, Fisch P, Timmer J, Veelken H: Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood 2007, 109:1202-1210
30. Chapiro E, Leporrier N, Radford-Weiss I, Bastard C, Mossafa H, Leroux D, Tigaud I, De Braekeleer M, Terré C, Brizard F, Callet-Bauchu E, Struski S, Veronese L, Fert-Ferrer S, Taviaux S, Lesty C, Davi F, Merle-Béral H, Bernard OA, Sutton L, Raynaud SD, Nguyen-Khac F: Gain of the short arm of chromosome 2 (2p) is a frequent recurring chromosome aberration in untreated chronic lymphocytic leukemia (CLL) at advanced stages. Leuk Res 2010, 34:63-68
31. Hewamana S, Lin TT, Rowntree C, Karunanithi K, Pratt G, Hills R, Fegan C, Brennan P, Pepper C: Rel a is an independent biomarker of clinical outcome in chronic lymphocytic leukemia. J Clin Oncol 2009, 27:763-769
32. Forconi F, Rinaldi A, Kwee I, Sozzi E, Sozzi E, Raspadori D, Rancoita PM, Scandurra M, Rossi D, Deambrogi C, Capello D, Zucca E, Marconi D, Bomben R, Gattei V, Lauria F, Gaidano G, Bertoni F: Genome-wide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion. Br J Haematol 2008, 143:532-536
33. Sellmann L, Gesk S, Walter C, Ritgen M, Harder L, Martín-Subero JI, Schroers R, Siemer D, Nückel H, Dyer MJ, Dührsen U, Siebert R, Dürig J, Küppers R: Trisomy 19 is associated with trisomy 12 and mutated IGHV genes in B-chronic lymphocytic leukaemia. Br J Haematol 2007, 138:217-220
34. Nayak BN, Sokal J, Ray M: Clonal chromosomal changes in chronic lymphocytic leukemia. Cancer Lett 1990, 49:99-105 (Pubitemid 20081015)
35. Hook EB: Exclusion of chromosomal mosaicism: tables of 90%, 95% and 99% confidence limits and comments on use. Am J Hum Genet 1977, 29:94-97
36. Cheung SW, Shaw CA, Scott DA, Patel A, Sahoo T, Bacino CA, Pursley A, Li J, Erickson R, Gropman AL, Miller DT, Seashore MR, Summers AM, Stankiewicz P, Chinault AC, Lupski JR, Beaudet AL, Sutton VR: Microarray-based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics. Am J Med Genet A 2007, 143A:1679-1686
37. Ou Z, Kang SH, Shaw CA, Carmack CE, White LD, Patel A, Beaudet AL, Cheung SW, Chinault AC: Bacterial artificial chromosome-emulation oligonucleotide arrays for targeted clinical array-comparative genomic hybridization analyses. Genet Med 2008, 10:278-289
38. Li J, Yang T, Wang L, Yan H, Zhang Y, Guo Y, Pan F, Zhang Z, Peng Y, Zhou Q, He L, Zhu X, Deng H, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Cheng J, Deng HW :Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. PLoS One 2009, 4(11):e7958
39. Tyybä kinoja A, Elonen E, Piippo K, Porkka K, Knuutila S: Oligonucleotide array-CGH reveals cryptic gene copy number alterations in karyotypically normal acute myeloid leukemia. Leukemia 2007, 21:571-574
40. Viny AD, Lichtin A, Pohlman B, Loughran T, Maciejewski J: Chronic B-cell dyscrasias are an important clinical feature of T-LGL leukemia. Leuk Lymphoma 2008, 49:932-938 (Pubitemid 351942747)
41. Juliusson G, Oscier DG, Fitchett M, Ross FM, Stockdill G, Mackie MJ, Parker AC, Castoldi GL, Guneo A, Knuutila S, Elonen E, Gahrton G: Prognostic subgroups in B-cell chronic lymphocytic leukemia defined by specific chromosomal abnormalities. N Engl J Med 1990, 323:720-724
42. Gunnarsson R, Isaksson A, Mansouri M, Göransson H, Jansson M, Cahill N, Rasmussen M, Staaf J, Lundin J, Norin S, Buhl AM, Smedby KE, Hjalgrim H, Karlsson K, Jurlander J, Juliusson G, Rosenquist R: Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients. Leukemia 2010, 24:211-215
43. Starczynowski DT, Vercauteren S, Telenius A, Sung S, Tohyama K, Brooks-Wilson A, Spinelli JJ, Eaves CJ, Eaves AC, Horsman DE, Lam WL, Karsan A: High-resolution whole genome tiling path array CGH analysis of CD34+ cells from patients with low-risk myelodysplastic syndromes reveals cryptic copy number alterations and predicts overall and leukemia-free survival. Blood 2008, 112:3412-3424
44. Kolomietz E, Al-Maghrabi J, Brennan S, Karaskova J, Minkin S, Lipton J, Squire JA: Primary chromosomal rearrangements of leukemia are frequently accompanied by extensive submicroscopic deletions and may lead to altered prognosis. Blood 2001, 97:3581-3588
45. De Melo VA, Milojkovic D, Marin D, Apperley JF, Nacheva EP, Reid AG: Deletions adjacent to BCR and ABL1 breakpoints occur in a substantial minority of chronic myeloid leukemia patients with masked Philadelphia rearrangements. Cancer Genet Cytogenet 2008, 182:1111-1115
46. Vaz de Campos MG, Montesano FT, Rodrigues MM, Chauffaille Mde L: Clinical implications of der(9q) deletions detected through dualfusion fluorescence in situ hybridization in patients with chronic myeloid leukemia. Cancer Genet Cytogenet 2007, 178:49-56
47. Kreil S, Pfirrmann M, Haferlach C, Waghorn K, Chase A, Hehlmann R, Reiter A, Hochhaus A, Cross NC; German Chronic Myelogenous Leukemia (CML) Study Group: Heterogeneous prognostic impact of derivative chromosome 9 deletions in chronic myelogenous leukemia. Blood 2007, 110:1283-1290
48. Fourouclas N, Campbell PJ, Bench AJ, Swanton S, Baxter EJ, Huntly BJ, Green AR: Size matters: the prognostic implications of large and small deletions of the derivative 9 chromosome in chronic myeloid leukemia. Haematologica 2006, 91:952-955 (Pubitemid 44023150)
49. Dolan M, Peterson B, Hirsch B: Array-based comparative genomic hybridization characterizes a deletion associated with a t(15;17) in acute promyelocytic leukemia. Am J Clin Pathol 2008, 130:818-823