Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia

Haematologica

Volumn 96, Issue 8, 2011, Pages 1161-1169

  Gunnarsson, Rebeqa ^a,b   Mansouri, Larry ^b   Isaksson, Anders ^b   Göransson, Hanna ^b   Cahill, Nicola ^b   Jansson, Mattias ^b   Rasmussen, Markus ^b   Lundin, Jeanette ^c   Norin, Stefan ^c   Buhl, Anne Mette ^d   Smedby, Karin Ekstr̈m ^e   Hjalgrim, Henrik ^f   Karlsson, Karin ^a   Jurlander, Jesper ^d   Geisler, Christian ^d   Juliusson, Gunnar ^a   Rosenquist, Richard ^b  

^a LUND UNIVERSITY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^d Rigshospitalet   (Denmark)

^e KAROLINSKA INSTITUTE   (Sweden)

^f STATENS SERUM INSTITUT   (Denmark)

Author keywords

Chronic lymphocytic leukemia; Clonal evolution; CNN LOH; Genomic aberrations; SNP array

Indexed keywords

IMMUNOGLOBULIN HEAVY CHAIN;

ADULT; AGED; ARTICLE; CHROMOSOME 10Q; CHROMOSOME 11Q; CHROMOSOME 13Q; CHROMOSOME 14; CHROMOSOME 17P; CHROMOSOME 2; CHROMOSOME 4; CHROMOSOME 6Q; CHROMOSOME 8; CHROMOSOME 8P; CHROMOSOME 9P; CHROMOSOME ABERRATION; CHROMOSOME DELETION; CHROMOSOME DELETION 11; CHROMOSOME DELETION 13; CHROMOSOME DELETION 17; CHRONIC LYMPHATIC LEUKEMIA; COHORT ANALYSIS; CONTROLLED STUDY; COPY NUMBER VARIATION; FOLLOW UP; GENE; GENE MUTATION; GENETIC SCREENING; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; IGHV GENE; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; OVERALL SURVIVAL; PROGNOSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TRISOMY 12;

ADOLESCENT; ADULT; AGED; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 13; DNA COPY NUMBER VARIATIONS; FOLLOW-UP STUDIES; GENOME, HUMAN; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; LOSS OF HETEROZYGOSITY; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROGNOSIS; SURVIVAL ANALYSIS; YOUNG ADULT;

EID: 79961059215     PISSN: 03906078     EISSN: 15928721     Source Type: Journal    
DOI: 10.3324/haematol.2010.039768     Document Type: Article

References (36)

1. Damle RN, Wasil T, Fais F, Ghiotto F, Valetto A, Allen SL, et al. Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood. 1999;94(6):1840-7.
2. Dohner H, Stilgenbauer S, Benner A, Leupolt E, Krober A, Bullinger L, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med. 2000;343(26):1910-6.
3. Hamblin TJ, Davis Z, Gardiner A, Oscier DG, Stevenson FK. Unmutated Ig V(H) genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood. 1999;94(6):1848-54.
4. Juliusson G, Oscier DG, Fitchett M, Ross FM, Stockdill G, Mackie MJ, et al. Prognostic subgroups in B-cell chronic lymphocytic leukemia defined by specific chromosomal abnormalities. N Engl J Med. 1990;323(11):720-4.
5. Juliusson G, Robert KH, Ost A, Friberg K, Biberfeld P, Nilsson B, et al. Prognostic information from cytogenetic analysis in chronic B-lymphocytic leukemia and leukemic immunocytoma. Blood. 1985;65 (1):134-41.
6. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA. 2002;99(24):15524-9.
7. Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med. 2005;353 (17):1793-801.
8. Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, Dumitru CD, et al. MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA. 2004;101(32):11755-60.
9. Cimmino A, Calin GA, Fabbri M, Iorio MV, Ferracin M, Shimizu M, et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA. 2005;102 (39):13944-9.
10. Klein U, Lia M, Crespo M, Siegel R, Shen Q, Mo T, et al. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell. 2010;17(1):28-40.
11. Dicker F, Herholz H, Schnittger S, Nakao A, Patten N, Wu L, et al. The detection of TP53 mutations in chronic lymphocytic leukemia independently predicts rapid disease progression and is highly correlated with a complex aberrant karyotype. Leu - kemia. 2009;23(1):117-24.
12. Forconi F, Rinaldi A, Kwee I, Sozzi E, Raspadori D, Rancoita PM, et al. Genomewide DNA analysis identifies recurrent imbalances predicting outcome in chronic lymphocytic leukaemia with 17p deletion. Br J Haematol. 2008;143(4):532-6.
13. Haferlach C, Dicker F, Schnittger S, Kern W, Haferlach T. Comprehensive genetic characterization of CLL: a study on 506 cases analysed with chromosome banding analysis, interphase FISH, IgV(H) status and immunophenotyping. Leukemia. 2007;21 (12):2442-51.
14. Chapiro E, Leporrier N, Radford-Weiss I, Bastard C, Mossafa H, Leroux D, et al. 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(1):63-8.
15. Gunn SR, Mohammed MS, Gorre ME, Cotter PD, Kim J, Bahler DW, et al. Wholegenome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J Mol Diagn. 2008;10(5):442-51.
16. Pfeifer D, Pantic M, Skatulla I, Rawluk J, Kreutz C, Martens UM, et al. Genomewide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood. 2007;109(3):1202-10.
17. Gunn SR, Bolla AR, Barron LL, Gorre ME, Mohammed MS, Bahler DW, et al. Array CGH analysis of chronic lymphocytic leukemia reveals frequent cryptic monoallelic and biallelic deletions of chromosome 22q11 that include the PRAME gene. Leuk Res. 2009;33(9):1276-81.
18. Gunnarsson R, Isaksson A, Mansouri M, Goransson H, Jansson M, Cahill N, et al. 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. 2009;24(1):211-5.
19. Mosca L, Fabris S, Lionetti M, Todoerti K, Agnelli L, Morabito F, et al. Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion. Clin Cancer Res. 2010;16(23):5641-53.
20. Ouillette P, Erba H, Kujawski L, Kaminski M, Shedden K, Malek SN. Integrated genomic profiling of chronic lymphocytic leukemia identifies subtypes of deletion 13q14. Cancer Res. 2008;68(4):1012-21.
21. Lehmann S, Ogawa S, Raynaud SD, Sanada M, Nannya Y, Ticchioni M, et al. Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia. Cancer. 2008;112(6):1296-305.
22. Berkova A, Zemanova Z, Trneny M, Schwarz J, Karban J, Cmunt E, et al. Clonal evolution in chronic lymphocytic leukemia studied by interphase fluorescence in-situ hybridization. Neoplasma. 2009;56(5):455-8.
23. Finn WG, Kay NE, Kroft SH, Church S, Peterson LC. Secondary abnormalities of chromosome 6q in B-cell chronic lymphocytic leukemia: a sequential study of karyotypic instability in 51 patients. Am J Hematol. 1998;59(3):223-9.
24. Juliusson G, Friberg K, Gahrton G. Consistency of chromosomal aberrations in chronic B-lymphocytic leukemia. A longitudinal cytogenetic study of 41 patients. Cancer. 1988;62(3):500-6.
25. Juliusson G, Friberg K, Gahrton G. Chromo somal aberrations in progressive and indolent chronic B-lymphocytic leu - kaemia. A longitudinal study. Acta Oncol. 1988;27(5):473-7.
26. Nowell PC, Moreau L, Growney P, Besa EC. Karyotypic stability in chronic B-cell leukemia. Cancer Genet Cytogenet. 1988; 33(2):155-60.
27. Oscier D, Fitchett M, Herbert T, Lambert R. Karyotypic evolution in B-cell chronic lymphocytic leukaemia. Genes Chromosomes Cancer. 1991;3(1):16-20.
28. Shanafelt TD, Witzig TE, Fink SR, Jenkins RB, Paternoster SF, Smoley SA, et al. Prospective evaluation of clonal evolution during long-term follow-up of patients with untreated early-stage chronic lymphocytic leukemia. J Clin Oncol. 2006;24(28): 4634-41.
29. Stilgenbauer S, Sander S, Bullinger L, Benner A, Leupolt E, Winkler D, et al. Clonal evolution in chronic lymphocytic leukemia: acquisition of high-risk genomic aberrations associated with unmutated VH, resistance to therapy, and short survival. Haematologica. 2007;92(9):1242-5.
30. Smedby KE, Hjalgrim H, Melbye M, Torrang A, Rostgaard K, Munksgaard L, et al. Ultraviolet radiation exposure and risk of malignant lymphomas. J Natl Cancer Inst. 2005;97(3):199-209.
31. Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio F, Dighiero G, Dohner H, et al. Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines. Blood. 2008;111 (12):5446-56.
32. Rabbee N, Speed TP. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics. 2006;22(1):7-12.
33. Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, et al. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res. 2006;16(9):1149-58.
34. Strefford JC, Parker H, Parker A, Robinson H, Chaplin T, Chen XH, et al. 13q deletion size predicts disease progression and response to treatment in patients with chronic lymphocytic leukaemia. Blood. 2009;114(22):280-1.
35. Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, et al. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood. 2009;113(6):1294-303.
36. Goransson H, Edlund K, Rydaker M, Rasmussen M, Winquist J, Ekman S, et al. Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data. PLoS One. 2009;4(6):e6057.