Exploring the genetic landscape in chronic lymphocytic leukemia using high-resolution technologies

References

• Dohner H, Stilgenbauer S, Benner A, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000; 343:1910–1916.
   PubMed Web of Science ®Google Scholar
• Gunnarsson R, Mansouri L, Isaksson A, et al. Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia. Haematologica 2011;96:1161–1169.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Coe BP, Ylstra B, Carvalho B, et al. Resolving the resolution of array CGH. Genomics 2007;89:647–653.
   PubMed Web of Science ®Google Scholar
• Gaasenbeek M, Howarth K, Rowan AJ, et al. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers. Cancer Res 2006;66:3471–3479.
   PubMed Web of Science ®Google Scholar
• Greshock J, Feng B, Nogueira C, et al. A comparison of DNA copy number profiling platforms. Cancer Res 2007;67:10173–10180.
   PubMed Web of Science ®Google Scholar
• Gunnarsson R, Staaf J, Jansson M, et al. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 2008;47:697–711.
   PubMed Web of Science ®Google Scholar
• Hagenkord JM, Monzon FA, Kash SF, et al. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. J Mol Diagn 2010;12:184–196.
   PubMed Web of Science ®Google Scholar
• Hehir-Kwa JY, Egmont-Petersen M, Janssen IM, et al. Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res 2007;14:1–11.
   PubMed Web of Science ®Google Scholar
• Kloth JN, Oosting J, van Wezel T, et al. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer. BMC Genomics 2007;8:53.
   PubMed Web of Science ®Google Scholar
• Wicker N, Carles A, Mills IG, et al. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 2007;8:84.
   PubMed Web of Science ®Google Scholar
• Patel A, Kang SH, Lennon PA, et al. Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia. Am J Hematol 2008;83:540–546.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Mosca L, Fabris S, Lionetti M, et al. Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion. Clin Cancer Res 2010;16:5641–5653.
   PubMed Web of Science ®Google Scholar
• Ouillette P, Erba H, Kujawski L, et al. Integrated genomic profiling of chronic lymphocytic leukemia identifies subtypes of deletion 13q14. Cancer Res 2008;68:1012–1021.
   PubMed Web of Science ®Google Scholar
• Calin GA, Dumitru CD, Shimizu M, 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; 99:15524–15529.
   PubMed Web of Science ®Google Scholar
• Cimmino A, Calin GA, Fabbri M, et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 2005;102: 13944–13949.
   PubMed Web of Science ®Google Scholar
• Kitada S, Andersen J, Akar S, et al. Expression of apoptosis-regulating proteins in chronic lymphocytic leukemia: correlations with in vitro and in vivo chemoresponses. Blood 1998;91:3379–3389.
   PubMed Web of Science ®Google Scholar
• Klein U, Lia M, Crespo M, et al. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 2010;17:28–40.
   PubMed Web of Science ®Google Scholar
• Lia M, Carette A, Tang H, et al. Functional dissection of the chromosome 13q14 tumor-suppressor locus using transgenic mouse lines. Blood 2012;119:2981–2990.
   PubMed Web of Science ®Google Scholar
• Mian M, Rinaldi A, Mensah AA, et al. Del(13q14.3) length matters: an integrated analysis of genomic, fluorescence in situ hybridization and clinical data in 169 chronic lymphocytic leukaemia patients with 13q deletion alone or a normal karyotype. Hematol Oncol 2012;30:46–49.
   PubMed Web of Science ®Google Scholar
• Parker H, Rose-Zerilli MJ, Parker A, et al. 13q deletion anatomy and disease progression in patients with chronic lymphocytic leukemia. Leukemia 2011;25:489–497.
   PubMed Web of Science ®Google Scholar
• Gunnarsson R, Isaksson A, Mansouri M, 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 2010;24:211–215.
   PubMed Web of Science ®Google Scholar
• Lehmann S, Ogawa S, Raynaud SD, et al. Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia. Cancer 2008;112:1296–1305.
   PubMed Web of Science ®Google Scholar
• Pfeifer D, Pantic M, Skatulla I, et al. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood 2007;109:1202–1210.
   PubMed Web of Science ®Google Scholar
• Chapiro E, Leporrier N, Radford-Weiss I, 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;34:63–68.
   PubMed Web of Science ®Google Scholar
• Grubor V, Krasnitz A, Troge JE, et al. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood 2009;113:1294–1303.
   PubMed Web of Science ®Google Scholar
• Deambrogi C, De Paoli L, Fangazio M, et al. Analysis of the REL, BCL11A, and MYCN proto-oncogenes belonging to the 2p amplicon in chronic lymphocytic leukemia. Am J Hematol 2010;85:541–544.
   PubMed Web of Science ®Google Scholar
• Brown JR, Hanna M, Tesar B, et al. Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res 2012;18:3791–3802.
   PubMed Web of Science ®Google Scholar
• Edelmann J, Holzmann K, Miller F, et al. High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Blood 2012 Oct 9. [Epub ahed of print]
   Web of Science ®Google Scholar
• Kujawski L, Ouillette P, Erba H, et al. Genomic complexity identifies patients with aggressive chronic lymphocytic leukemia. Blood 2008;112:1993–2003.
   PubMed Web of Science ®Google Scholar
• Stephens PJ, Greenman CD, Fu B, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011;144:27–40.
   PubMed Web of Science ®Google Scholar
• Berkova A, Zemanova Z, Trneny M, et al. Clonal evolution in chronic lymphocytic leukemia studied by interphase fluorescence in-situ hybridization. Neoplasma 2009;56:455–458.
   PubMed Web of Science ®Google Scholar
• Finn WG, Kay NE, Kroft SH, et al. Secondary abnormalities of chromosome 6q in B-cell chronic lymphocytic leukemia: a sequential study of karyotypic instability in 51 patients. Am J Hematol 1998;59:223–229.
   PubMed Web of Science ®Google Scholar
• Juliusson G, Friberg K, Gahrton G. Consistency of chromosomal aberrations in chronic B-lymphocytic leukemia. A longitudinal cytogenetic study of 41 patients. Cancer 1988;62:500–506.
   PubMed Web of Science ®Google Scholar
• Juliusson G, Friberg K, Gahrton G. Chromosomal aberrations in progressive and indolent chronic B-lymphocytic leukaemia. A longitudinal study. Acta Oncol 1988;27:473–477.
   PubMed Web of Science ®Google Scholar
• Nowell PC, Moreau L, Growney P, et al. Karyotypic stability in chronic B-cell leukemia. Cancer Genet Cytogenet 1988;33:155–160.
   PubMed Web of Science ®Google Scholar
• Oscier D, Fitchett M, Herbert T, et al. Karyotypic evolution in B-cell chronic lymphocytic leukaemia. Genes Chromosomes Cancer 1991;3:16–20.
   PubMed Web of Science ®Google Scholar
• Shanafelt TD, Witzig TE, Fink SR, 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;24:4634–4641.
   PubMed Web of Science ®Google Scholar
• Stilgenbauer S, Sander S, Bullinger L, 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;92:1242–1245.
   PubMed Web of Science ®Google Scholar
• Dicker F, Herholz H, Schnittger S, 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. Leukemia 2009;23:117–124.
   PubMed Web of Science ®Google Scholar
• Malcikova J, Smardova J, Rocnova L, et al. Monoallelic and biallelic inactivation of TP53 gene in chronic lymphocytic leukemia: selection, impact on survival, and response to DNA damage. Blood 2009;114:5307–5314.
   PubMed Web of Science ®Google Scholar
• Rossi D, Cerri M, Deambrogi C, et al. The prognostic value of TP53 mutations in chronic lymphocytic leukemia is independent of del17p13: implications for overall survival and chemorefractoriness. Clin Cancer Res 2009;15:995–1004.
   PubMed Web of Science ®Google Scholar
• Zenz T, Krober A, Scherer K, et al. Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: results from a detailed genetic characterization with long-term follow-up. Blood 2008;112:3322–3329.
   PubMed Web of Science ®Google Scholar
• Zainuddin N, Murray F, Kanduri M, et al. TP53 mutations are infrequent in newly diagnosed chronic lymphocytic leukemia. Leuk Res 2011;35:272–274.
   PubMed Web of Science ®Google Scholar
• Zenz T, Habe S, Denzel T, et al. Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial. Blood 2009;114:2589–2597.
   PubMed Web of Science ®Google Scholar
• Zenz T, Vollmer D, Trbusek M, et al. TP53 mutation profile in chronic lymphocytic leukemia: evidence for a disease specific profile from a comprehensive analysis of 268 mutations. Leukemia 2010;24:2072–2079.
   PubMed Web of Science ®Google Scholar
• Gonzalez D, Martinez P, Wade R, et al. Mutational status of the TP53 gene as a predictor of response and survival in patients with chronic lymphocytic leukemia: results from the LRF CLL4 trial. J Clin Oncol 2011;29:2223–2229.
   PubMed Web of Science ®Google Scholar
• Zenz T, Eichhorst B, Busch R, et al. TP53 mutation and survival in chronic lymphocytic leukemia. J Clin Oncol 2010;28:4473–4479.
   PubMed Web of Science ®Google Scholar
• Pospisilova S, Gonzalez D, Malcikova J, et al. ERIC recommendations on TP53 mutation analysis in chronic lymphocytic leukemia. Leukemia 2012;26:1458–1461.
   PubMed Web of Science ®Google Scholar
• Rossi D, Fangazio M, Rasi S, et al. Disruption of BIRC3 associates with fludarabine chemorefractoriness in TP53 wild-type chronic lymphocytic leukemia. Blood 2012;119:2854–2862.
   PubMed Web of Science ®Google Scholar
• Fabbri G, Rasi S, Rossi D, et al. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. J Exp Med 2011;208:1389–1401.
   PubMed Web of Science ®Google Scholar
• Puente XS, Pinyol M, Quesada V, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011;475:101–105.
   PubMed Web of Science ®Google Scholar
• Quesada V, Conde L, Villamor N, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 2012;44:47–52.
   PubMed Web of Science ®Google Scholar
• Di Ianni M, Baldoni S, Rosati E, et al. A new genetic lesion in B-CLL: a NOTCH1 PEST domain mutation. Br J Haematol 2009;146:689–691.
   PubMed Web of Science ®Google Scholar
• Wang L, Lawrence MS, Wan Y, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 2011;365:2497–2506.
   PubMed Web of Science ®Google Scholar
• Rosati E, Sabatini R, Rampino G, et al. Constitutively activated Notch signaling is involved in survival and apoptosis resistance of B-CLL cells. Blood 2009;113:856–865.
   PubMed Web of Science ®Google Scholar
• Balatti V, Bottoni A, Palamarchuk A, et al. NOTCH1 mutations in CLL associated with trisomy 12. Blood 2012;119:329–331.
   PubMed Web of Science ®Google Scholar
• Del Giudice I, Rossi D, Chiaretti S, et al. NOTCH1 mutations in + 12 chronic lymphocytic leukemia (CLL) confer an unfavorable prognosis, induce a distinctive transcriptional profiling and refine the intermediate prognosis of + 12 CLL. Haematologica 2012; 97:437–441.
   PubMed Web of Science ®Google Scholar
• Rossi D, Rasi S, Fabbri G, et al. Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood 2012;119:521–529.
   PubMed Web of Science ®Google Scholar
• Lopez C, Delgado J, Costa D, et al. Different distribution of NOTCH1 mutations in chronic lymphocytic leukemia with isolated trisomy 12 or associated with other chromosomal alterations. Genes Chromosomes Cancer 2012;51:881–889.
   PubMed Web of Science ®Google Scholar
• Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136:701–718.
   PubMed Web of Science ®Google Scholar
• Kotake Y, Sagane K, Owa T, et al. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol 2007;3:570–575.
   PubMed Web of Science ®Google Scholar
• Rossi D, Bruscaggin A, Spina V, et al. Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: association with progression and fludarabine-refractoriness. Blood 2011;118: 6904–6908.
   PubMed Web of Science ®Google Scholar
• Mansouri L, Cahill N, Gunnarsson R, et al. NOTCH1 and SF3B1 mutations can be added to the hierarchical prognostic classification in chronic lymphocytic leukemia. Leukemia 2012 Nov 6. [Epub ahead of print]
   Web of Science ®Google Scholar
• Coste I, Le Corf K, Kfoury A, et al. Dual function of MyD88 in RAS signaling and inflammation, leading to mouse and human cell transformation. J Clin Invest 2010;120:3663–3667.
   PubMed Web of Science ®Google Scholar
• Ngo VN, Young RM, Schmitz R, et al. Oncogenically active MYD88 mutations in human lymphoma. Nature 2011;470: 115–119.
   PubMed Web of Science ®Google Scholar
• Domenech E, Gomez-Lopez G, Gzlez-Pena D, et al. New mutations in chronic lymphocytic leukemia identified by target enrichment and deep sequencing. PLoS One 2012;7:e38158.
   PubMed Web of Science ®Google Scholar
• Mansouri L, Gunnarsson R, Sutton LA, et al. Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia. Am J Hematol 2012;87:737–740.
   PubMed Web of Science ®Google Scholar
• Kharas MG, Lengner CJ, Al-Shahrour F, et al. Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia. Nat Med 2010;16:903–908.
   PubMed Web of Science ®Google Scholar