A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: An integrated genomics approach reveals a wide gene dosage effect

Genes Chromosomes and Cancer

Volumn 48, Issue 7, 2009, Pages 603-614

  Agnelli, Luca ^a   Mosca, Laura ^a   Fabris, Sonia ^a   Lionetti, Marta ^a   Andronache, Adrian ^a   Kwee, Ivo ^b   Todoerti, Katia ^a   Verdelli, Donata ^a   Battaglia, Cristina ^c   Bertoni, Francesco ^b   Deliliers, Giorgio Lambertenghi ^a   Neri, Antonino ^a,c  

^a FONDAZIONE IRCCS CA GRANDA OSPEDALE MAGGIORE POLICLINICO   (Italy)

^b ONCOLOGY INSTITUTE OF SOUTHERN SWITZERLAND   (Switzerland)

^c UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ALLELE; ANEUPLOIDY; ARTICLE; CHROMOSOME 13; CHROMOSOME 14; CHROMOSOME 1Q; CHROMOSOME 22; CHROMOSOME ABERRATION; CLINICAL ARTICLE; CONTROLLED STUDY; DIPLOIDY; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE DELETION; GENE DOSAGE; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE NUMBER; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; HETEROZYGOSITY; HUMAN; MALE; MICROARRAY ANALYSIS; MULTIPLE MYELOMA; PLASMA CELL LEUKEMIA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TETRAPLOIDY;

AGED; AGED, 80 AND OVER; ALLELIC IMBALANCE; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; LOSS OF HETEROZYGOSITY; MALE; MIDDLE AGED; MULTIPLE MYELOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDOREDUCTASES; POLYMORPHISM, SINGLE NUCLEOTIDE; RETINOBLASTOMA PROTEIN; TUMOR SUPPRESSOR PROTEINS;

EID: 67449107983     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20668     Document Type: Article

References (38)

1. Agnelli L, Bicciato S, Mattioli M, Fabris S, Intini D, Verdelli D, Baldini L, Morabito F, Callea V, Lombardi L, Neri A. 2005. Molecular classification of multiple myeloma: A distinct transcriptional profile characterizes patients expressing CCND1 and negative for 14q32 translocations. J Clin Oncol 23:7296-7306.
2. Agnelli L, Bicciato S, Fabris S, Baldini L, Morabito F, Intini D, Verdelli D, Callegaro A, Bertoni F, Lambertenghi-Deliliers G, Lombardi L, Neri A. 2007a. Integrative genomic analysis reveals distinct transcriptional and genetic features associated with chromosome 13 deletion in multiple myeloma. Haematologica 92:56-65.
3. Agnelli L, Fabris S, Bicciato S, Basso D, Baldini L, Morabito F, Verdelli D, Todoerti K, Lambertenghi-Deliliers G, Lombardi L, Neri A. 2007b. Upregulation of translational machinery and distinct genetic subgroups characterise hyperdiploidy in multiple myeloma. Br J Haematol 136:565-573.
4. Bea S, Salaverria I, Armengol L, Pinyol M, Fernandez V, Hartmann EM, Jares P, Amador V, Hernandez L, Navarro A, Ott G, Rosenwald A, Estivill X, Campo E. 2009. Uniparental disomies, homozygous deletions, amplifications and target genes in mantle cell lymphoma revealed by integrative high-resolution whole genome profiling. Blood 113:3059-3069.
5. Bergsagel PL, Kuehl WM. 2005. Molecular pathogenesis and a consequent classification of multiple myeloma. J Clin Oncol 23:6333-6338.
6. Bieche I, Lidereau R. 2000. Loss of heterozygosity at 13q14 correlates with RB1 gene underexpression in human breast cancer. Mol Carcinog 29:151-158.
7. Brunet JP, Tamayo P, Golub TR, Mesirov JP. 2004. Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci USA 101:4164-4169.
8. Carrasco DR, Tonon G, Huang Y, Zhang Y, Sinha R, Feng B, Stewart JP, Zhan F, Khatry D, Protopopova M. 2006. High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cells 9:313-325.
9. Chng WJ, Kumar S, Vanwier S, Ahmann G, Price-Troska T, Henderson K, Chung TH, Kim S, Mulligan G, Bryant B, Carpten J, Gertz M, Rajkumar SV, Lacy M, Dispenzieri A, Kyle R, Greipp P, Bergsagel PL, Fonseca R. 2007. Molecular dissection of hyperdiploid multiple myeloma by gene expression profiling. Cancer Res 67:2982-2989.
10. Cigudosa JC, Rao PH, Calasanz MJ, Odero MD, Michaeli J, Jhanwar SC, Chaganti RS. 1998. Characterization of nonrandom chromosomal gains and losses in multiple myeloma by comparative genomic hybridization. Blood 91:3007-3010.
11. Debes-Marun CS, Dewald GW, Bryant S, Picken E, Santana-Davila R, Gonzalez-Paz N, Winkler JM, Kyle RA, Gertz MA, Witzig TE, Dispenzieri A, Lacy MQ, Rajkumar SV, Lust JA, Greipp PR, Fonseca R. 2003. Chromosome abnormalities clustering and its implications for pathogenesis and prognosis in myeloma. Leukemia 17:427-436.
12. Durig J, Bug S, Klein-Hitpass L, Boes T, Jons T, Martin-Subero JI, Harder L, Baudis M, Duhrsen U, Siebert R. 2007. Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocyte leukemia with inv(14)(q11q32). Leukemia 21:2153-2163.
13. Fabris S, Agnelli L, Mattioli M, Baldini L, Ronchetti D, Morabito F, Verdelli D, Nobili L, Intini D, Callea V, Stelitano C, Lombardi L, Neri A. 2005. Characterization of oncogene dysregulation in multiple myeloma by combined FISH and DNA microarray analyses. Genes Chromosomes Cancer 42:117-127.
14. Fabris S, Ronchetti D, Agnelli L, Baldini L, Morabito F, Bicciato S, Basso D, Todoerti K, Lombardi L, Lambertenghi-Deliliers G, Neri A. 2007a. Transcriptional features of multiple myeloma patients with chromosome 1q gain. Leukemia 21:1113-1116.
15. Fabris S, Todoerti K, Mosca L, Agnelli L, Intini D, Lionetti M, Guerneri S, Lambertenghi-Deliliers G, Bertoni F, Neri A. 2007b. Molecular and transcriptional characterization of the novel 17p11.2-p12 amplicon in multiple myeloma. Genes Chromosomes Cancer 46:1109-1118.
16. Ferrari F, Bortoluzzi S, Coppe A, Sirota A, Safran M, Shmoish M, Ferrari S, Lancet D, Danieli GA, Bicciato S. 2007. Novel definition files for human GeneChips based on GeneAnnot. BMC Bioinformatics 8:446.
17. Fonseca R, Barlogie B, Bataille R, Bastard C, Bergsagel PL, Chesi M, Davies FE, Drach J, Greipp PR, Kirsch IR, Kuehl WM, Hernandez JM, Minvielle S, Pilarski LM, Shaughnessy JD, Jr., Stewart AK, Avet-Loiseau H. 2004. Genetics and cytogenetics of multiple myeloma: A workshop report. Cancer Res 64:1546-1558.
18. Gutierrez NC, Garcia JL, Hernandez JM, Lumbreras E, Castellanos M, Rasillo A, Mateo G, Hernandez JM, Perez S, Orfao A, San Miguel JF. 2004. Prognostic and biologic significance of chromosomal imbalances assessed by comparative genomic hybridization in multiple myeloma. Blood 104:2661-2666.
19. Hideshima T, Bergsagel PL, Kuehl WM, Anderson KC. 2004. Advances in biology of multiple myeloma: Clinical applications. Blood 104:607-618.
20. Jenner MW, Leone PE, Walker BA, Ross FM, Johnson DC, Gonzalez D, Chiecchio L, Dachs CE, Dagrada GP, Nightingale M, Protheroe RK, Stockley D, Else M, Dickens NJ, Cross NC, Davies FE, Morgan GJ. 2007. Gene mapping and expression analysis of 16q loss of heterozygosity identifies WWOX and CYLD as being important in determining clinical outcome in multiple myeloma. Blood 110:3291-3300.
21. Keats JJ, Fonseca R, Chesi M, Schop R, Baker A, Chng WJ, Van WS, Tiedemann R, Shi CX, Sebag M, Braggio E, Henry T, Zhu YX, Fogle H, Price-Troska T, Ahmann G, Mancini C, Brents LA, Kumar S, Greipp P, Dispenzieri A, Bryant B, Mulligan G, Bruhn L, Barrett M, Valdez R, Trent J, Stewart AK, Carpten J, Bergsagel PL. 2007. Promiscuous mutations activate the noncanonical NF-kappaB pathway in multiple myeloma. Cancer Cells 12:131-144.
22. Koren-Michowitz M, Hardan I, Berghoff J, Yshoev G, Amariglio N, Rechavi G, Nagler A, Trakhtenbrot L. 2007. Chromosome 13q deletion and IgH abnormalities may be both masked by near-tetraploidy in a high proportion of multiple myeloma patients: A combined morphology and I-FISH analysis. Cancer Lett 255:307-314.
23. Largo C, Alvarez S, Saez B, Blesa D, Martin-Subero JI, Gonzalez-Garcia I, Brieva JA, Dopazo J, Siebert R, Calasanz MJ, Cigudosa JC. 2006. Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma. Haematologica 91:184-191.
24. Largo C, Saez B, Alvarez S, Suela J, Ferreira B, Blesa D, Prosper F, Calasanz MJ, Cigudosa JC. 2007. Multiple myeloma primary cells show a highly rearranged unbalanced genome with amplifications and homozygous deletions irrespective of the presence of immunoglobulin-related chromosome translocations. Haematologica 92:795-802.
25. Liebisch P, Dohner H. 2006. Cytogenetics and molecular cytogenetics in multiple myeloma. Eur J Cancer 42:1520-1529.
26. Liebisch P, Viardot A, Bassermann N, Wendl C, Roth K, Goldschmidt H, Einsele H, Straka C, Stilgenbauer S, Dohner H, Bentz M. 2003. Value of comparative genomic hybridization and fluorescence in situ hybridization for molecular diagnostics in multiple myeloma. Br J Haematol 122:193-201.
27. Lombardi L, Poretti G, Mattioli M, Fabris S, Agnelli L, Bicciato S, Kwee I, Rinaldi A, Ronchetti D, Verdelli D, Lambertenghi-Deliliers G, Bertoni F, Neri A. 2007. Molecular characterization of human multiple myeloma cell lines by integrative genomics: Insights into the biology of the disease. Genes Chromosomes Cancer 46:226-238.
28. Mattioli M, Agnelli L, Fabris S, Baldini L, Morabito F, Bicciato S, Verdelli D, Intini D, Nobili L, Cro L, Pruneri G, Callea V, Stelitano C, Maiolo AT, Lombardi L, Neri A. 2005. Gene expression profiling of plasma cell dyscrasias reveals molecular patterns associated with distinct IGH translocations in multiple myeloma. Oncogene 24:2461-2473.
29. Olshen AB, Venkatraman ES, Lucito R, Wigler M. 2004. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5:557-572.
30. Rhodes DR, Chinnaiyan AM. 2005. Integrative analysis of the cancer transcriptome. Nat Genet 37 Suppl:S31-S37.
31. Ronchetti D, Lionetti M, Mosca L, Agnelli L, Andronache A, Fabris S, Lambertenghi DG, Neri A. 2008. An integrative genomic approach reveals coordinated expression of intronic miR-335, miR-342, and miR-561 with deregulated host genes in multiple myeloma. BMC Med Genomics 1:37.
32. Shaughnessy J, Tian E, Sawyer J, McCoy J, Tricot G, Jacobson J, Anaissie E, Zangari M, Fassas A, Muwalla F, Morris C, Barlogie B. 2003. Prognostic impact of cytogenetic and interphase fluorescence in situ hybridization-defined chromosome 13 deletion in multiple myeloma: Early results of total therapy II. Br J Haematol 120:44-52.
33. Shaughnessy JD, Zhan F, Burington BE, Huang Y, Colla S, Hanamura I, Stewart JP, Kordsmeier B, Randolph C, Williams DR, Xiao Y, Xu H, Epstein J, Anaissie E, Krishna SG, Cottler-Fox M, Hollmig K, Mohiuddin A, Pineda-Roman M, Tricot G, Van Rhee F, Sawyer J, Alsayed Y, Walker R, Zangari M, Crowley J, Barlogie B. 2007. A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1. Blood 109:2276-2284.
34. Smadja NV, Fruchart C, Isnard F, Louvet C, Dutel JL, Cheron N, Grange MJ, Monconduit M, Bastard C. 1998. Chromosomal analysis in multiple myeloma: Cytogenetic evidence of two different diseases. Leukemia 12:960-969.
35. Song J, Salek-Ardakani S, Rogers PR, Cheng M, Van PL, Croft M. 2004. The costimulation-regulated duration of PKB activation controls T cell longevity. Nat Immunol 5:150-158.
36. Walker BA, Morgan GJ. 2006. Use of single nucleotide polymorphism-based mapping arrays to detect copy number changes and loss of heterozygosity in multiple myeloma. Clin Lymphoma Myeloma 7:186-191.
37. Walker BA, Leone PE, Jenner MW, Li C, Gonzalez D, Johnson DC, Ross FM, Davies FE, Morgan GJ. 2006. Integration of global SNP-based mapping and expression arrays reveals key regions, mechanisms, and genes important in the pathogenesis of multiple myeloma. Blood 108:1733-1743.
38. Zhan F, Huang Y, Colla S, Stewart JP, Hanamura I, Gupta S, Epstein J, Yaccoby S, Sawyer J, Burington B, Anaissie E, Hollmig K, Pineda-Roman M, Tricot G, Van Rhee F, Walker R, Zangari M, Crowley J, Barlogie B, Shaughnessy JD, Jr. 2006. The molecular classification of multiple myeloma. Blood 108:2020-2028.