Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide single nucleotide polymorphism array analysis

Cancer Research

Volumn 69, Issue 10, 2009, Pages 4143-4149

  Volchenboum, Samuel L ^a   Li, Cheng ^b   Li, Shuli ^b   Attiyeh, Edward F ^d   Reynolds, C Patrick ^e   Maris, John M ^d   Look, A Thomas ^c   George, Rani E ^c  

^a UNIVERSITY OF CHICAGO   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

^e TEXAS TECH UNIVERSITY HEALTH SCIENCES CENTER SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME BANDING PATTERN; CONTROLLED STUDY; GENE AMPLIFICATION; GENOMICS; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; HUMAN TISSUE; MOLECULAR CLONING; NEUROBLASTOMA; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STROMA;

ALGORITHMS; CELL LINE; CELL LINE, TUMOR; CHILD; CHROMOSOME ABERRATIONS; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 1; CHROMOSOMES, HUMAN, PAIR 11; CHROMOSOMES, HUMAN, PAIR 14; CHROMOSOMES, HUMAN, PAIR 15; DNA, NEOPLASM; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LOSS OF HETEROZYGOSITY; NEUROBLASTOMA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; STROMAL CELLS;

EID: 66249114997     PISSN: 00085472     EISSN: 15387445     Source Type: Journal    
DOI: 10.1158/0008-5472.CAN-08-3112     Document Type: Article

References (27)

1. Matthay K. Neuroblastoma: a clinical challenge and biologic puzzle. CA Cancer J Clin 1995;45:179-192
2. George RE, Attiyeh EF, Li S, et al. Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays. PLoSONE 2007;2:e255.
3. Attiyeh EF, Diskin SJ, Attiyeh MA, et al. Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. Genome Res 2009;19:276-283
4. Zhao X, Weir BA, LaFramboise T, et al. Homozygous deletions and chromosome amplifications in human lung carcinomas revealed by single nucleotide polymorphism array analysis. Cancer Res 2005;65:5561-5570 (Pubitemid 40911156)
5. Brodeur G, Pritchard J, Berthold F, et al. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. J Clin Oncol 1993;11:1466-1477 (Pubitemid 23228250)
6. Shimada H, Chatten J, Newton W, et al. Histopathologic prognostic factors in neuroblastic tumors: definition of subtypes of ganglioneuroblastoma and an age-linked classification of neuroblastomas. J Natl Cancer Inst 1984;73:405-416 (Pubitemid 14055221)
7. Look A, Hayes F, Shuster J, et al. Clinical relevance of tumor cell ploidy and N-myc gene amplification in childhood neuroblastoma: a Pediatric Oncology Group study. J Clin Oncol 1991;9:581-591
8. Mathew P, Valentine M, Bowman L, et al. Detection of MYCN gene amplification in neuroblastoma by fluorescence in situ hybridization: a pediatric oncology group study. Neoplasia 2001;3:105-109 (Pubitemid 32410350)
9. Beroukhim R, Lin M, Park Y, et al. Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2006;2:e41. (Pubitemid 43794326)
10. Lin M, Wei LJ, Sellers WR, Lieberfarb M, Wong WH, Li C. dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004;20:1233-1240 (Pubitemid 38807579)
11. Zhou X, Mok S, Chen Z, Li Y, Wong D. Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet 2004;115:327-330 (Pubitemid 39247874)
12. Demichelis F, Greulich H, Macoska JA, et al. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res 2008;36:2446-2456
13. Emmert-Buck MR, Bonner RF, Smith PD, et al. Laser capture microdissection. Science 1996;274:998-1001. (Pubitemid 26398425)
14. Lieberfarb ME, Lin M, Lechpammer M, et al. Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP. Cancer Res 2003;63:4781-4785 (Pubitemid 37022605)
15. Lazcoz P, Munoz J, Nistal M, Pestana A, Encio IJ, Castresana JS. Loss of heterozygosity and microsatellite instability on chromosome arm 10q in neuroblastoma. Cancer Genet Cytogenet 2007;174:1-8. (Pubitemid 46365973)
16. Mosse YP, Diskin SJ, Wasserman N, et al. Neuroblastomas have distinct genomic DNA profiles that predict clinical phenotype and regional gene expression. Genes Chromosomes Cancer 2007;46:936-949 (Pubitemid 47435023)
17. Thompson PM, Seifried BA, Kyemba SK, et al. Loss of heterozygosity for chromosome 14q in neuroblastoma. Med Pediatr Oncol 2001;36:28-31. (Pubitemid 32052991)
18. Attiyeh E, London W, Mossé Y, et al. Chromosome 1p and 11q deletions and outcome in neuroblastoma. N Engl J Med 2005;353:2243-2253 (Pubitemid 41697287)
19. Lastowska M, Cotterill S, Pearson A, et al. Gain of chromosome arm 17q predicts unfavourable outcome in neuroblastoma patients. U K. Children's Cancer Study Group and the U K. Cancer Cytogenetics Group. Eur J Cancer 1997;33:1627-1633
20. Hirai M, Yoshida S, Kashiwagi H, et al. 1q23 gain is associated with progressive neuroblastoma resistant to aggressive treatment. Genes Chromosomes Cancer 1999;25:261-269 (Pubitemid 29266695)
21. Michels E, Vandesompele J, De Preter K, et al. ArrayCGH-based classification of neuroblastoma into genomic subgroups. Genes Chromosomes Cancer 2007;46:1098-1108 (Pubitemid 47614544)
22. Mosse YP, Greshock J, Margolin A, et al. High-resolution detection and mapping of genomic DNA alterations in neuroblastoma. Genes Chromosomes Cancer 2005;43:390-403. (Pubitemid 40946474)
23. Iguchi H, Urashima Y, Inagaki Y, et al. SOX6 suppresses cyclin D1 promoter activity by interacting with β -catenin and histone deacetylase 1 and its downregulation induces pancreatic β-cell proliferation. J Biol Chem 2007;282:19052-19061 (Pubitemid 47100155)
24. George RE, Sanda T, Hanna M, et al. Activating mutations in ALK provide a therapeutic target in neuroblastoma. Nature 2008;455:975-978
25. Schlisio S, Kenchappa RS, Vredeveld LC, et al. The kinesin KIF1Bβ acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressor. Genes Dev 2008;22:884-893
26. Bagchi A, Papazoglu C, Wu Y, et al. CHD5 is a tumor suppressor at human 1p36. Cell 2007;128:459-475 (Pubitemid 46198889)
27. Cunsolo CL, Bicocchi MP, Petti AR, Tonini GP. Numerical and structural aberrations in advanced neuroblastoma tumours by CGH analysis;survival correlates with chromosome 17 status. Br J Cancer 2000;83:1295-1300