Genomics of medulloblastoma: From Giemsa-banding to next-generation sequencing in 20 years

Neurosurgical Focus

Volumn 28, Issue 1, 2010, Pages

  Northcott, Paul A ^a,b,c   Rutka, James T ^a,c   Taylor, Michael D ^a,b,c  

^a UNIVERSITY OF TORONTO   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

Genomics; Medulloblastoma; Microarrays; Next generation sequencing

Indexed keywords

DIAGNOSTIC AGENT; MICRORNA; TUMOR MARKER;

BRAIN TUMOR; CHROMOSOME ANALYSIS; CHROMOSOME BANDING PATTERN; DNA MICROARRAY; DNA SEQUENCE; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; GENOMICS; GIEMSA STAIN; HISTORY; HUMAN; HUMAN GENOME; KARYOTYPING; MEDULLOBLASTOMA; METHODOLOGY; MUTATION; ONCOGENE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; REVIEW;

AZURE STAINS; BRAIN NEOPLASMS; CHROMOSOME BANDING; CYTOGENETIC ANALYSIS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOME, HUMAN; GENOMICS; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; HUMANS; KARYOTYPING; MEDULLOBLASTOMA; MICRORNAS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ONCOGENES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SEQUENCE ANALYSIS, DNA; TUMOR MARKERS, BIOLOGICAL;

EID: 76549086016     PISSN: None     EISSN: 10920684     Source Type: Journal    
DOI: 10.3171/2009.10.FOCUS09218     Document Type: Review

References (177)

1. Adesina AM, Nguyen Y, Mehta V, Takei H, Stangeby P, Crabtree S, et al: FOXG1 dysregulation is a frequent event in medulloblastoma. J Neurooncol 85:111-122, 2007.
2. Aldosari N, Wiltshire RN, Dutra A, Schrock E, McLendon RE, Friedman HS, et al: Comprehensive molecular cytogenetic investigation of chromosomal abnormalities in human medulloblastoma cell lines and xenograft. Neuro Oncol 4:75-85, 2002.
3. Ambros V: The functions of animal microRNAs. Nature 431:350-355, 2004.
4. Anderton JA, Lindsey JC, Lusher ME, Gilbertson RJ, Bailey S, Ellison DW, et al: Global analysis of the medulloblastoma epigenome identifies disease-subgroup-specific inactivation of COL1A2. Neuro Oncol 10:981-994, 2008.
5. Ansorge WJ: Next-generation DNA sequencing techniques. N Biotechnol 25:195-203, 2009.
6. Attard TM, Giglio P, Koppula S, Snyder C, Lynch HT: Brain tumors in individuals with familial adenomatous polyposis: a cancer registry experience and pooled case report analysis. Cancer 109:761-766, 2007.
7. Avet-Loiseau H, Vénuat AM, Terrier-Lacombe MJ, Lellouch-Tubiana A, Zerah M, Vassal G: Comparative genomic hybridization detects many recurrent imbalances in central nervous system primitive neuroectodermal tumours in children. Br J Cancer 79:1843-1847, 1999.
8. Badiali M, Pession A, Basso G, Andreini L, Rigobello L, Galassi E, et al: N-myc and c-myc oncogenes amplification in medulloblastomas. Evidence of particularly aggressive behavior of a tumor with c-myc amplification. Tumori 77:118-121, 1991.
9. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al: High-resolution profiling of histone methylations in the human genome. Cell 129:823-837, 2007.
10. Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell 136:215-233, 2009.
11. Bayani J, Squire JA: Traditional banding of chromosomes for cytogenetic analysis. Curr Protoc Cell Biol Chapter 22:Unit 22.3, 2004.
12. Bayani J, Zielenska M, Marrano P, Kwan Ng Y, Taylor MD, Jay V, et al: Molecular cytogenetic analysis of medulloblastomas and supratentorial primitive neuroectodermal tumors by using conventional banding, comparative genomic hybridization, and spectral karyotyping. J Neurosurg 93:437-448, 2000.
13. Bayani JM, Squire JA: Applications of SKY in cancer cytogenetics. Cancer Invest 20:373-386, 2002.
14. Behesti H, Marino S: Cerebellar granule cells: insights into proliferation, differentiation, and role in medulloblastoma pathogenesis. Int J Biochem Cell Biol 41:435-445, 2009.
15. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59, 2008.
16. Bernstein BE, Meissner A, Lander ES: The mammalian epigenome. Cell 128:669-681, 2007.
17. Biegel JA, Rorke LB, Packer RJ, Sutton LN, Schut L, Bonner K, et al: Isochromosome 17q in primitive neuroectodermal tumors of the central nervous system. Genes Chromosomes Cancer 1:139-147, 1989.
18. Bigner SH, Friedman HS, Vogelstein B, Oakes WJ, Bigner DD: Amplification of the c-myc gene in human medulloblastoma cell lines and xenografts. Cancer Res 50:2347-2350, 1990.
19. Bigner SH, Mark J, Friedman HS, Biegel JA, Bigner DD: Structural chromosomal abnormalities in human medulloblastoma. Cancer Genet Cytogenet 30:91-101, 1988.
20. Bigner SH, McLendon RE, Fuchs H, McKeever PE, Friedman HS: Chromosomal characteristics of childhood brain tumors. Cancer Genet Cytogenet 97:125-134, 1997.
21. Boon K, Eberhart CG, Riggins GJ: Genomic amplification of orthodenticle homologue 2 in medulloblastomas. Cancer Res 65:703-707, 2005.
22. Boon K, Edwards JB, Siu IM, Olschner D, Eberhart CG, Marra MA, et al: Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes. Oncogene 22:7687-7694, 2003.
23. Brena RM, Costello JF: Genome-epigenome interactions in cancer. Hum Mol Genet 16 (Spec No 1):R96-R105, 2007.
24. Calin GA, Croce CM: MicroRNA signatures in human cancers. Nat Rev Cancer 6:857-866, 2006.
25. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, et al: Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40:722-729, 2008.
26. Cancer Genome Atlas Research Network: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061-1068, 2008.
27. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, et al: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 6:99-103, 2009.
28. Clifford SC, Lusher ME, Lindsey JC, Langdon JA, Gilbertson RJ, Straughton D, et al: Wnt/Wingless pathway activation and chromosome 6 loss characterize a distinct molecular subgroup of medulloblastomas associated with a favorable prognosis. Cell Cycle 5:2666-2670, 2006.
29. Cogen PH, Daneshvar L, Metzger AK, Duyk G, Edwards MS, Sheffield VC: Involvement of multiple chromosome 17p loci in medulloblastoma tumorigenesis. Am J Hum Genet 50:584-589, 1992.
30. Cogen PH, Daneshvar L, Metzger AK, Edwards MS: Deletion mapping of the medulloblastoma locus on chromosome 17p. Genomics 8:279-285, 1990.
31. Cohen BH, Zeltzer PM, Boyett JM, Geyer JR, Allen JC, Finlay JL, et al: Prognostic factors and treatment results for supratentorial primitive neuroectodermal tumors in children using radiation and chemotherapy: a Childrens Cancer Group randomized trial. J Clin Oncol 13:1687-1696, 1995.
32. Cohen N, Betts DR, Tavori U, Toren A, Ram T, Constantini S, et al: Karyotypic evolution pathways in medulloblastoma/primitive neuroectodermal tumor determined with a combination of spectral karyotyping, G-banding, and fluorescence in situ hybridization. Cancer Genet Cytogenet 149:44-52, 2004.
33. Coombs A: The sequencing shakeup. Nat Biotechnol 26: 1109-1112, 2008.
34. Davies JJ, Wilson IM, Lam WL: Array CGH technologies and their applications to cancer genomes. Chromosome Res 13:237-248, 2005.
35. Di C, Liao S, Adamson DC, Parrett TJ, Broderick DK, Shi Q, et al: Identification of OTX2 as a medulloblastoma oncogene whose product can be targeted by all-trans retinoic acid. Cancer Res 65:919-924, 2005.
36. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, et al: Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455:1069-1075, 2008.
37. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al: A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26:779-785, 2008.
38. Eberhart CG, Kratz JE, Schuster A, Goldthwaite P, Cohen KJ, Perlman EJ, et al: Comparative genomic hybridization detects an increased number of chromosomal alterations in large cell/anaplastic medulloblastomas. Brain Pathol 12: 36-44, 2002.
39. Ehrbrecht A, Müller U, Wolter M, Hoischen A, Koch A, Radlwimmer B, et al: Comprehensive genomic analysis of desmoplastic medulloblastomas: identification of novel amplified genes and separate evaluation of the different histological components. J Pathol 208:554-563, 2006.
40. Ellison DW, Clifford SC, Gajjar A, Gilbertson RJ: What's new in neuro-oncology? Recent advances in medulloblastoma. Eur J Paediatr Neurol 7:53-66, 2003.
41. Esquela-Kerscher A, Slack FJ: Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer 6:259-269, 2006.
42. Esteller M: Epigenetics in cancer. N Engl J Med 358:1148-1159, 2008.
43. Fattet S, Haberler C, Legoix P, Varlet P, Lellouch-Tubiana A, Lair S, et al: Beta-catenin status in paediatric medulloblastomas: correlation of immunohistochemical expression with mutational status, genetic profiles, and clinical characteristics. J Pathol 218:86-94, 2009.
44. Ferretti E, De Smaele E, Miele E, Laneve P, Po A, Pelloni M, et al: Concerted microRNA control of Hedgehog signalling in cerebellar neuronal progenitor and tumour cells. EMBO J 27:2616-2627, 2008.
45. Ferretti E, De Smaele E, Po A, Di Marcotullio L, Tosi E, Espinola MS, et al: MicroRNA profiling in human medulloblastoma. Int J Cancer 124:568-577, 2009.
46. Finlay JL, Erdreich-Epstein A, Packer RJ: Progress in the treatment of childhood brain tumors: no room for complacency. Pediatr Hematol Oncol 24:79-84, 2007.
47. Fogarty MP, Kessler JD, Wechsler-Reya RJ: Morphing into cancer: the role of developmental signaling pathways in brain tumor formation. J Neurobiol 64:458-475, 2005.
48. Friedman HS, Burger PC, Bigner SH, Trojanowski JQ, Brodeur GM, He XM, et al: Phenotypic and genotypic analysis of a human medulloblastoma cell line and transplantable xenograft (D341 Med) demonstrating amplification of c-myc. Am J Pathol 130:472-484, 1988.
49. Frühwald MC, O'Dorisio MS, Dai Z, Tanner SM, Balster DA, Gao X, et al: Aberrant promoter methylation of previously unidentified target genes is a common abnormality in medulloblastomas-implications for tumor biology and potential clinical utility. Oncogene 20:5033-5042, 2001.
50. Fults DW: Modeling medulloblastoma with genetically engineered mice. Neurosurg Focus 19(5):E7, 2005.
51. Gailani MR, Bale SJ, Leffell DJ, DiGiovanna JJ, Peck GL, Poliak S, et al: Developmental defects in Gorlin syndrome related to a putative tumor suppressor gene on chromosome 9. Cell 69:111-117, 1992.
52. Gajjar A, Chintagumpala M, Ashley D, Kellie S, Kun LE, Merchant TE, et al: Risk-adapted craniospinal radiotherapy followed by high-dose chemotherapy and stem-cell rescue in children with newly diagnosed medulloblastoma (St Jude Medulloblastoma-96): long-term results from a prospective, multicentre trial. Lancet Oncol 7:813-820, 2006.
53. Gajjar A, Hernan R, Kocak M, Fuller C, Lee Y, McKinnon PJ, et al: Clinical, histopathologic, and molecular markers of prognosis: toward a new disease risk stratification system for medulloblastoma. J Clin Oncol 22:984-993, 2004.
54. Gilbertson RJ, Clifford SC: PDGFRB is overexpressed in metastatic medulloblastoma. Nat Genet 35:197-198, 2003.
55. Gilbertson RJ, Ellison DW: The origins of medulloblastoma subtypes. Annu Rev Pathol 3:341-365, 2008.
56. Gilhuis HJ, Anderl KL, Boerman RH, Jeuken JM, James CD, Raffel C, et al: Comparative genomic hybridization of medulloblastomas and clinical relevance: eleven new cases and a review of the literature. Clin Neurol Neurosurg 102: 203-209, 2000.
57. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, et al: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286:531-537, 1999.
58. Gonzalez-Gomez P, Bello MJ, Inda MM, Alonso ME, Arjona D, Amiñoso C, et al: Deletion and aberrant CpG island methylation of Caspase 8 gene in medulloblastoma. Oncol Rep 12:663-666, 2004.
59. Griffin CA, Hawkins AL, Packer RJ, Rorke LB, Emanuel BS: Chromosome abnormalities in pediatric brain tumors. Cancer Res 48:175-180, 1988.
60. Grimmer MR, Weiss WA: Childhood tumors of the nervous system as disorders of normal development. Curr Opin Pediatr 18:634-638, 2006.
61. Grotzer MA, Eggert A, Zuzak TJ, Janss AJ, Marwaha S, Wiewrodt BR, et al: Resistance to TRAIL-induced apoptosis in primitive neuroectodermal brain tumor cells correlates with a loss of caspase-8 expression. Oncogene 19:4604-4610, 2000.
62. Hahn H, Wicking C, Zaphiropoulous PG, Gailani MR, Shanley S, Chidambaram A, et al: Mutations of the human homolog of Drosophila patched in the nevoid basal cell carcinoma syndrome. Cell 85:841-851, 1996.
63. Hamilton SR, Liu B, Parsons RE, Papadopoulos N, Jen J, Powell SM, et al: The molecular basis of Turcot's syndrome. N Engl J Med 332:839-847, 1995.
64. Hammond SM: MicroRNAs as oncogenes. Curr Opin Genet Dev 16:4-9, 2006.
65. Harada K, Toyooka S, Maitra A, Maruyama R, Toyooka KO, Timmons CF, et al: Aberrant promoter methylation and silencing of the RASSF1A gene in pediatric tumors and cell lines. Oncogene 21:4345-4349, 2002.
66. He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, et al: A microRNA polycistron as a potential human oncogene. Nature 435:828-833, 2005.
67. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, et al: Genome-wide in situ exon capture for selective resequencing. Nat Genet 39:1522-1527, 2007.
68. Horiguchi K, Tomizawa Y, Tosaka M, Ishiuchi S, Kurihara H, Mori M, et al: Epigenetic inactivation of RASSF1A candidate tumor suppressor gene at 3p21.3 in brain tumors. Oncogene 22:7862-7865, 2003.
69. Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, et al: Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1:287-299, 2004.
70. Hui AB, Takano H, Lo KW, Kuo WL, Lam CN, Tong CY, et al: Identification of a novel homozygous deletion region at 6q23.1 in medulloblastomas using high-resolution array comparative genomic hybridization analysis. Clin Cancer Res 11:4707-4716, 2005.
71. International Human Genome Sequencing Consortium: Finishing the euchromatic sequence of the human genome. Nature 431:931-945, 2004.
72. James CD, He J, Carlbom E, Mikkelsen T, Ridderheim PA, Cavenee WK, et al: Loss of genetic information in central nervous system tumors common to children and young adults. Genes Chromosomes Cancer 2:94-102, 1990.
73. Jemal A, Siegel R, Ward E, Hao Y, Xu J, Murray T, et al: Cancer statistics, 2008. CA Cancer J Clin 58:71-96, 2008.
74. Johnson DS, Mortazavi A, Myers RM, Wold B: Genomewide mapping of in vivo protein-DNA interactions. Science 316:1497-1502, 2007.
75. Jones PA, Baylin SB: The epigenomics of cancer. Cell 128:683-692, 2007.
76. Jones PA, Baylin SB: The fundamental role of epigenetic events in cancer. Nat Rev Genet 3:415-428, 2002.
77. Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, et al: Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 324:217, 2009.
78. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, et al: Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321:1801-1806, 2008.
79. Kasuga C, Nakahara Y, Ueda S, Hawkins C, Taylor MD, Smith CA, et al: Expression of MAGE and GAGE genes in medulloblastoma and modulation of resistance to chemotherapy. Laboratory investigation. J Neurosurg Pediatr 1:305-313, 2008.
80. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, et al: A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011-1015, 2009.
81. Kongkham PN, Northcott PA, Ra YS, Nakahara Y, Mainprize TG, Croul SE, et al: An epigenetic genome-wide screen identifies SPINT2 as a novel tumor suppressor gene in pediatric medulloblastoma. Cancer Res 68:9945-9953, 2008.
82. Kool M, Koster J, Bunt J, Hasselt NE, Lakeman A, van Sluis P, et al: Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoS One 3:e3088, 2008.
83. Kortmann RD, Kühl J, Timmermann B, Mittler U, Urban C, Budach V, et al: Postoperative neoadjuvant chemotherapy before radiotherapy as compared to immediate radiotherapy followed by maintenance chemotherapy in the treatment of medulloblastoma in childhood: results of the German prospective randomized trial HIT '91. Int J Radiat Oncol Biol Phys 46:269-279, 2000.
84. Kouzarides T: Chromatin modifications and their function. Cell 128:693-705, 2007.
85. LaFramboise T: Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res 37:4181-4193, 2009.
86. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, et al: Initial sequencing and analysis of the human genome. Nature 409:860-921, 2001.
87. Leary RJ, Cummins J, Wang TL, Velculescu VE: Digital karyotyping. Nat Protoc 2:1973-1986, 2007.
88. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:66-72, 2008.
89. Li MH, Bouffet E, Hawkins CE, Squire JA, Huang A: Molecular genetics of supratentorial primitive neuroectodermal tumors and pineoblastoma. Neurosurg Focus 19(5):E3, 2005.
90. Lindsey JC, Anderton JA, Lusher ME, Clifford SC: Epigenetic events in medulloblastoma development. Neurosurg Focus 19(5):E10, 2005.
91. Lindsey JC, Lusher ME, Anderton JA, Bailey S, Gilbertson RJ, Pearson AD, et al: Identification of tumour-specific epigenetic events in medulloblastoma development by hypermethylation profiling. Carcinogenesis 25:661-668, 2004.
92. Lo KC, Rossi MR, Eberhart CG, Cowell JK: Genome wide copy number abnormalities in pediatric medulloblastomas as assessed by array comparative genome hybridization. Brain Pathol 17:282-296, 2007.
93. Lusher ME, Lindsey JC, Latif F, Pearson AD, Ellison DW, Clifford SC: Biallelic epigenetic inactivation of the RASSF1A tumor suppressor gene in medulloblastoma development. Cancer Res 62:5906-5911, 2002.
94. MacDonald TJ, Brown KM, LaFleur B, Peterson K, Lawlor C, Chen Y, et al: Expression profiling of medulloblastoma: PDGFRA and the RAS/MAPK pathway as therapeutic targets for metastatic disease. Nat Genet 29:143-152, 2001.
95. Malkin D, Li FP, Strong LC, Fraumeni JF Jr, Nelson CE, Kim DH, et al: Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science 250: 1233-1238, 1990.
96. Marino S: Medulloblastoma: developmental mechanisms out of control. Trends Mol Med 11:17-22, 2005.
97. Marrett LD, De P, Airia P, Dryer D: Cancer in Canada in 2008. CMAJ 179:1163-1170, 2008.
98. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, et al: Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 1:109-111, 2004.
99. Matsuzaki H, Loi H, Dong S, Tsai YY, Fang J, Law J, et al: Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res 14:414-425, 2004.
100. McCabe MG, Ichimura K, Liu L, Plant K, Bäcklund LM, Pearson DM, et al: High-resolution array-based comparative genomic hybridization of medulloblastomas and supratentorial primitive neuroectodermal tumors. J Neuropathol Exp Neurol 65:549-561, 2006.
101. McNeil DE, Coté TR, Clegg L, Rorke LB: Incidence and trends in pediatric malignancies medulloblastoma/primitive neuroectodermal tumor: a SEER update. Surveillance Epidemiology and End Results. Med Pediatr Oncol 39:190-194, 2002.
102. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, et al: Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770, 2008.
103. Mendell JT: miRiad roles for the miR-17-92 cluster in development and disease. Cell 133:217-222, 2008.
104. Mendrzyk F, Radlwimmer B, Joos S, Kokocinski F, Benner A, Stange DE, et al: Genomic and protein expression profiling identifies CDK6 as novel independent prognostic marker in medulloblastoma. J Clin Oncol 23:8853-8862, 2005.
105. Mertens F, Johansson B, Mitelman F: Isochromosomes in neoplasia. Genes Chromosomes Cancer 10:221-230, 1994.
106. Metzker ML: Emerging technologies in DNA sequencing. Genome Res 15:1767-1776, 2005.
107. Michiels EM, Oussoren E, Van Groenigen M, Pauws E, Bossuyt PM, Voûte PA, et al: Genes differentially expressed in medulloblastoma and fetal brain. Physiol Genomics 1:83-91, 1999.
108. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560, 2007.
109. Mischel PS, Cloughesy TF, Nelson SF: DNA-microarray analysis of brain cancer: molecular classification for therapy. Nat Rev Neurosci 5:782-792, 2004.
110. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, et al: Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18:610-621, 2008.
111. Morozova O, Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255-264, 2008.
112. Morozova O, Marra MA: From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumors. Biochem Cell Biol 86:81-91, 2008.
113. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNASeq. Nat Methods 5:621-628, 2008.
114. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al: The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349, 2008.
115. Neben K, Korshunov A, Benner A, Wrobel G, Hahn M, Kokocinski F, et al: Microarray-based screening for molecular markers in medulloblastoma revealed STK15 as independent predictor for survival. Cancer Res 64:3103-3111, 2004.
116. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, et al: Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461:272-276, 2009.
117. Nicholson J, Wickramasinghe C, Ross F, Crolla J, Ellison D: Imbalances of chromosome 17 in medulloblastomas determined by comparative genomic hybridisation and fluorescence in situ hybridisation. Mol Pathol 53:313-319, 2000.
118. Northcott PA, Fernandez-L A, Hagan JP, Ellison DW, Grajkowska W, Gillespie Y, et al: The miR-17/92 polycistron is up-regulated in sonic hedgehog-driven medulloblastomas and induced by N-myc in sonic hedgehog-treated cerebellar neural precursors. Cancer Res 69:3249-3255, 2009.
119. Northcott PA, Nakahara Y, Wu X, Feuk L, Ellison DW, Croul S, et al: Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat Genet 41:465-472, 2009.
120. Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, Ladd C, et al: Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res 63:1602-1607, 2003.
121. Ogawa H, Ishiguro K, Gaubatz S, Livingston DM, Nakatani Y: A complex with chromatin modifiers that occupies E2F- and Myc-responsive genes in G0 cells. Science 296:1132-1136, 2002.
122. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40:1413-1415, 2008.
123. Park PC, Taylor MD, Mainprize TG, Becker LE, Ho M, Dura WT, et al: Transcriptional profiling of medulloblastoma in children. J Neurosurg 99:534-541, 2003.
124. Parmigiani G, Boca S, Lin J, Kinzler KW, Velculescu V, Vogelstein B: Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics 93:17-21, 2009.
125. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, et al: An integrated genomic analysis of human glioblastoma multiforme. Science 321:1807-1812, 2008.
126. Pfister S, Remke M, Benner A, Mendrzyk F, Toedt G, Felsberg J, et al: Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci. J Clin Oncol 27:1627-1636, 2009.
127. Pfister S, Remke M, Toedt G, Werft W, Benner A, Mendrzyk F, et al: Supratentorial primitive neuroectodermal tumors of the central nervous system frequently harbor deletions of the CDKN2A locus and other genomic aberrations distinct from medulloblastomas. Genes Chromosomes Cancer 46:839-851, 2007.
128. Pfister S, Schlaeger C, Mendrzyk F, Wittmann A, Benner A, Kulozik A, et al: Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma. Nucleic Acids Res 35:e51, 2007.
129. Piedimonte LR, Wailes IK, Weiner HL: Medulloblastoma: mouse models and novel targeted therapies based on the Sonic hedgehog pathway. Neurosurg Focus 19(5):E8, 2005.
130. Pietsch T, Scharmann T, Fonatsch C, Schmidt D, Ockler R, Freihoff D, et al: Characterization of five new cell lines derived from human primitive neuroectodermal tumors of the central nervous system. Cancer Res 54:3278-3287, 1994.
131. Polyak K, Riggins GJ: Gene discovery using the serial analysis of gene expression technique: implications for cancer research. J Clin Oncol 19:2948-2958, 2001.
132. Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, et al: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415:436-442, 2002.
133. Pruitt KD, Tatusova T, Maglott DR: NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35 (Database issue):D61-D65, 2007.
134. Raffel C: Medulloblastoma: molecular genetics and animal models. Neoplasia 6:310-322, 2004.
135. Raffel C, Gilles FE, Weinberg KI: Reduction to homozygosity and gene amplification in central nervous system primitive neuroectodermal tumors of childhood. Cancer Res 50:587-591, 1990.
136. Reardon DA, Michalkiewicz E, Boyett JM, Sublett JE, Entrekin RE, Ragsdale ST, et al: Extensive genomic abnormalities in childhood medulloblastoma by comparative genomic hybridization. Cancer Res 57:4042-4047, 1997.
137. Reddy AT, Janss AJ, Phillips PC, Weiss HL, Packer RJ: Outcome for children with supratentorial primitive neuroectodermal tumors treated with surgery, radiation, and chemotherapy. Cancer 88:2189-2193, 2000.
138. Rickert CH, Paulus W: Comparative genomic hybridization in central and peripheral nervous system tumors of childhood and adolescence. J Neuropathol Exp Neurol 63:399-417, 2004.
139. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, et al: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657, 2007.
140. Rood BR, Zhang H, Weitman DM, Cogen PH: Hypermethylation of HIC-1 and 17p allelic loss in medulloblastoma. Cancer Res 62:3794-3797, 2002.
141. Rorke LB: Classification and grading of childhood brain tumors. Overview and statement of the problem. Cancer 56 (7 Suppl):1848-1849, 1985.
142. Rossi MR, Conroy J, McQuaid D, Nowak NJ, Rutka JT, Cowell JK: Array CGH analysis of pediatric medulloblastomas. Genes Chromosomes Cancer 45:290-303, 2006.
143. Rusk N, Kiermer V: Primer: Sequencing-the next generation. Nat Methods 5:15, 2008.
144. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, et al: Using the transcriptome to annotate the genome. Nat Biotechnol 20:508-512, 2002.
145. Schuster SC: Next-generation sequencing transforms today's biology. Nat Methods 5:16-18, 2008.
146. Shendure J, Ji H: Next-generation DNA sequencing. Nat Biotechnol 26:1135-1145, 2008.
147. Speicher MR, Carter NP: The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 6:782-792, 2005.
148. Srivastava S, Zou ZQ, Pirollo K, Blattner W, Chang EH: Germline transmission of a mutated p53 gene in a cancer-prone family with Li-Fraumeni syndrome. Nature 348:747-749, 1990.
149. Stratton MR, Campbell PJ, Futreal PA: The cancer genome. Nature 458:719-724, 2009.
150. Tachibana M, Ueda J, Fukuda M, Takeda N, Ohta T, Iwanari H, et al: Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev 19:815-826, 2005.
151. Taylor MD, Mainprize TG, Rutka JT: Molecular insight into medulloblastoma and central nervous system primitive neuroectodermal tumor biology from hereditary syndromes: a review. Neurosurgery 47:888-901, 2000.
152. Taylor RE, Bailey CC, Robinson KJ, Weston CL, Walker DA, Ellison D, et al: Outcome for patients with metastatic (M2-3) medulloblastoma treated with SIOP/UKCCSG PNET-3 chemotherapy. Eur J Cancer 41:727-734, 2005.
153. Thomas GA, Raffel C: Loss of heterozygosity on 6q, 16q, and 17p in human central nervous system primitive neuroectodermal tumors. Cancer Res 51:639-643, 1991.
154. Thompson MC, Fuller C, Hogg TL, Dalton J, Finkelstein D, Lau CC, et al: Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations. J Clin Oncol 24:1924-1931, 2006.
155. Timmermann B, Kortmann RD, Kühl J, Meisner C, Dieckmann K, Pietsch T, et al: Role of radiotherapy in the treatment of supratentorial primitive neuroectodermal tumors in childhood: results of the prospective German brain tumor trials HIT 88/89 and 91. J Clin Oncol 20:842-849, 2002.
156. Ting AH, McGarvey KM, Baylin SB: The cancer epigenome-components and functional correlates. Genes Dev 20:3215-3231, 2006.
157. Tomlinson FH, Jenkins RB, Scheithauer BW, Keelan PA, Ritland S, Parisi JE, et al: Aggressive medulloblastoma with high-level N-myc amplification. Mayo Clin Proc 69:359-365, 1994.
158. Uziel T, Karginov FV, Xie S, Parker JS, Wang YD, Gajjar A, et al: The miR-17~92 cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma. Proc Natl Acad Sci U S A 106:2812-2817, 2009.
159. van Ruissen F, Baas F: Serial analysis of gene expression (SAGE). Methods Mol Biol 383:41-66, 2007.
160. Velculescu VE: Essay: Amersham Pharmacia Biotech & Science prize. Tantalizing transcriptomes-SAGE and its use in global gene expression analysis. Science 286:1491-1492, 1999.
161. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW: Serial analysis of gene expression. Science 270:484-487, 1995.
162. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, et al: Characterization of the yeast transcriptome. Cell 88:243-251, 1997.
163. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al: The sequence of the human genome. Science 291:1304-1351, 2001.
164. von Stein OD: Isolation of differentially expressed genes through subtractive suppression hybridization. Methods Mol Biol 175:263-278, 2001.
165. Waha A, Koch A, Hartmann W, Milde U, Felsberg J, Hübner A, et al: SGNE1/7B2 is epigenetically altered and transcription ally downregulated in human medulloblastomas. Oncogene 26:5662-5668, 2007.
166. Waha A, Waha A, Koch A, Meyer-Puttlitz B, Weggen S, Sörensen N, et al: Epigenetic silencing of the HIC-1 gene in human medulloblastomas. J Neuropathol Exp Neurol 62:1192-1201, 2003.
167. Wang J, Wang W, Li R, Li Y, Tian G, Goodman L, et al: The diploid genome sequence of an Asian individual. Nature 456:60-65, 2008.
168. Wang TL, Maierhofer C, Speicher MR, Lengauer C, Vogelstein B, Kinzler KW, et al: Digital karyotyping. Proc Natl Acad Sci U S A 99:16156-16161, 2002.
169. Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63, 2009.
170. Wechsler-Reya R, Scott MP: The developmental biology of brain tumors. Annu Rev Neurosci 24:385-428, 2001.
171. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, et al: The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872-876, 2008.
172. Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, et al: Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453:1239-1243, 2008.
173. Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, et al: The genomic landscapes of human breast and colorectal cancers. Science 318:1108-1113, 2007.
174. Yan PS, Potter D, Deatherage DE, Huang TH, Lin S: Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray. Methods Mol Biol 507:89-106, 2009.
175. Yokota N, Mainprize TG, Taylor MD, Kohata T, Loreto M, Ueda S, et al: Identification of differentially expressed and developmentally regulated genes in medulloblastoma using suppression subtraction hybridization. Oncogene 23:3444-3453, 2004.
176. Yoshimoto M, Bayani J, Nuin PA, Silva NS, Cavalheiro S, Stavale JN, et al: Metaphase and array comparative genomic hybridization: unique copy number changes and gene amplification of medulloblastomas in South America. Cancer Genet Cytogenet 170:40-47, 2006.
177. Zeltzer PM, Boyett JM, Finlay JL, Albright AL, Rorke LB, Milstein JM, et al: Metastasis stage, adjuvant treatment, and residual tumor are prognostic factors for medulloblastoma in children: conclusions from the Children's Cancer Group 921 randomized phase III study. J Clin Oncol 17:832-845, 1999.