Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

Nature

Volumn 488, Issue 7409, 2012, Pages 106-110

  Pugh, Trevor J ^a,b,c   Weeraratne, Shyamal Dilhan ^c,d   Archer, Tenley C ^c,d   Pomeranz Krummel, Daniel A ^e   Auclair, Daniel ^a   Bochicchio, James ^a   Carneiro, Mauricio O ^a   Carter, Scott L ^a   Cibulskis, Kristian ^a   Erlich, Rachel L ^a   Greulich, Heidi ^a,b,c   Lennon, Niall J ^a   Mc Kenna, Aaron ^a   Meldrim, James ^a   Ramos, Alex H ^a,b,c   Ross, Michael G ^a   Russ, Carsten ^a   Shefler, Erica ^a   Sivachenko, Andrey ^a   Sogoloff, Brian ^a   Stojanov, Petar ^a   Tamayo, Pablo ^a   Mesirov, Jill P ^a   Amani, Vladimir ^c,d   Teider, Natalia ^c,d   Sengupta, Soma ^c,d   Francois, Jessica Pierre ^c,d   Northcott, Paul A ^f   Taylor, Michael D ^f   Yu, Furong ^g   Crabtree, Gerald R ^g,h   Kautzman, Amanda G ^g   Gabriel, Stacey B ^a   Getz, Gad ^a   Jäger, Natalie ⁱ   Jones, David T W ⁱ   Lichter, Peter ⁱ   Pfister, Stefan M ⁱ   Roberts, Thomas M ^b,c   Dangl, Jeffery L ^j   Pomeroy, Scott L ^a,c,d   Cho, Yoon Jae ^a,c,d,g   more..

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d BOSTON CHILDREN S HOSPITAL   (United States)

^e BRANDEIS UNIVERSITY   (United States)

^f HOSPITAL FOR SICK CHILDREN   (Canada)

^g STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h STANFORD UNIVERSITY   (United States)

ⁱ GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^j BRIGHAM AND WOMEN S HOSPITAL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BCOR PROTEIN, HUMAN; BETA CATENIN; CELL SURFACE RECEPTOR; CTNNB1 PROTEIN, HUMAN; DDX3X PROTEIN, HUMAN; DEAD BOX PROTEIN; DNA BINDING PROTEIN; GPS2 PROTEIN, HUMAN; HELICASE; HISTONE LYSINE METHYLTRANSFERASE; HISTONE METHYLTRANSFERASE; LDB1 PROTEIN, HUMAN; LIM PROTEIN; MLL2 PROTEIN, HUMAN; NUCLEAR PROTEIN; ONCOPROTEIN; PATCHED RECEPTORS; PROTEIN P53; REPRESSOR PROTEIN; SHH PROTEIN, HUMAN; SIGNAL PEPTIDE; SMARCA4 PROTEIN, HUMAN; SONIC HEDGEHOG PROTEIN; T CELL FACTOR PROTEIN; TP53 PROTEIN, HUMAN; TRANSCRIPTION FACTOR; TUMOR PROTEIN; WNT PROTEIN; BRG1 PROTEIN; RNA HELICASE;

ARTICLE; CEREBELLUM TUMOR; CHEMICAL STRUCTURE; CHEMISTRY; CHILD; CLASSIFICATION; EXOME; GENETICS; HUMAN; HUMAN GENOME; MEDULLOBLASTOMA; METABOLISM; MUTATION; PROMOTER REGION; PROTEIN TERTIARY STRUCTURE; SIGNAL TRANSDUCTION; CELL VIABILITY; CTNNB1 GENE; DDX3X GENE; GENE MUTATION; GENE SEQUENCE; HEDGEHOG; HISTONE METHYLATION; HUMAN TISSUE; MLL2 GENE; MUTANT; PRIORITY JOURNAL; PTCH1 GENE; SOMATIC MUTATION; SUPPRESSOR GENE; TUMOR GENE; WILD TYPE;

BETA CATENIN; CEREBELLAR NEOPLASMS; CHILD; DEAD-BOX RNA HELICASES; DNA HELICASES; DNA-BINDING PROTEINS; EXOME; GENOME, HUMAN; HEDGEHOG PROTEINS; HISTONE-LYSINE N-METHYLTRANSFERASE; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LIM DOMAIN PROTEINS; MEDULLOBLASTOMA; MODELS, MOLECULAR; MUTATION; NEOPLASM PROTEINS; NUCLEAR PROTEINS; PROMOTER REGIONS, GENETIC; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS; RECEPTORS, CELL SURFACE; REPRESSOR PROTEINS; SIGNAL TRANSDUCTION; TCF TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS; TUMOR SUPPRESSOR PROTEIN P53; WNT PROTEINS;

BRAIN; CHILD HEALTH; DISEASE TREATMENT; ENZYME ACTIVITY; GENETIC ANALYSIS; GENOMICS; MOLECULAR ANALYSIS; MUTATION; PHYSIOLOGY; SIGNALING; TUMOR;

ERINACEIDAE;

EID: 84864492215     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature11329     Document Type: Letter

References (29)

1. Central Brain Tumor Registry of the United States. Statistical Report: Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2004-2007 http://www.cbtrus.org/2011-NPCR-SEER/WEB-0407-Report-3-3-2011.pdf (CBTRUS, 2011).
2. Cho, Y.-J. et al. Integrative genomic analysis of medulloblastoma identifiesa molecular subgroup that drives poor clinical outcome. J. Clin. Oncol. 29, 1424-1430 (2011).
3. Kool, M. et al. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles, pathway signatures and clinicopathological features. PLoSONE 3, e3088 (2008).
4. Remke, M. et al. Adult medulloblastoma comprises three major molecularvariants. J. Clin. Oncol. 29, 2717-2723 (2011).
5. Taylor, M. D. et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 123, 465-472 (2012).
6. Smoll, N. R. Relative survival of childhood and adult medulloblastomas and primitive neuroectodermal tumors (PNETs). Cancer 118, 1313-1322 (2012).
7. Parsons, D. W. et al. The genetic landscape of the childhood cancer medulloblastoma. Science 331, 435-439 (2011).
8. Getz, G. et al. Comment on ‘The consensus coding sequences of human breast and colorectal cancers.''. Science 317, 1500 (2007).
9. Ming, J. E. et al. Mutations in PATCHED-1, the receptor for SONIC HEDGEHOG, are associated with holoprosencephaly. Hum. Genet 110, 297-301 (2002).
10. Zhang, J. et al. A novel retinoblastoma therapy from genomic and epigenetic analyses. Nature 481, 329-334 (2012).
11. Grossmann, V. et al. Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood 118, 6153-6163 (2011).
12. Oberoi, J. et al. Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nature Struct Mol. Biol. 18, 177-184(2011).
13. Baek, S. H. et al. Regulated subset of G1 growth-control genes in response to derepression by the Wnt pathway. Proc. Natl Acad. Sci. USA 100, 3245-3250 (2003).
14. Wilson, B. G. & Roberts, C. W. M. SWI/SNF nucleosome remodellers and cancer. Nature Rev. Cancer 11, 481-492 (2011).
15. Futreal, P. A. et al. A census of human cancer genes. Nature Rev. Cancer 4, 177-183 (2004).
16. Satow, R., Kurisaki, A., Chan, T.-C., Hamazaki, T. S. & Asashima, M. Dullard promotes degradation and dephosphorylation of BMP receptors and is required for neural induction. Dev. Cell 11, 763-774 (2006).
17. Peterson, T. R. et al. mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway. Cell 146, 408-420 (2011).
18. Garbelli, A., Beermann, S., Di Cicco, G., Dietrich, U.& Maga, G. A motif unique to the human dead-box protein DDX3 is important for nucleic acid binding, ATP hydrolysis, RNA/DNA unwinding and HIV-1 replication. PLoS ONE 6, e19810(2011).
19. Hogbom, M. et al. Crystal structure of conserved domains 1 and 2 of the human DEAD-box helicase DDX3X in complex with the mononucleotide AMP. J. Mol. Biol. 372, 150-159 (2007).
20. Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S. & Yokoyama, S. Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell 125, 287-300 (2006).
21. Wang, L. et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N. Engl. J. Med. 365, 2497-2506 (2011).
22. Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157-1160 (2011).
23. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
24. Genome Reference Consortium. Human Genome Overview http:// www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ (2012).
25. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
26. Ramos, A. et al. Oncotator http://www.broadinstitute.org/oncotator/ (2012).
27. Robinson, J. T. et al. Integrative genomics viewer. Nature Biotechnol. 29, 24-26 (2011).
28. Ren, J. et al. DOG 1.0: illustrator of protein domain structures. Cell Res. 19, 271-273 (2009).
29. Pettersen, E. F. et al. UCSFChimera-a visualization system forexploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).