Clonal architectures and driver mutations in metastatic melanomas

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Ding, Li ^a   Kim, Minjung ^b   Kanchi, Krishna L ^a   Dees, Nathan D ^a   Lu, Charles ^a   Griffith, Malachi ^a   Fenstermacher, David ^b   Sung, Hyeran ^b   Miller, Christopher A ^a   Goetz, Brian ^a   Wendl, Michael C ^a   Griffith, Obi ^a   Cornelius, Lynn A ^a   Linette, Gerald P ^a   McMichael, Joshua F ^a   Sondak, Vernon K ^b   Fields, Ryan C ^a   Ley, Timothy J ^a   Mulé, James J ^b   Wilson, Richard K ^a   Weber, Jeffrey S ^b   more..

^a WASHINGTON UNIVERSITY   (United States)

^b H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; CYCLIN DEPENDENT KINASE INHIBITOR 2A; EPHRIN RECEPTOR A3; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN P53; TUMOR SUPPRESSOR PROTEIN; BRAF PROTEIN, HUMAN; EPHA3 PROTEIN, HUMAN; GUANOSINE TRIPHOSPHATASE; MEMBRANE PROTEIN; NRAS PROTEIN, HUMAN; PROTEIN TYROSINE KINASE;

ARID2 GENE; ARTICLE; ASXL3 GENE; BRAF GENE; CANCER GENETICS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CLONAL VARIATION; CONTROLLED STUDY; DRIVER MUTATION; EPHA3 GENE; GENE; GENE IDENTIFICATION; GENE MUTATION; GENE SEQUENCE; GENOME; HUMAN; HUMAN CELL; HUMAN TISSUE; METASTATIC MELANOMA; MLL2 GENE; NRAS GENE; ONCOGENE N RAS; PHENOTYPE; PHYLOGENY; PTEN GENE; PTPRB GENE; PTPRD GENE; PTPRT GENE; RB1 GENE; TUMOR SUPPRESSOR GENE; VALIDATION PROCESS; DNA MUTATIONAL ANALYSIS; DNA SEQUENCE; GENETICS; HUMAN GENOME; MELANOMA; NUCLEOTIDE SEQUENCE; SKIN TUMOR;

BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; GENES, P16; GENOME, HUMAN; GTP PHOSPHOHYDROLASES; HUMANS; MELANOMA; MEMBRANE PROTEINS; PHOSPHOPROTEIN PHOSPHATASES; PROTO-ONCOGENE PROTEINS B-RAF; RECEPTOR PROTEIN-TYROSINE KINASES; SEQUENCE ANALYSIS, DNA; SKIN NEOPLASMS; TUMOR SUPPRESSOR PROTEINS;

EID: 84911941605     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0111153     Document Type: Article

References (45)

1. Siegel R, Naishadham D, Jemal A (2013) Cancer statistics, 2013. CA: a cancer journal for clinicians 63: 11-30.
2. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, et al. (2011) Improved survival with vemurafenib in melanoma with BRAF V600E mutation. The New England journal of medicine 364: 2507-2516.
3. Hodi FS, O'Day SJ, McDermott DF, Weber RW, Sosman JA, et al. (2010) Improved survival with ipilimumab in patients with metastatic melanoma. The New England journal of medicine 363: 711-723.
4. Davies MA, Samuels Y (2010) Analysis of the genome to personalize therapy for melanoma. Oncogene 29: 5545-5555.
5. Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, et al. (2005) Distinct sets of genetic alterations in melanoma. The New England journal of medicine 353: 2135-2147.
6. Bauer J, Curtin JA, Pinkel D, Bastian BC (2007) Congenital melanocytic nevi frequently harbor NRAS mutations but no BRAF mutations. The Journal of investigative dermatology 127: 179-182.
7. Pollock PM, Harper UL, Hansen KS, Yudt LM, Stark M, et al. (2003) High frequency of BRAF mutations in nevi. Nature genetics 33: 19-20.
8. Michaloglou C, Vredeveld LC, Soengas MS, Denoyelle C, Kuilman T, et al. (2005) BRAFE600-associated senescence-like cell cycle arrest of human naevi. Nature 436: 720-724.
9. Wajapeyee N, Serra RW, Zhu X, Mahalingam M, Green MR (2008) Oncogenic BRAF induces senescence and apoptosis through pathways mediated by the secreted protein IGFBP7. Cell 132: 363-374.
10. Bennett DC (2003) Human melanocyte senescence and melanoma susceptibility genes. Oncogene 22: 3063-3069.
11. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463: 191-196.
12. Hocker T, Tsao H (2007) Ultraviolet radiation and melanoma: a systematic review and analysis of reported sequence variants. Human mutation 28: 578-588.
13. Prickett TD, Agrawal NS, Wei X, Yates KE, Lin JC, et al. (2009) Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4. Nature genetics 41: 1127-1132.
14. Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, et al. (2011) The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature 471: 513-517.
15. Stark MS, Woods SL, Gartside MG, Bonazzi VF, Dutton-Regester K, et al. (2011) Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing. Nature genetics 44: 165-169.
16. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nature genetics 43: 442-446.
17. Prickett TD, Wei X, Cardenas-Navia I, Teer JK, Lin JC, et al. (2011) Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nature genetics 43: 1119-1126.
18. Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, et al. (2012) A landscape of driver mutations in melanoma. Cell 150: 251-263.
19. Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, et al. (2012) Melanoma genome sequencing reveals frequent PREX2 mutations. Nature 485: 502-506.
20. Turajlic S, Furney SJ, Lambros MB, Mitsopoulos C, Kozarewa I, et al. (2012) Whole genome sequencing of matched primary and metastatic acral melanomas. Genome research 22: 196-207.
21. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome research 20: 1297-1303.
22. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865-2871.
23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
24. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6: 677-681.
25. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, et al. (2011) SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics.
26. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, et al. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481: 506-510.
27. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461: 809-813.
28. Ding L, Ellis MJ, Li S, Larson DE, Chen K, et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464: 999-1005.
29. Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, et al. (2013) Highly recurrent TERT promoter mutations in human melanoma. Science 339: 957-959.
30. Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, et al. (2013) TERT promoter mutations in familial and sporadic melanoma. Science 339: 959-961.
31. Killela PJ, Reitman ZJ, Jiao Y, Bettegowda C, Agrawal N, et al. (2013) TERT promoter mutations occur frequently in gliomas and a subset of tumors derived from cells with low rates of self-renewal. Proceedings of the National Academy of Sciences of the United States of America 110: 6021-6026.
32. Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, et al. (2012) MuSiC: Identifying mutational significance in cancer genomes. Genome research 22: 1589-1598.
33. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455: 1069-1075.
34. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, et al. (2013) The somatic genomic landscape of glioblastoma. Cell 155: 462-477.
35. Gray-Schopfer V, Wellbrock C, Marais R (2007) Melanoma biology and new targeted therapy. Nature 445: 851-857.
36. Smalley KS (2010) Understanding melanoma signaling networks as the basis for molecular targeted therapy. The Journal of investigative dermatology 130: 28-37.
37. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic acids research 39: D945-950.
38. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome research.
39. Shi H, Moriceau G, Kong X, Lee MK, Lee H, et al. (2012) Melanoma whole-exome sequencing identifies (V600E)B-RAF amplification-mediated acquired B-RAF inhibitor resistance. Nat Commun 3: 724.
40. Grafstrom E, Egyhazi S, Ringborg U, Hansson J, Platz A (2005) Biallelic deletions in INK4 in cutaneous melanoma are common and associated with decreased survival. Clinical cancer research: an official journal of the American Association for Cancer Research 11: 2991-2997.
41. Kamb A, Shattuck-Eidens D, Eeles R, Liu Q, Gruis NA, et al. (1994) Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. Nature genetics 8: 23-26.
42. Turajlic S, Furney SJ, Lambros MB, Mitsopoulos C, Kozarewa I, et al. Whole genome sequencing of matched primary and metastatic acral melanomas. Genome Res 22: 196-207.
43. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 43: 442-446.
44. Prickett TD, Wei X, Cardenas-Navia I, Teer JK, Lin JC, et al. Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nat Genet 43: 1119-1126.
45. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, et al. (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361: 1058-1066.