Integrative analysis of the melanoma transcriptome

Genome Research

Volumn 20, Issue 4, 2010, Pages 413-427

  Berger, Michael F ^a   Levin, Joshua Z ^a   Vijayendran, Krishna ^a,b   Sivachenko, Andrey ^a   Adiconis, Xian ^a   Maguire, Jared ^a   Johnson, Laura A ^a,b   Robinson, James ^a   Verhaak, Roel G ^a,b   Sougnez, Carrie ^a   Onofrio, Robert C ^a   Ziaugra, Liuda ^a   Cibulskis, Kristian ^a   Laine, Elisabeth ^c   Barretina, Jordi ^a   Winckler, Wendy ^a   Fisher, David E ^d,e   Getz, Gad ^a   Meyerson, Matthew ^a,b   Jaffe, David B ^a   Gabriel, Stacey B ^a   Lander, Eric S ^a,b,f   Dummer, Reinhard ^c   Gnirke, Andreas ^a   Nusbaum, Chad ^a   Garraway, Levi A ^a,b   more..

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

^b HARVARD MEDICAL SCHOOL   (United States)

^c UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e BOSTON CHILDREN S HOSPITAL   (United States)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; RNA; TRANSCRIPTOME;

ARTICLE; CANCER GROWTH; CHROMOSOME ANALYSIS; DNA SEQUENCE; GENE FUSION; GENE MAPPING; GENE NUMBER; GENE STRUCTURE; GENETIC TRANSCRIPTION; HUMAN; MELANOMA; PRIORITY JOURNAL; SOMATIC MUTATION;

BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE FUSION; GENOMICS; HUMANS; K562 CELLS; MATCHED-PAIR ANALYSIS; MELANOMA; POLYMORPHISM, GENETIC; PROTEIN ISOFORMS; SEQUENCE ANALYSIS, DNA; SKIN NEOPLASMS; SYSTEMS INTEGRATION; TUMOR CELLS, CULTURED;

EID: 77950633122     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.103697.109     Document Type: Article

References (67)

1. Albert TJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, et al. 2007. Direct selection of human genomic loci by microarray hybridization. Nat Methods 4: 903-905.
2. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
3. Blacker D, Wilcox MA, Laird NM, Rodes L, Horvath SM, Go RC, Perry R, Watson B Jr, Bassett SS, McInnis MG, et al. 1998. Alpha-2 macroglobulin is genetically associated with Alzheimer disease. Nat Genet 19: 357-360.
4. Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, et al. 2008. Identification of somatically acquired rearrangements in cancer using genomewide massively parallel paired-end sequencing. Nat Genet 40: 722-729.
5. Cancer Genome Atlas Research Network. 2008. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
6. Chen YZ, Bennett CL, Huynh HM, Blair IP, Puls I, Irobi J, Dierick I, Abel A, Kennerson ML, Rabin BA, et al. 2004. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). Am J Hum Genet 74: 1128-1135.
7. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, et al. 2008. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5: 613-619.
8. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, et al. 2008. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5: 887-893.
9. Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Brocker EB, LeBoit PE, et al. 2005. Distinct sets of genetic alterations in melanoma. N Engl J Med 353: 2135-2147.
10. Drobetsky EA, Grosovsky AJ, Glickman BW. 1987. The specificity of UV-induced mutations at an endogenous locus in mammalian cells. Proc Natl Acad Sci 84: 9103-9107.
11. Du J, Widlund HR, Horstmann MA, Ramaswamy S, Ross K, Huber WE, Nishimura EK, Golub TR, Fisher DE. 2004. Critical role of CDK2 for melanoma growth linked to its melanocyte-specific transcriptional regulation by MITF. Cancer Cell 6: 565-576.
12. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR. 2008. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet 57: 10.11.1-10.11.26.
13. Futreal PA, Coin L, Marshall M, Down T, Hubbard T,Wooster R, Rahman N, Stratton MR. 2004. A census of human cancer genes. Nat Rev Cancer 4: 177-183.
14. Garraway LA, Widlund HR, Rubin MA, Getz G, Berger AJ, Ramaswamy S, Beroukhim R, Milner DA, Granter SR, Du J, et al. 2005. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436: 117-122.
15. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, et al. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27: 182-189.
16. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, et al. 2007. Patterns of somatic mutation in human cancer genomes. Nature 446: 153-158.
17. Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. 2009. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res 19: 657-666.
18. Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, et al. 2007. Genome-wide in situ exon capture for selective resequencing. Nat Genet 39: 1522-1527.
19. Hoek KS, Schlegel NC, Eichhoff OM, Widmer DS, Praetorius C, Einarsson SO, Valgeirsdottir S, Bergsteinsdottir K, Schepsky A, Dummer R, et al. 2008. Novel MITF targets identified using a two-step DNA microarray strategy. Pigment Cell Melanoma Res 21: 665-676.
20. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, et al. 2008. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321: 1801-1806.
21. Kantarjian H, Sawyers C, Hochhaus A, Guilhot F, Schiffer C, Gambacorti- Passerini C, Niederwieser D, Resta D, Capdeville R, Zoellner U, et al. 2002. Hematologic and cytogenetic responses to imatinib mesylate in chronic myelogenous leukemia. N Engl J Med 346: 645-652.
22. Krishnakumar S, Zheng J, Wilhelmy J, Faham M, Mindrinos M, Davis R. 2008. A comprehensive assay for targeted multiplex amplification of human DNA sequences. Proc Natl Acad Sci 105: 9296-9301.
23. Kwiatkowski TJ Jr, Bosco DA, Leclerc AL, Tamrazian E, Vanderburg CR, Russ C, Davis A, Gilchrist J, Kasarskis EJ, Munsat T, et al. 2009. Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis. Science 323: 1205-1208.
24. Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A. 2009. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol 10: R115. doi: 10.1186/gb-2009-10-10-r115.
25. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, et al. 2008. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456: 66-72.
26. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
27. Li H, Wang J, Mor G, Sklar J. 2008. A neoplastic gene fusion mimics transsplicing of RNAs in normal human cells. Science 321: 1357-1361.
28. Lin WM, Baker AC, Beroukhim R, Winckler W, Feng W, Marmion JM, Laine E, Greulich H, Tseng H, Gates C, et al. 2008. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res 68: 664-673.
29. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
30. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM. 2009a. Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
31. Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, Barrette TR, Grasso C, Yu J, et al. 2009b. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci 106: 12353-12358.
32. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, et al. 2009. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361: 1058-1066.
33. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. 2008. RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
34. Matsuda S, Giliberto L, Matsuda Y, Davies P, McGowan E, Pickford F, Ghiso J, Frangione B, D'Adamio L. 2005. The familial dementia BRI2 gene binds the Alzheimer gene amyloid-b precursor protein and inhibits amyloid-β production. J Biol Chem 280: 28912-28916.
35. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, et al. 2008. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
36. Mitelman F, Johansson B, Mertens F. 2007. The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7: 233-245.
37. Moreira MC,Klur S,Watanabe M,Nemeth AH, Le Ber I,Moniz JC,Tranchant C, Aubourg P, Tazir M, Schols L, et al. 2004. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia-ocular apraxia 2. Nat Genet 36: 225-227.
38. Morin R, Bainbridge M, Fejes A, Hirst M, Krzywinski M, Pugh T, McDonald H, Varhol R, Jones S, Marra M. 2008. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques 45: 81-94.
39. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
40. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
41. Ng SB, Turner EH, Robertson PD, Flygare SD, Bigham AW, Lee C, Shaffer T, Wong M, Bhattacharjee A, Eichler EE, et al. 2009. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276.
42. Nibbe RK, Markowitz S, Myeroff L, Ewing R, Chance MR. 2009. Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol Cell Proteomics 8: 827-845.
43. Nowell PC, Hungerford DA. 1960. A minute chromosome in human chronic leukemia. Science 132: 1497.
44. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. 2007. Microarray-based genomic selection for high-throughput resequencing. Nat Methods 4: 907-909.
45. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40: 1413-1415.
46. Perner S,Wagner PL, Demichelis F, Mehra R, Lafargue CJ, Moss BJ, Arbogast S, Soltermann A, Weder W, Giordano TJ, et al. 2008. EML4-ALK fusion lung cancer: A rare acquired event. Neoplasia 10: 298-302.
47. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, et al. 2007. Multiplex amplification of large sets of human exons. Nat Methods 4: 931-936.
48. Prensner JR, Chinnaiyan AM. 2009. Oncogenic gene fusions in epithelial carcinomas. Curr Opin Genet Dev 19: 82-91.
49. Rabbitts TH, Forster A, Larson R, Nathan P. 1993. Fusion of the dominant negative transcription regulator CHOP with a novel gene FUS by translocation t(12;16) in malignant liposarcoma. Nat Genet 4: 175-180.
50. Rowley JD. 1973. A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 243: 290-293.
51. Sawyers CL. 2008. The cancer biomarker problem. Nature 452: 548-552.
52. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, et al. 2009. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461: 809-813.
53. Shendure J, Ji H. 2008. Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
54. Sherry ST,Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
55. Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG. 2005. Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma. Oncogene 24: 4232-4242.
56. Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, et al. 2007. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 448: 561-566.
57. Stratton MR, Campbell PJ, Futreal PA. 2009. The cancer genome. Nature 458: 719-724.
58. Stuart D, Sellers WR. 2009. Linking somatic genetic alterations in cancer to therapeutics. Curr Opin Cell Biol 21: 304-310.
59. Sugarbaker DJ, Richards WG, Gordon GJ, Dong L, De Rienzo A, Maulik G, Glickman JN, Chirieac LR, Hartman ML, Taillon BE, et al. 2008. Transcriptome sequencing of malignant pleural mesothelioma tumors. Proc Natl Acad Sci 105: 3521-3526.
60. Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, et al. 2008. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321: 956-960.
61. Takahashi C, Sheng Z, Horan TP, Kitayama H, Maki M, Hitomi K, Kitaura Y, Takai S, Sasahara RM, Horimoto A, et al. 1998. Regulation of matrix metalloproteinase-9 and inhibition of tumor invasion by the membrane-anchored glycoprotein RECK. Proc Natl Acad Sci 95: 13221-13226.
62. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, et al. 2005. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644-648.
63. Vance C, Rogelj B, Hortobagyi T, De Vos KJ, Nishimura AL, Sreedharan J, Hu X, Smith B, Ruddy D, Wright P, et al. 2009. Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6. Science 323: 1208-1211
64. Vrieling H, Venema J, van Rooyen ML, van Hoffen A, Menichini P, Zdzienicka MZ, Simons JW, Mullenders LH, van Zeeland AA. 1991. Strand specificity for UV-induced DNA repair and mutations in the Chinese hamster HPRT gene. Nucleic Acids Res 19: 2411-2415.
65. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
66. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, et al. 2009. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci 106: 3264-3269.
67. Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, et al. 2009. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci 106: 1886-1891