Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Gartner, Jared J ^a   Davis, Sean ^b   Wei, Xiaomu ^a   Lin, Jimmy C ^c   Trivedi, Niraj S ^a   Teer, Jamie K ^a   Meltzer, Paul S ^b   Rosenberg, Steven A ^b   Samuels, Yardena ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CLONE; CONTROLLED STUDY; COPY NUMBER VARIATION; DISTANT METASTASIS; EXOME; HUMAN; HUMAN TISSUE; MELANOMA; METASTASIS; SEQUENCE ANALYSIS; SOMATIC MUTATION; TUMOR GROWTH; WHOLE EXOME SEQUENCING;

EID: 84866495931     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-505     Document Type: Article

References (26)

1. Jemal A, Siegel R, Xu J, Ward E. Cancer statistics, 2010. CA Cancer J Clin 2010, 60(5):277-300. 10.3322/caac.20073, 20610543.
2. SEER Cancer Statistics Review, 1975-2008 http://seer.cancer.gov/csr/1975_2008/.
3. Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, O'Dwyer PJ, Lee RJ, Grippo JF, Nolop K, et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med 2010, 363(9):809-819. 10.1056/NEJMoa1002011, 20818844.
4. Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27(2):182-189. 10.1038/nbt.1523, 2663421, 19182786.
5. Wei X, Walia V, Lin JC, Teer JK, Prickett TD, Gartner J, Davis S, Stemke-Hale K, Davies MA, Gershenwald JE, et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 2011, 43(5):442-446. 10.1038/ng.810, 3161250, 21499247.
6. Kim YH, Girard L, Giacomini CP, Wang P, Hernandez-Boussard T, Tibshirani R, Minna JD, Pollack JR. Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification. Oncogene 2005, 25(1):130-138.
7. King M-C, Marks JH, Mandell JB, Group TNYBCS Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science (New York, NY) 2003, 302(5645):643-646. Group TNYBCS.
8. Prickett TD, Agrawal NS, Wei X, Yates KE, Lin JC, Wunderlich JR, Cronin JC, Cruz P, Rosenberg SA, Samuels Y. Analysis of the tyrosine kinome in melanoma reveals recurrent mutations in ERBB4. Nat Genet 2009, 41(10):1127-1132. 10.1038/ng.438, 2897709, 19718025.
9. Prickett TD, Wei X, Cardenas-Navia I, Teer JK, Lin JC, Walia V, Gartner J, Jiang J, Cherukuri PF, Molinolo A, et al. Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma. Nat Genet 2011, 43(11):1119-1126. 10.1038/ng.950, 3376644, 21946352.
10. Dahia PL. PTEN, a unique tumor suppressor gene. Endocr Relat Cancer 2000, 7(2):115-129. 10.1677/erc.0.0070115, 10903528.
11. Wei X, Moncada-Pazos A, Cal S, Soria-Valles C, Gartner J, Rudloff U, Lin JC, Rosenberg SA, Lopez-Otin C, Samuels Y. Analysis of the disintegrin-metalloproteinases family reveals ADAM29 and ADAM7 are often mutated in melanoma. Hum Mutat 2011, 32(6):E2148-2175. 10.1002/humu.21477, 3103704, 21618342.
12. Mochizuki S, Okada Y. ADAMs in cancer cell proliferation and progression. Cancer Sci 2007, 98(5):621-628. 10.1111/j.1349-7006.2007.00434.x, 17355265.
13. Leong KG. KA: Recent insights into the role of Notch signalling in tumorgenesis. Blood 2006, 107(6):2223-2233. 10.1182/blood-2005-08-3329, 16291593.
14. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, et al. The consensus coding sequences of human breast and colorectal cancers. Science (New York, NY) 2006, 314(5797):268-274.
15. Greenman C, Stephens P, Smith R, Dalgliesh GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C, et al. Patterns of somatic mutation in human cancer genomes. Nature 2007, 446(7132):153-158. 10.1038/nature05610, 2712719, 17344846.
16. Abdel-Rahman MH, Craig EL, Davidorf FH, Eng C. Expression of vascular endothelial growth factor in uveal melanoma is independent of 6p21-region copy number. Clin Cancer Res 2005, 11(1):73-78.
17. Stark M, Hayward N. Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Res 2007, 67(6):2632-2642. 10.1158/0008-5472.CAN-06-4152, 17363583.
18. Miller AJ, Mihm MC. Melanoma. N Engl J Med 2006, 355(1):51-65. 10.1056/NEJMra052166, 16822996.
19. Saeki H, Kitao H, Yoshinaga K, Nakanoko T, Kubo N, Kakeji Y, Morita M, Maehara Y. Copy-neutral loss of heterozygosity at the p53 locus in carcinogenesis of esophageal squamous cell carcinomas associated with p53 mutations. Clin Cancer Res 2011, 17(7):1731-1740. 10.1158/1078-0432.CCR-10-1996, 21325068.
20. Tuna M, Knuutila S, Mills GB. Uniparental disomy in cancer. Trends Mol Med 2009, 15(3):120-128. 10.1016/j.molmed.2009.01.005, 19246245.
21. Christensen C, Guldberg P. Growth factors rescue cutaneous melanoma cells from apoptosis induced by knockdown of mutated (V 600 E) B-RAF. Oncogene 2005, 24(41):6292-6302. 10.1038/sj.onc.1208758, 16007203.
22. Wan P, Hu Y, He L. Regulation of melanocyte pivotal transcription factor MITF by some other transcription factors. Mol Cell Biochem 2011, 354(1-2):241-246.
23. Palavalli LH, Prickett TD, Wunderlich JR, Wei X, Burrell AS, Porter-Gill P, Davis S, Wang C, Cronin JC, Agrawal NS, et al. Analysis of the matrix metalloproteinase family reveals that MMP8 is often mutated in melanoma. Nat Genet 2009, 41(5):518-520. 10.1038/ng.340, 2748394, 19330028.
24. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, Swift AJ, Abaan HO, Albert TJ, Margulies EH, Green ED, et al. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 2010, 20(11):1420-1431. 2945191, 20810667.
25. Biesecker LG, Mullikin JC, Facio FM, Turner C, Cherukuri PF, Blakesley RW, Bouffard GG, Chines PS, Cruz P, Hansen NF, et al. The ClinSeq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res 2009, 19(9):1665-1674. 10.1101/gr.092841.109, 2752125, 19602640.
26. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res 2009, 19(9):1639-1645. 10.1101/gr.092759.109, 2752132, 19541911.