{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T03:18:24Z","timestamp":1789010304386,"version":"build-2803163510"},"reference-count":46,"publisher":"Association for Research in Vision and Ophthalmology (ARVO)","issue":"2","license":[{"start":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T00:00:00Z","timestamp":1555459200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Trans. Vis. Sci. Tech."],"published-print":{"date-parts":[[2019,4,17]]},"DOI":"10.1167\/tvst.8.2.18","type":"journal-article","created":{"date-parts":[[2019,4,17]],"date-time":"2019-04-17T21:33:16Z","timestamp":1555536796000},"page":"18","source":"Crossref","is-referenced-by-count":59,"title":["Next-Generation Sequencing of Uveal Melanoma for Detection of Genetic Alterations Predicting Metastasis"],"prefix":"10.1167","volume":"8","author":[{"given":"Armin R.","family":"Afshar","sequence":"first","affiliation":[{"name":"Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertil E.","family":"Damato","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay M.","family":"Stewart","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lydia B.","family":"Zablotska","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ritu","family":"Roy","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Computational Biology and Informatics, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam B.","family":"Olshen","sequence":"additional","affiliation":[{"name":"Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Computational Biology and Informatics, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nancy M.","family":"Joseph","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boris C.","family":"Bastian","sequence":"additional","affiliation":[{"name":"Hellen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Department of Pathology, University of California, San Francisco, San Francisco, CA, USA"},{"name":"Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"27","reference":[{"key":"i2164-2591-8-2-18-b01","doi-asserted-by":"crossref","unstructured":"Damato B, Eleuteri A, Taktak AFG, Coupland SE. Estimating prognosis for survival after treatment of choroidal melanoma. Prog Retin Eye Res. 2011; 30: 285\u2013295.","DOI":"10.1016\/j.preteyeres.2011.05.003"},{"key":"i2164-2591-8-2-18-b02","doi-asserted-by":"crossref","unstructured":"Damato B, Duke C, Coupland SE, et al. Cytogenetics of uveal melanoma: a 7-year clinical experience. Ophthalmology. 2007; 114: 1925\u20131931.","DOI":"10.1016\/j.ophtha.2007.06.012"},{"key":"i2164-2591-8-2-18-b03","doi-asserted-by":"crossref","unstructured":"Damato B, Eleuteri A, Fisher AC, Coupland SE, Taktak AF. Artificial neural networks estimating survival probability after treatment of choroidal melanoma. Ophthalmology. 2008; 115: 1598\u20131607.","DOI":"10.1016\/j.ophtha.2008.01.032"},{"key":"i2164-2591-8-2-18-b04","doi-asserted-by":"crossref","unstructured":"Cook SA, Damato B, Marshall E, Salmon P. Psychological aspects of cytogenetic testing of uveal melanoma: preliminary findings and directions for future research. Eye(Lond). 200923: 581\u2013585.","DOI":"10.1038\/eye.2008.54"},{"key":"i2164-2591-8-2-18-b05","doi-asserted-by":"crossref","unstructured":"Dogrusoz M, Bagger M, van Duinen SG, et al. The prognostic value of AJCC staging in uveal melanoma is enhanced by adding chromosome 3 and 8q status. Invest Ophthalmol Vis Sci. 2017; 58: 833\u2013842.","DOI":"10.1167\/iovs.16-20212"},{"key":"i2164-2591-8-2-18-b06","doi-asserted-by":"crossref","unstructured":"Finger PT. The 7th edition AJCC staging system for eye cancer: an international language for ophthalmic oncology. Arch Pathol Lab Med. 2009; 133: 1197\u20131198.","DOI":"10.5858\/133.8.1197"},{"key":"i2164-2591-8-2-18-b07","doi-asserted-by":"crossref","unstructured":"Prescher G, Bornfeld N, Hirche H, et al. Prognostic implications of monosomy 3 in uveal melanoma. Lancet. 1996; 347: 1222\u20131225.","DOI":"10.1016\/S0140-6736(96)90736-9"},{"key":"i2164-2591-8-2-18-b08","doi-asserted-by":"crossref","unstructured":"Onken MD, Worley LA, Char DH, et al. Collaborative Ocular Oncology Group report number 1: prospective validation of a multi-gene prognostic assay in uveal melanoma. Ophthalmology. 2012; 119: 1596\u20131603.","DOI":"10.1016\/j.ophtha.2012.02.017"},{"key":"i2164-2591-8-2-18-b09","unstructured":"White, VA, Chambers, J., Courtright, PD, et al. Correlation of cytogenetic abnormalities with the outcome of patients with uveal melanoma. Cancer. 1998; 83, 354e359."},{"key":"i2164-2591-8-2-18-b10","doi-asserted-by":"crossref","unstructured":"Damato B, Dopierala JA, Coupland SE. Genotypic profiling of 452 choroidal melanomas with multiplex ligation-dependent probe amplification. Clin Cancer Res. 2010; 16: 6083\u20136092.","DOI":"10.1158\/1078-0432.CCR-10-2076"},{"key":"i2164-2591-8-2-18-b11","doi-asserted-by":"crossref","unstructured":"Shields CL, Say EAT, Hasanreisoglu M, et al. Personalized prognosis of uveal melanoma based on cytogenetic profile in 1059 patients over an 8 year period. Ophthalmology. 2017; 124: 1523\u20131531.","DOI":"10.1016\/j.ophtha.2017.04.003"},{"key":"i2164-2591-8-2-18-b12","doi-asserted-by":"crossref","unstructured":"Van Raamsdonk, CD, Bezrookove V, Green G, et al. Frequent somatic mutations of GNAQ in uveal melanoma and blue nevi. Nature. 2009; 457: 599\u2013602.","DOI":"10.1038\/nature07586"},{"key":"i2164-2591-8-2-18-b13","doi-asserted-by":"crossref","unstructured":"Van Raamsdonk CD, Griewank KG, Crosby MB, et al. Mutations in GNA11 in uveal melanoma. N Engl J Med 2010; 363: 2191\u20132199.","DOI":"10.1056\/NEJMoa1000584"},{"key":"i2164-2591-8-2-18-b14","doi-asserted-by":"crossref","unstructured":"Harbour JW, Onken MD, Roberson ED, et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science. 2010; 330: 1410\u20131413.","DOI":"10.1126\/science.1194472"},{"key":"i2164-2591-8-2-18-b15","doi-asserted-by":"crossref","unstructured":"Martin M, Masshofer L, Temming P, et al. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat Genet. 2013; 45: 933\u2013936.","DOI":"10.1038\/ng.2674"},{"key":"i2164-2591-8-2-18-b16","doi-asserted-by":"crossref","unstructured":"Harbour JW, Roberson ED, Anbunathan H, et al. Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma. Nat Genet. 2013; 45: 133\u2013135.","DOI":"10.1038\/ng.2523"},{"key":"i2164-2591-8-2-18-b17","doi-asserted-by":"crossref","unstructured":"Ewens KG, Kanetsky PA, Richards-Yutz J, et al. Chromosome 3 status combined with BAP1 and EIF1AX mutation profiles are associated with metastasis in uveal melanoma. Invest Ophthalmol Vis Sci. 2014; 55: 5160\u20135167.","DOI":"10.1167\/iovs.14-14550"},{"key":"i2164-2591-8-2-18-b18","doi-asserted-by":"crossref","unstructured":"Robertson AG, Shih J, Yau C, et al. Integrative analysis identifies four molecular and clinical subsets in uveal melanoma. Cancer Cell. 2017; 32: 204\u2013220.e15.","DOI":"10.1016\/j.ccell.2017.07.003"},{"key":"i2164-2591-8-2-18-b19","doi-asserted-by":"crossref","unstructured":"Yavuzyiqitoqlu S, Koopmans AE, Verdijk RM, et al. Uveal melanomas with SF3B1 mutations: a distinct subclass associated with late-onset metastases. Ophthalmology. 2016; 123: 1118\u20131128.","DOI":"10.1016\/j.ophtha.2016.01.023"},{"key":"i2164-2591-8-2-18-b20","doi-asserted-by":"crossref","unstructured":"Johansson P, Aoude LG, Wadt K, et al. Deep sequencing of uveal melanoma identifies a recurrent mutation in PLCB4. Oncotarget. 2016; 7: 4624\u20134631.","DOI":"10.18632\/oncotarget.6614"},{"key":"i2164-2591-8-2-18-b21","doi-asserted-by":"crossref","unstructured":"Moore AM , Ceraudo E, Sher JJ, et al. Recurrent activating mutations of G-protein-coupled receptor CYSLTR2 in uveal melanoma. Nat Genet. 2016; 48: 675\u2013680.","DOI":"10.1038\/ng.3549"},{"key":"i2164-2591-8-2-18-b22","doi-asserted-by":"crossref","unstructured":"Talevich ES, Shain AH, Bastian BC. CNVkit: genome wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput Biol. 2016; 12: e1004873.","DOI":"10.1371\/journal.pcbi.1004873"},{"key":"i2164-2591-8-2-18-b23","unstructured":"Kline CN, Joseph NM, Grenert JP, et al. Targeted next-generation sequencing of pediatric neuro-oncology patients improves diagnosis, identifies pathogenic germline mutations, and directs targeted therapy. Neuro Oncol. 2017; 19: 699\u2013709."},{"key":"i2164-2591-8-2-18-b24","unstructured":"Afshar AR. \u201cNext-generation sequencing of uveal melanoma.\u201d Presented at the American Society of Retinal Specialists Annual Meeting, San Francisco, CA, August 12, 2016."},{"key":"i2164-2591-8-2-18-b25","doi-asserted-by":"crossref","unstructured":"Sen J, Groenewald C, Hiscott PS, et al. Transretinal choroidal tumor biopsy with a 25-gauge vitrector. Ophthalmology. 2006; 113: 1028\u20131031.","DOI":"10.1016\/j.ophtha.2006.02.048"},{"key":"i2164-2591-8-2-18-b26","doi-asserted-by":"crossref","unstructured":"McLean IW, Foster WD, Zimmerman LE, et al. Modifications of Callender's classification of uveal melanoma at the Armed Forces Institute of Pathology. Am J Ophthalmol 1983; 96: 502\u2013509.","DOI":"10.1016\/S0002-9394(14)77914-0"},{"key":"i2164-2591-8-2-18-b27","doi-asserted-by":"crossref","unstructured":"Wagle N, Berger MF, Davis MJ, et al. High- throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2012; 2: 82\u201393.","DOI":"10.1158\/2159-8290.CD-11-0184"},{"key":"i2164-2591-8-2-18-b28","doi-asserted-by":"crossref","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26: 589\u2013595.","DOI":"10.1093\/bioinformatics\/btp698"},{"key":"i2164-2591-8-2-18-b29","doi-asserted-by":"crossref","unstructured":"Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics. 2009; 25: 2078\u20132079.","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"i2164-2591-8-2-18-b30","doi-asserted-by":"crossref","unstructured":"Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015; 10: 1556\u20131566.","DOI":"10.1038\/nprot.2015.105"},{"key":"i2164-2591-8-2-18-b31","doi-asserted-by":"crossref","unstructured":"Rausch T, Zichner T, Schlattl A, et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012; 28: i333\u2013i9.","DOI":"10.1093\/bioinformatics\/bts378"},{"key":"i2164-2591-8-2-18-b32","unstructured":"Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM: Broad Institute. Available at: http:\/\/broadinstitute.github.io\/picard."},{"key":"i2164-2591-8-2-18-b33","unstructured":"Garrison E, Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv. 2012 (1207.3907 [q-bio.GN])."},{"key":"i2164-2591-8-2-18-b34","doi-asserted-by":"crossref","unstructured":"McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20: 1297\u20131303.","DOI":"10.1101\/gr.107524.110"},{"key":"i2164-2591-8-2-18-b35","doi-asserted-by":"crossref","unstructured":"DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011; 43: 491\u2013498.","DOI":"10.1038\/ng.806"},{"key":"i2164-2591-8-2-18-b36","doi-asserted-by":"crossref","unstructured":"Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013; 43: 11.10.1\u201333.","DOI":"10.1002\/0471250953.bi1110s43"},{"key":"i2164-2591-8-2-18-b37","doi-asserted-by":"crossref","unstructured":"Ye K, Schulz MH, Long Q, et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009; 25: 2865\u20132871.","DOI":"10.1093\/bioinformatics\/btp394"},{"key":"i2164-2591-8-2-18-b38","unstructured":"R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2016. Available at: https:\/\/www.R-project.org."},{"key":"i2164-2591-8-2-18-b39","doi-asserted-by":"crossref","unstructured":"Hothorn T, Hornik K, van de Wiel MA, Zeileis A. A lego system for conditional interference. Am Stat. 2006; 60: 257\u2013263.","DOI":"10.1198\/000313006X118430"},{"key":"i2164-2591-8-2-18-b40","doi-asserted-by":"crossref","unstructured":"Damato B, Coupland SE. A reappraisal of the significance of largest basal diameter of posterior uveal melanoma. Eye (Lond). 2009; 23: 2152\u20132160; quiz 2161\u20132162.","DOI":"10.1038\/eye.2009.235"},{"key":"i2164-2591-8-2-18-b41","doi-asserted-by":"crossref","unstructured":"Kalirai H, Dodson A, Faqir S, et al. Lack of BAP1 protein expression in uveal melanoma is associated with increased metastatic risk and has utility in routine prognostic testing. Br J Cancer. 2014; 111: 1373\u20131380.","DOI":"10.1038\/bjc.2014.417"},{"key":"i2164-2591-8-2-18-b42","doi-asserted-by":"crossref","unstructured":"Bhattacharya A, Roy R, Snijders AM, Hamilton G. Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res. 2011; 17: 7024\u20137034.","DOI":"10.1158\/1078-0432.CCR-11-1944"},{"key":"i2164-2591-8-2-18-b43","doi-asserted-by":"crossref","unstructured":"Furney SJ, Pedersen M, Gentien D. SF3B1 mutations are associated with alternative splicing in uveal melanoma. Cancer Discov. 2013; 3: 1122\u20131129.","DOI":"10.1158\/2159-8290.CD-13-0330"},{"key":"i2164-2591-8-2-18-b44","doi-asserted-by":"crossref","unstructured":"Field MG, Durante MA, Anbunathan H, et al. Punctuated evolution of canonical genomic aberrations in uveal melanoma. Nat Comm. 2018: 9, 116.","DOI":"10.1038\/s41467-017-02428-w"},{"key":"i2164-2591-8-2-18-b45","doi-asserted-by":"crossref","unstructured":"Smit KN, van Poppelen NM, Vaarwater J, et al. Combined mutation and copy-number variation detection by targeted next-generation sequencing in uveal melanoma. Mod Path. 2018; 31: 763\u2013771.","DOI":"10.1038\/modpathol.2017.187"},{"key":"i2164-2591-8-2-18-b46","doi-asserted-by":"crossref","unstructured":"Eleuteri A, Damato B, Coupland SE, Taktak A. Enhancing survival prognostication in patients with choroidal melanoma by integrating pathologic clinical and genetic predictors of metastases. Int J Biomed Eng Technol. 2012; 8: 18\u201335.","DOI":"10.1504\/IJBET.2012.045355"}],"container-title":["Translational Vision Science & Technology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/tvst.arvojournals.org\/article.aspx?articleid=2731609","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T05:40:49Z","timestamp":1663306849000},"score":1,"resource":{"primary":{"URL":"http:\/\/tvst.arvojournals.org\/article.aspx?doi=10.1167\/tvst.8.2.18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,17]]},"references-count":46,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2019,3,1]]}},"URL":"https:\/\/doi.org\/10.1167\/tvst.8.2.18","relation":{},"ISSN":["2164-2591"],"issn-type":[{"value":"2164-2591","type":"print"}],"subject":[],"published":{"date-parts":[[2019,4,17]]}}}