Erratum: Unraveling the clonal hierarchy of somatic genomic aberrations. [Genome Biol. 15, (2014), (439)]DOI:10.1186/s13059-014-0439-6;Unraveling the clonal hierarchy of somatic genomic aberrations

Genome Biology

Volumn 15, Issue 8, 2014, Pages

  Prandi, Davide ^a   Baca, Sylvan C 760 766 ^b,c,d   Romanel, Alessandro ^a   Barbieri, Christopher E ^e   Mosquera, Juan Miguel ^e   Fontugne, Jacqueline ^e   Beltran, Himisha ^e   Sboner, Andrea ^e   Garraway, Levi A ^b,c,d   Rubin, Mark A ^e   Demichelis, Francesca ^a,e  

^a UNIVERSITY OF TRENTO   (Italy)

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

^c DANA FARBER CANCER INSTITUTE   (United States)

^d HARVARD MEDICAL SCHOOL   (United States)

^e WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; TRANSCRIPTION FACTOR ERG;

ANEUPLOIDY; ARTICLE; CELL HETEROGENEITY; CLONAL EVOLUTION; CLONAL VARIATION; COPY NUMBER VARIATION; GENE DELETION; GENE MUTATION; GENOMICS; HUMAN; LUNG ADENOCARCINOMA; MATHEMATICAL MODEL; METASTATIC MELANOMA; MOLECULARLY TARGETED THERAPY; PATIENT SELECTION; POINT MUTATION; POLYPLOIDY; PROSTATE CANCER; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC ABERRATION; WHOLE GENOME SEQUENCING; ADENOCARCINOMA; ALGORITHM; BIOLOGY; GENETIC VARIABILITY; GENETICS; HUMAN GENOME; LUNG TUMOR; MALE; MELANOMA; PROCEDURES; PROSTATE TUMOR;

ADENOCARCINOMA; ALGORITHMS; CLONAL EVOLUTION; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; GENOME, HUMAN; HUMANS; LUNG NEOPLASMS; MALE; MELANOMA; PROSTATIC NEOPLASMS;

EID: 84964314022     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-017-1183-5     Document Type: Erratum

References (48)

1. Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR: PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 2010, 11:164-175.
2. Li A, Liu Z, Lezon-Geyda K, Sarkar S, Lannin D, Schulz V, Krop I, Winer E, Harris L, Tuck D: GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Res 2011, 39:4928-4941.
3. Van Loo P, Nordgard SH, Lingjaerde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale A-L, Kristensen VN: Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A 2010, 107:16910-16915.
4. Yau C, Mouradov D, Jorissen RN, Colella S, Mirza G, Steers G, Harris A, Ragoussis J, Sieber O, Holmes CC: A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol 2010, 11:R92.
5. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G: Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol 2012, 30:413-421.
6. Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, Raine K, Jones D, Marshall J, Ramakrishna M, Shlien A, Cooke SL, Hinton J, Menzies A, Stebbings LA, Leroy C, Jia M, Rance R, Mudie LJ, Gamble SJ, Stephens PJ, McLaren S, Tarpey PS, Papaemmanuil E, Davies HR, Varela I, McBride DJ, Bignell GR, Leung K, Butler AP, et al: The life history of 21 breast cancers. Cell 2012, 149:994-1007.
7. Oesper L, Mahmoody A, Raphael BJ: THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol 2013, 14:R80.
8. Strino F, Parisi F, Micsinai M, Kluger Y: TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res 2013, 41:e165.
9. Yau C: OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes. Bioinformatics 2013, 29:2482-2484.
10. Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat J-P, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, et al: Punctuated evolution of prostate cancer genomes. Cell 2013, 153:666-677.
11. Berger MF, Hodis E, Heffernan TP, Deribe YL, Lawrence MS, Protopopov A, Ivanova E, Watson IR, Nickerson E, Ghosh P, Zhang H, Zeid R, Ren X, Cibulskis K, Sivachenko AY, Wagle N, Sucker A, Sougnez C, Onofrio R, Ambrogio L, Auclair D, Fennell T, Carter SL, Drier Y, Stojanov P, Singer MA, Voet D, Jing R, Saksena G, Barretina J, et al: Melanoma genome sequencing reveals frequent PREX2 mutations. Nature 2012, 485:502-506.
12. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, et al: Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 2012, 150:1107-1120.
13. Kennedy J: Particle swarm optimization. In Encyclopedia of Machine Learning. Edited by Sammut C, Webb G. US: Springer; 2010:760-766.
14. Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G: Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res 2013, 23:228-235.
15. Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005, 310:644-648.
16. Perner S, Demichelis F, Beroukhim R, Schmidt FH, Mosquera JM, Setlur S, Tchinda J, Tomlins SA, Hofer MD, Pienta KG, Kuefer R, Vessella R, Sun X-W, Meyerson M, Lee C, Sellers WR, Chinnaiyan AM, Rubin MA: TMPRSS2:ERG fusion-associated deletions provide insight into the heterogeneity of prostate cancer. Cancer Res 2006, 66:8337-8341.
17. Barbieri CE, Baca SC, Lawrence MS, Demichelis F, Blattner M, Theurillat JP, White TA, Stojanov P, Van Allen E, Stransky N, Nickerson E, Chae S-S, Boysen G, Auclair D, Onofrio RC, Park K, Kitabayashi N, MacDonald TY, Sheikh K, Vuong T, Guiducci C, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Hussain WM, Ramos AH, Winckler W, Redman MC, et al: Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012, 44:685-689.
18. Pruitt KD, Tatusova T, Brown GR, Maglott DR: NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 2012, 40:D130-D135.
19. Bhatia-Gaur R, Donjacour AA, Sciavolino PJ, Kim M, Desai N, Young P, Norton CR, Gridley T, Cardiff RD, Cunha GR, Abate-Shen C, Shen MM: Roles for Nkx3.1 in prostate development and cancer. Genes Dev 1999, 13:966-977.
20. Chitale D, Gong Y, Taylor BS, Broderick S, Brennan C, Somwar R, Golas B, Wang L, Motoi N, Szoke J, Reinersman JM, Major J, Sander C, Seshan VE, Zakowski MF, Rusch V, Pao W, Gerald W, Ladanyi M: An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene 2009, 28:2773-2783.
21. Paolini JB, Mancini J, Genestal M, Gonzalez H, McKay RE, Samii K, Fourcade OA: Predictive value of abdominal obesity vs. body mass index for determining risk of intensive care unit mortality. Crit Care Med 2010, 38:1308-1314.
22. Jepson S, Komatsu M, Haq B, Arango ME, Huang D, Carraway CA, Carraway KL: Muc4/sialomucin complex, the intramembrane ErbB2 ligand, induces specific phosphorylation of ErbB2 and enhances expression of p27(kip), but does not activate mitogen-activated kinase or protein kinaseB/Akt pathways. Oncogene 2002, 21:7524-7532.
23. Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, et al: SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet 2009, 41:1238-1242.
24. Sholl LM, Barletta JA, Yeap BY, Chirieac LR, Hornick JL: Sox2 protein expression is an independent poor prognostic indicator in stage I lung adenocarcinoma. Am J Surg Pathol 2010, 34:1193-1198.
25. Davoli T, Xu AW, Mengwasser KE, Sack LM, Yoon JC, Park PJ, Elledge SJ: Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 2013, 155:948-962.
26. Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N: IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods 2013, 10:1081-1082.
27. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012, 366:883-892.
28. Fontugne J, Lee D, Cantaloni C, Barbieri CE, Caffo O, Hanspeter E, Mazzoleni G, Dalla Palma P, Rubin MA, Fellin G, Mosquera JM, Barbareschi M, Demichelis F: Recurrent prostate cancer genomic alterations predict response to brachytherapy treatment. Cancer Epidemiol Biomarkers Prev 2014, 23:594-600.
29. Krohn A, Freudenthaler F, Harasimowicz S, Kluth M, Fuchs S, Burkhardt L, Stahl P, CT M, Bauer M, Tennstedt P, Graefen M, Steurer S, Sirma H, Sauter G, Schlomm T, Simon R, Minner S: Heterogeneity and chronology of PTEN deletion and ERG fusion in prostate cancer. Mod Pathol 2014. doi:10.1038/modpathol.2014.70.
30. Hodis E, Watson IR, Kryukov GV, Arold ST, Imielinski M, Theurillat JP, Nickerson E, Auclair D, Li L, Place C, Dicara D, Ramos AH, Lawrence MS, Cibulskis K, Sivachenko A, Voet D, Saksena G, Stransky N, Onofrio RC, Winckler W, Ardlie K, Wagle N, Wargo J, Chong K, Morton DL, Stemke-Hale K, Chen G, Noble M, Meyerson M, Ladbury JE, et al: A landscape of driver mutations in melanoma. Cell 2012, 150:251-263.
31. Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G: Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014, 505:495-501.
32. Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N: Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep 2013, 3:2650.
33. Yang Q, Ota K, Tian Y, Kumar A, Wada J, Kashihara N, Wallner E, Kanwar YS: Cloning of rat fibrillin-2 cDNA and its role in branching morphogenesis of embryonic lung. Dev Biol 1999, 212:229-242.
34. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer 2004, 4:177-183.
35. Karin M: Nuclear factor-kappaB in cancer development and progression. Nature 2006, 441:431-436.
36. Lee DF, Kuo HP, Chen CT, Hsu JM, Chou CK, Wei Y, Sun HL, Li LY, Ping B, Huang WC, He X, Hung J-Y, Lai C-C, Ding Q, Su J-L, Yang J-Y, Sahin AA, Hortobagyi GN, Tsai F-J, Tsai C-H, Hung M-C: IKK beta suppression of TSC1 links inflammation and tumor angiogenesis via the mTOR pathway. Cell 2007, 130:440-455.
37. Mosquera JM, Beltran H, Park K, MacDonald TY, Robinson BD, Tagawa ST, Perner S, Bismar TA, Erbersdobler A, Dhir R, Nelson JB, Nanus DM, Rubin MA: Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. Neoplasia 2013, 15:1-IN4.
38. Carreira S, Romanel A, Goodall J, Grist E, Ferraldeschi R, Miranda S, Prandi D, Lorente D, Frenel J-S, Pezaro C, Omlin A, Rodrigues DN, Flohr P, Tunariu N, de Bono JS, Demichelis F, Attard G: Tumor clone dynamics in lethal prostate cancer. Sci Transl Med 2014. in press.
39. Chiang DY, Getz G, Jaffe DB, O'Kelly MJ, Zhao X, Carter SL, Russ C, Nusbaum C, Meyerson M, Lander ES: High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods 2009, 6:99-103.
40. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AWC, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME: Origins and functional impact of copy number variation in the human genome. Nature 2010, 464:704-712.
41. Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, Onofrio R, Carter SL, Park K, Habegger L, Ambrogio L, Fennell T, Parkin M, Saksena G, Voet D, Ramos AH, Pugh TJ, Wilkinson J, Fisher S, Winckler W, Mahan S, Ardlie K, Baldwin J, Simons JW, Kitabayashi N, MacDonald TY, et al: The genomic complexity of primary human prostate cancer. Nature 2011, 470:214-220.
42. Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA: Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer 2009, 48:366-380.
43. Alkodsi A, Louhimo R, Hautaniemi S: Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data. Brief Bioinform 2014, [Epub ahead of print].
44. Degner JF, Marioni JC, Pai AA, Pickrell JK, Nkadori E, Gilad Y, Pritchard JK: Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 2009, 25:3207-3212.
45. Chakravarti IM, Laha RG: Handbook of Methods of Applied Statistics. New York: John Wiley & Sons; 1967.
46. Moore RE, Kearfott RB, Cloud MJ: Introduction to Interval Analysis. Philadelphia: Society for Industrial and Applied Mathematics; 2009.
47. CLONET: CLONality Estimate in Tumors. [ http://demichelislab.unitn.it/CLONET ]
48. Bitbucket: CLONET. [ https://bitbucket.org/deid00/clonet ]