Transflip mutations produce deletions in pancreatic cancer

Genes Chromosomes and Cancer

Volumn 54, Issue 8, 2015, Pages 472-481

  Norris, Alexis L ^a   Kamiyama, Hirohiko ^a   Makohon Moore, Alvin ^a   Pallavajjala, Aparna ^a   Morsberger, Laura A ^a   Lee, Kurt ^a   Batista, Denise ^a   Iacobuzio Donahue, Christine A ^a   Lin, Ming Tseh ^a   Klein, Alison P ^a   Hruban, Ralph H ^a   Wheelan, Sarah J ^a   Eshleman, James R ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; NUCLEOTIDE; SMAD4 PROTEIN;

ARTICLE; CENTROMERE; CLINICAL ARTICLE; GENE DELETION; GENE MUTATION; GENE SEQUENCE; GENOME; HOMOZYGOUS DELETION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PANCREAS CANCER; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TANSFLIP MUTATION; TELOMERE; TUMOR SUPPRESSOR GENE;

EID: 84931058980     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.22258     Document Type: Article

References (28)

1. Ali H, Daser A, Dear P, Wood H, Rabbitts P, Rabbitts T. 2013. Nonreciprocal chromosomal translocations in renal cancer involve multiple DSBs and NHEJ associated with breakpoint inversion but not necessarily with transcription. Genes Chromosomes Cancer 52:402-409.
2. 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 JP, 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, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA. 2013. Punctuated evolution of prostate cancer genomes. Cell 153:666-677.
3. Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Nones K, Fink JL, Christ A, Bruxner T, Cloonan N, Kolle G, Newell F, Pinese M, Mead RS, Humphris JL, Kaplan W, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chou A, Chin VT, Chantrill LA, Mawson A, Samra JS, Kench JG, Lovell JA, Daly RJ, Merrett ND, Toon C, Epari K, Nguyen NQ, Barbour A, Zeps N, Australian Pancreatic Cancer Genome I, Kakkar N, Zhao F, Wu YQ, Wang M, Muzny DM, Fisher WE, Brunicardi FC, Hodges SE, Reid JG, Drummond J, Chang K, Han Y, Lewis LR, Dinh H, Buhay CJ, Beck T, Timms L, Sam M, Begley K, Brown A, Pai D, Panchal A, Buchner N, De Borja R, Denroche RE, Yung CK, Serra S, Onetto N, Mukhopadhyay D, Tsao MS, Shaw PA, Petersen GM, Gallinger S, Hruban RH, Maitra A, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL, Morgan RA, Lawlor RT, Capelli P, Corbo V, Scardoni M, Tortora G, Tempero MA, Mann KM, Jenkins NA, Perez-Mancera PA, Adams DJ, Largaespada DA, Wessels LF, Rust AG, Stein LD, Tuveson DA, Copeland NG, Musgrove EA, Scarpa A, Eshleman JR, Hudson TJ, Sutherland RL, Wheeler DA, Pearson JV, McPherson JD, Gibbs RA, Grimmond SM. 2012. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 491:399-405.
4. Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, Widaa S, Hinton J, Fahey C, Fu B, Swamy S, Dalgliesh GL, Teh BT, Deloukas P, Yang F, Campbell PJ, Futreal PA, Stratton MR. 2010. Signatures of mutation and selection in the cancer genome. Nature 463:893-898.
5. Caldas C, Hahn SA, da Costa LT, Redston MS, Schutte M, Seymour AB, Weinstein CL, Hruban RH, Yeo CJ, Kern SE. 1994. Frequent somatic mutations and homozygous deletions of the p16 (MTS1) gene in pancreatic adenocarcinoma. Nat Genet 8:27-32.
6. Campbell PJ, Yachida S, Mudie LJ, Stephens PJ, Pleasance ED, Stebbings LA, Morsberger LA, Latimer C, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal SA, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Griffin CA, Burton J, Swerdlow H, Quail MA, Stratton MR, Iacobuzio-Donahue C, Futreal PA. 2010. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature 467:1109-1113.
7. Cayuela JM, Gardie B, Sigaux F. 1997. Disruption of the multiple tumor suppressor gene MTS1/p16(INK4a)/CDKN2 by illegitimate V(D)J recombinase activity in T-cell acute lymphoblastic leukemias. Blood 90:3720-3726.
8. Chiang C, Jacobsen JC, Ernst C, Hanscom C, Heilbut A, Blumenthal I, Mills RE, Kirby A, Lindgren AM, Rudiger SR, McLaughlan CJ, Bawden CS, Reid SJ, Faull RL, Snell RG, Hall IM, Shen Y, Ohsumi TK, Borowsky ML, Daly MJ, Lee C, Morton CC, MacDonald ME, Gusella JF, Talkowski ME. 2012. Complex reorganization and predominant non-homologous repair following chromosomal breakage in karyotypically balanced germline rearrangements and transgenic integration. Nat Genet 44:390-397, S391.
9. Cox C, Bignell G, Greenman C, Stabenau A, Warren W, Stephens P, Davies H, Watt S, Teague J, Edkins S, Birney E, Easton DF, Wooster R, Futreal PA, Stratton MR. 2005. A survey of homozygous deletions in human cancer genomes. Proc Natl Acad Sci USA 102:4542-4547.
10. Embuscado EE, Laheru D, Ricci F, Yun KJ, de Boom Witzel S, Seigel A, Flickinger K, Hidalgo M, Bova GS, Iacobuzio-Donahue CA. 2005. Immortalizing the complexity of cancer metastasis: Genetic features of lethal metastatic pancreatic cancer obtained from rapid autopsy. Cancer Biol Ther 4:548-554.
11. Farmer H, McCabe N, Lord CJ, Tutt AN, Johnson DA, Richardson TB, Santarosa M, Dillon KJ, Hickson I, Knights C, Martin NM, Jackson SP, Smith GC, Ashworth A. 2005. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434:917-921.
12. Griffin CA, Hruban RH, Long PP, Morsberger LA, Douna-Issa F, Yeo CJ. 1994. Chromosome abnormalities in pancreatic adenocarcinoma. Genes Chromosomes Cancer 9:93-100.
13. Griffin CA, Morsberger L, Hawkins AL, Haddadin M, Patel A, Ried T, Schrock E, Perlman EJ, Jaffee E. 2007. Molecular cytogenetic characterization of pancreas cancer cell lines reveals high complexity chromosomal alterations. Cytogenet Genome Res 118:148-156.
14. Hahn SA, Schutte M, Hoque AT, Moskaluk CA, da Costa LT, Rozenblum E, Weinstein CL, Fischer A, Yeo CJ, Hruban RH, Kern SE. 1996. DPC4, a candidate tumor suppressor gene at human chromosome 18q21.1. Science 271:350-353.
15. Herholz H, Kern W, Schnittger S, Haferlach T, Dicker F, Haferlach C. 2007. Translocations as a mechanism for homozygous deletion of 13q14 and loss of the ATM gene in a patient with B-cell chronic lymphocytic leukemia. Cancer Genet Cytogenet 174:57-60.
16. Hustinx SR, Hruban RH, Leoni LM, Iacobuzio-Donahue C, Cameron JL, Yeo CJ, Brown PN, Argani P, Ashfaq R, Fukushima N, Goggins M, Kern SE, Maitra A. 2005. Homozygous deletion of the MTAP gene in invasive adenocarcinoma of the pancreas and in periampullary cancer: A potential new target for therapy. Cancer Biol Ther 4:83-86.
17. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. 2008. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321:1801-1806.
18. Kamiyama H, Rauenzahn S, Shim JS, Karikari CA, Feldmann G, Hua L, Kamiyama M, Schuler FW, Lin MT, Beaty RM, Karanam B, Liang H, Mullendore ME, Mo G, Hidalgo M, Jaffee E, Hruban RH, Jinnah HA, Roden RB, Jimeno A, Liu JO, Maitra A, Eshleman JR. 2013. Personalized chemotherapy profiling using cancer cell lines from selectable mice. Clin Cancer Res 19:1139-1146.
19. Leary RJ, Kinde I, Diehl F, Schmidt K, Clouser C, Duncan C, Antipova A, Lee C, McKernan K, De La Vega FM, Kinzler KW, Vogelstein B, Diaz LA, Jr., Velculescu VE. 2010. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med 2:20ra14.
20. Lee WH, Bookstein R, Hong F, Young LJ, Shew JY, Lee EY. 1987. Human retinoblastoma susceptibility gene: Cloning, identification, and sequence. Science 235:1394-1399.
21. Misawa A, Hosoi H, Imoto I, Iehara T, Sugimoto T, Inazawa J. 2004. Translocation (1;22)(p36;q11.2) with concurrent del(22)(q11.2) resulted in homozygous deletion of SNF5/INI1 in a newly established cell line derived from extrarenal rhabdoid tumor. J Hum Genet 49:586-589.
22. Norris AL, Roberts NJ, Jones S, Wheelan SJ, Papadopoulos N, Vogelstein B, Kinzler KW, Hruban RH, Klein AP, Eshleman JR. 2015. Familial and sporadic pancreatic cancer share the same molecular pathogenesis. Fam Cancer 14:95-103.
23. Raschke S, Balz V, Efferth T, Schulz WA, Florl AR. 2005. Homozygous deletions of CDKN2A caused by alternative mechanisms in various human cancer cell lines. Genes Chromosomes Cancer 42:58-67.
24. Sasaki S, Kitagawa Y, Sekido Y, Minna JD, Kuwano H, Yokota J, Kohno T. 2003. Molecular processes of chromosome 9p21 deletions in human cancers. Oncogene 22:3792-3798.
25. Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. 2015. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Nucleic Acids Res 43:2188-2198.
26. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, Campbell PJ. 2011. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27-40.
27. Tubio JM, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Group IBC, Group IBC, Group IPC, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, van't Veer L, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjord JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Borresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ. 2014. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345:1251343.
28. Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JA. 2007. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35:W71-W74.