High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

Genome Research

Volumn 21, Issue 12, 2011, Pages 2181-2189

  Koudijs, Marco J ^a,c   Klijn, Christiaan ^a   Van Der Weyden, Louise ^b   Kool, Jaap ^a,d   Ten Hoeve, Jelle ^a   Sie, Daoud ^a,e   Prasetyanti, Pramudita R ^a   Schut, Eva ^a   Kas, Sjors ^a   Whipp, Theodore ^b   Cuppen, Edwin ^c   Wessels, Lodewyk ^a   Adams, David J ^b   Jonkers, Jos ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^d Intervet Innovation GmbH   (Germany)

^e VU UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANALYTIC METHOD; ARTICLE; CELL CLONE; CLONAL VARIATION; GENE AMPLIFICATION; GENE INSERTION; GENE MUTATION; HIGH THROUGHPUT SCREENING; MOUSE MAMMARY TUMOR ONCOVIRUS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SHEAR SPLINK METHOD; TRANSPOSON; TUMOR GENE;

EID: 83055187859     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.112763.110     Document Type: Article

References (26)

1. Amsterdam A, Burgess S, Golling G, ChenW, Sun Z, Townsend K, Farrington S, Haldi M, Hopkins N. 1999. A large-scale insertional mutagenesis screen in zebrafish. Genes Dev 13: 2713-2724. (Pubitemid 29508558)
2. Bouwman P, Aly A, Escandell JM, Pieterse M, Bartkova J, van der Gulden H, Hiddingh S, Thanasoula M, Kulkarni A, Yang Q, et al. 2010. 53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol 17: 688-695.
3. Carette JE, Guimaraes CP, Varadarajan M, Park AS,Wuethrich I, Godarova A, Kotecki M, Cochran BH, Spooner E, Ploegh HL, et al. 2009. Haploid genetic screens in human cells identify host factors used by pathogens. Science 326: 1231-1235.
4. Collier LS, Carlson CM, Ravimohan S, Dupuy AJ, Largaespada DA. 2005. Cancer gene discovery in solid tumors using transposon-based somatic mutagenesis in the mouse. Nature 436: 272-276. (Pubitemid 41021279)
5. Copeland NG, Jenkins NA. 2010. Harnessing transposons for cancer gene discovery. Nat Rev Cancer 10: 696-706.
6. de Ridder J, Uren A, Kool J, Reinders M, Wessels L. 2006. Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens. PLoS Comput Biol 2: e166. doi: 10.1371/ journal.pcbi.0020166.
7. de Ridder J, Gerrits A, Bot J, de Haan G, Reinders M, Wessels L. 2010. Inferring combinatorial association logic networks in multimodal genome-wide screens. Bioinformatics 26: i149-i157.
8. de Wit T, Dekker S,Maas A, Breedveld G, Knoch TA, Langeveld A, Szumska D,Craig R, Bhattacharya S, Grosveld F, et al. 2010. Taggedmutagenesis by efficient Minos-based germ line transposition. Mol Cell Biol 30: 68-77.
9. Ding S,Wu X, Li G, Han M, Zhuang Y, Xu T. 2005. Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell 122: 473-483. (Pubitemid 41127147)
10. Dupuy AJ, Akagi K, Largaespada DA, Copeland NG, Jenkins NA. 2005. Mammalian mutagenesis using a highly mobile somatic Sleeping Beauty transposon system. Nature 436: 221-226. (Pubitemid 41021267)
11. Dupuy AJ, Rogers LM, Kim J, Nannapaneni K, Starr TK, Liu P, Largaespada DA, Scheetz TE, Jenkins NA, Copeland NG. 2009. A modified Sleeping Beauty transposon system that can be used to model a wide variety of human cancers in mice. Cancer Res 69: 8150-8156.
12. Golling G, Amsterdam A, Sun Z, Antonelli M, Maldonado E, Chen W, Burgess S, Haldi M, Artzt K, Farrington S, et al. 2002. Insertional mutagenesis in zebrafish rapidly identifies genes essential for early vertebrate development. Nat Genet 31: 135-140.
13. Jat PS, Sharp PA. 1986. Large Tantigens of simian virus 40 and polyomavirus efficiently establish primary fibroblasts. J Virol 59: 746-750. (Pubitemid 16011141)
14. KengVW, Yae K, Hayakawa T, Mizuno S, Uno Y, Yusa K, Kokubu C, Kinoshita T, Akagi K, Jenkins NA, et al. 2005. Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system. Nat Methods 2: 763-769. (Pubitemid 41486208)
15. Keng VW, Villanueva A, Chiang DY, Dupuy AJ, Ryan BJ, Matise I, Silverstein KA, Sarver A, Starr TK, Akagi K, et al. 2009. A conditional transposonbased insertional mutagenesis screen for genes associated with mouse hepatocellular carcinoma. Nat Biotechnol 27: 264-274.
16. Kool J, Berns A. 2009. High-throughput insertional mutagenesis screens in mice to identify oncogenic networks. Nat Rev Cancer 9: 389-399.
17. Kool J, Uren AG, Martins CP, Sie D, de Ridder J, Turner G, van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, et al. 2010. Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res 70: 520-531.
18. Kwan H, Pecenka V, Tsukamoto A, Parslow TG, Guzman R, Lin TP, Muller WJ, Lee FS, Leder P, Varmus HE. 1992. Transgenes expressing the Wnt-1 and int-2 proto-oncogenes cooperate during mammary carcinogenesis in doubly transgenic mice. Mol Cell Biol 12: 147-154.
19. Largaespada DA, Collier LS. 2008. Transposon-mediated mutagenesis in somatic cells: Identification of transposon-genomic DNA junctions. Methods Mol Biol 435: 95-108.
20. Lauchle JO, Kim D, Le DT, Akagi K, Crone M, Krisman K,Warner K, Bonifas JM, Li Q, Coakley KM, et al. 2009. Response and resistance to MEK inhibition in leukemias initiated by hyperactive Ras. Nature 461: 411-414.
21. Mikkers H, Berns A. 2003. Retroviral insertional mutagenesis: Tagging cancer pathways. Adv Cancer Res 88: 53-99. (Pubitemid 36343279)
22. Rad R, Rad L,WangW, Cadinanos J, Vassiliou G, Rice S, Campos LS, Yusa K, Banerjee R, Li MA, et al. 2010. PiggyBac transposon mutagenesis: A tool for cancer gene discovery in mice. Science 330: 1104-1107.
23. Starr TK, Allaei R, Silverstein KA, Staggs RA, Sarver AL, Bergemann TL, Gupta M, O'Sullivan MG, Matise I, Dupuy AJ, et al. 2009. A transposon-based genetic screen in mice identifies genes altered in colorectal cancer. Science 323: 1747-1750.
24. Theodorou V, Kimm MA, Boer M,Wessels L, TheelenW, Jonkers J, Hilkens J. 2007. MMTV insertional mutagenesis identifies genes, gene families, and pathways involved in mammary cancer. Nat Genet 39: 759-769. (Pubitemid 46848585)
25. Uren AG, Kool J, Matentzoglu K, de Ridder J, Mattison J, van Uitert M, LagcherW, Sie D, Tanger E, Cox T, et al. 2008. Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks. Cell 133: 727-741. (Pubitemid 351637624)
26. Uren AG, Mikkers H, Kool J, van derWeyden L, Lund AH,Wilson CH, Rance R, Jonkers J, van Lohuizen M, Berns A, et al. 2009. A high-throughput splinkerette-PCR method for the isolation and sequencing of retroviral insertion sites. Nat Protoc 4: 789-798.