Next-Generation Sequence Analysis of Cancer Xenograft Models

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Rossello, Fernando J ^a   Tothill, Richard W ^b,c   Britt, Kara ^a,b   Marini, Kieren D ^a   Falzon, Jeanette ^a   Thomas, David M ^b,c   Peacock, Craig D ^d   Marchionni, Luigi ^d   Li, Jason ^b,c   Bennett, Samara ^a   Tantoso, Erwin ^e   Brown, Tracey ^a   Chan, Philip ^a   Martelotto, Luciano G ^a,f   Watkins, D Neil ^a  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c PETER MACCALLUM CANCER CENTRE   (Australia)

^d JOHNS HOPKINS UNIVERSITY   (United States)

^e Partek SG Private Limited   (Singapore)

^f MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RNA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CANCER CELL CULTURE; CANCER RESEARCH; CELL POPULATION; COMPARATIVE STUDY; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; DISEASE MODEL; FINE NEEDLE ASPIRATION BIOPSY; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HUMAN TISSUE; LUNG BIOPSY; LUNG SMALL CELL CANCER; MOUSE; NONHUMAN; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STROMA CELL; TUMOR XENOGRAFT;

ANIMALS; CELL LINE, TUMOR; DISEASE MODELS, ANIMAL; DNA COPY NUMBER VARIATIONS; EXOME; GENE EXPRESSION PROFILING; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MICE, NUDE; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECIES SPECIFICITY; XENOGRAFT MODEL ANTITUMOR ASSAYS;

EID: 84884597613     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0074432     Document Type: Article

References (35)

1. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46 doi:10.1038/nrg2626.
2. Biankin AV, Waddell N, Kassahn KS, Gingras M-C, Muthuswamy LB, et al. (2012) Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 491: 399-405 doi:10.1038/nature11547.
3. Decaudin D, (2011) Primary human tumor xenografted models ("tumorgrafts") for good management of patients with cancer. Anticancer Drugs 22: 827-841 doi:10.1097/CAD.0b013e3283475f70.
4. Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, et al. (2009) A Primary Xenograft Model of Small-Cell Lung Cancer Reveals Irreversible Changes in Gene Expression Imposed by Culture In vitro. Cancer Research 69: 3364-3373 doi:10.1158/0008-5472.CAN-08-4210.
5. Pandita A, Aldape KD, Zadeh G, Guha A, James CD, (2004) Contrasting in vivo and in vitro fates of glioblastoma cell subpopulations with amplified EGFR. Genes Chromosomes Cancer 39: 29-36 doi:10.1002/gcc.10300.
6. Lee J, Kotliarova S, Kotliarov Y, Li A, Su Q, et al. (2006) Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines. Cancer Cell 9: 391-403 doi:10.1016/j.ccr.2006.03.030.
7. DeRose YS, Wang G, Lin Y-C, Bernard PS, Buys SS, et al. (2011) Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes. Nat Med 17: 1514-1520 doi:10.1038/nm.2454.
8. Ding L, Ellis MJ, Li S, Larson DE, Chen K, et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464: 999-1005 doi:10.1038/nature08989.
9. Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, et al. (2012) Xenome--a tool for classifying reads from xenograft samples. Bioinformatics 28: i172-i178 doi:10.1093/bioinformatics/bts236.
10. Raskatov JAJ, Nickols NGN, Hargrove AEA, Marinov GKG, Wold BB, et al. (2012) Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A 109: 16041-16045 doi:10.1073/pnas.1214267109.
11. Watkins DN, Berman DM, Burkholder SG, Wang B, Beachy PA, et al. (2003) Hedgehog signalling within airway epithelial progenitors and in small-cell lung cancer. Nature 422: 313-317 doi:10.1038/nature01493.
12. Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622-W627 doi:10.1093/nar/gks540.
13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079 doi:10.1093/bioinformatics/btp352.
14. Li J-W, Schmieder R, Ward RM, Delenick J, Olivares EC, et al. (2012) SEQanswers: an open access community for collaboratively decoding genomes. Bioinformatics 28: 1272-1273 doi:10.1093/bioinformatics/bts128.
15. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111 doi:10.1093/bioinformatics/btp120.
16. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25 doi:10.1186/gb-2009-10-3-r25.
17. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B, (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628 doi:10.1038/nmeth.1226.
18. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 36: D13-D21 doi:10.1093/nar/gkm1000.
19. Casey T, Bond J, Tighe S, Hunter T, Lintault L, et al. (2009) Molecular signatures suggest a major role for stromal cells in development of invasive breast cancer. Breast Cancer Res Treat 114: 47-62 doi:10.1007/s10549-008-9982-8.
20. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264 doi:10.1093/biostatistics/4.2.249.
21. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760 doi:10.1093/bioinformatics/btp324.
22. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303 doi:10.1101/gr.107524.110.
23. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498 doi:10.1038/ng.806.
24. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92 doi:10.4161/fly.19695.
25. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24-26 doi:10.1038/nbt.1754.
26. Thorvaldsdottir H, Robinson JT, Mesirov JP, (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 14: 178-192 doi:10.1093/bib/bbs017.
27. Ge H, Liu K, Juan T, Fang F, Newman M, et al. (2011) FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 27: 1922-1928 doi:10.1093/bioinformatics/btr310.
28. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19: 1639-1645 doi:10.1101/gr.092759.109.
29. Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, et al. (2012) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28: 423-425 doi:10.1093/bioinformatics/btr670.
30. Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, Meynert A, et al. (2009) A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463: 184-190 doi:10.1038/nature08629.
31. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, et al. (2012) Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing. The New England journal of medicine 366: 883-892 doi:10.1056/NEJMoa1113205.
32. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, et al. (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61-70 doi:10.1038/nature11412.
33. Yachida S, Jones S, Bozic I, Antal T, Leary R, et al. (2010) Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467: 1114-1117 doi:10.1038/nature09515.
34. Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, et al. (2012) Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet 44: 1104-1110 doi:10.1038/ng.2396.
35. Song S, Nones K, Miller D, Harliwong I, Kassahn KS, et al. (2012) qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS ONE 7: e45835 doi:10.1371/journal.pone.0045835.