|
1
|
Jemal A, Bray F, Center MM, Ferlay J, Ward
E and Forman D: Global cancer statistics. CA Cancer J Clin.
61:69–90. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Wu XR: Urothelial tumorigenesis: A tale of
divergent pathways. Nat Rev Cancer. 5:713–725. 2005. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Haimovich AD: Methods, challenges, and
promise of next-generation sequencing in cancer biology. Yale J
Biol Med. 84:439–446. 2011.PubMed/NCBI
|
|
4
|
Mardis ER, Ding L, Dooling DJ, Larson DE,
McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath
SD, et al: Recurring mutations found by sequencing an acute myeloid
leukemia genome. N Engl J Med. 361:1058–1066. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Ley TJ, Mardis ER, Ding L, Fulton B,
McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S,
Hickenbotham M, et al: DNA sequencing of a cytogenetically normal
acute myeloid leukaemia genome. Nature. 456:66–72. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Stephens PJ, McBride DJ, Lin ML, Varela I,
Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie
LJ, et al: Complex landscapes of somatic rearrangement in human
breast cancer genomes. Nature. 462:1005–1010. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Ding L, Ellis MJ, Li S, Larson DE, Chen K,
Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, et al:
Genome remodelling in a basal-like breast cancer metastasis and
xenograft. Nature. 464:999–1005. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
8
|
Shah SP, Morin RD, Khattra J, Prentice L,
Pugh T, Burleigh A, Delaney A, Gelmon K, Guliany R, Senz J, et al:
Mutational evolution in a lobular breast tumour profiled at single
nucleotide resolution. Nature. 461:809–813. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Pleasance ED, Cheetham RK, Stephens PJ,
McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin ML, Ordóñez GR,
Bignell GR, et al: A comprehensive catalogue of somatic mutations
from a human cancer genome. Nature. 463:191–196. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
10
|
Pleasance ED, Stephens PJ, O'Meara S,
McBride DJ, Meynert A, Jones D, Lin ML, Beare D, Lau KW, Greenman
C, et al: A small-cell lung cancer genome with complex signatures
of tobacco exposure. Nature. 463:184–190. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Campbell PJ, Stephens PJ, Pleasance ED,
O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S,
Hardy C, et al: Identification of somatically acquired
rearrangements in cancer using genome-wide massively parallel
paired-end sequencing. Nat Genet. 40:722–729. 2008. View Article : Google Scholar : PubMed/NCBI
|
|
12
|
Xu X, Hou Y, Yin X, Bao L, Tang A, Song L,
Li F, Tsang S, Wu K, Wu H, et al: Single-cell exome sequencing
reveals single-nucleotide mutation characteristics of a kidney
tumor. Cell. 148:886–895. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Jones S, Wang TL, Shih IEM, Mao TL,
Nakayama K, Roden R, Glas R, Slamon D, Diaz LA Jr, Vogelstein B, et
al: Frequent mutations of chromatin remodeling gene ARID1A in
ovarian clear cell carcinoma. Science. 330:228–231. 2010.
View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Gui Y, Guo G, Huang Y, Hu X, Tang A, Gao
S, Wu R, Chen C, Li X, Zhou L, et al: Frequent mutations of
chromatin remodeling genes in transitional cell carcinoma of the
bladder. Nat Genet. 43:875–878. 2011. View
Article : Google Scholar : PubMed/NCBI
|
|
15
|
Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S,
Li F, Im KM, Wu K, Wu H, et al: Single-cell sequencing analysis
characterizes common and cell-lineage-specific mutations in a
muscle-invasive bladder cancer. Gigascience. 1:122012. View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Guo G, Sun X, Chen C, Wu S, Huang P, Li Z,
Dean M, Huang Y, Jia W, Zhou Q, et al: Whole-genome and whole-exome
sequencing of bladder cancer identifies frequent alterations in
genes involved in sister chromatid cohesion and segregation. Nat
Genet. 45:1459–1463. 2013. View
Article : Google Scholar : PubMed/NCBI
|
|
17
|
El Gendy H, Madkour B, Abdelaty S, Essawy
F, Khattab D, Hammam O, El Kholy A and Nour HH: Galectin 3 for the
diagnosis of bladder cancer. Arab J Urol. 12:178–181. 2014.
View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Li H and Durbin R: Fast and accurate short
read alignment with Burrows-Wheeler transform. Bioinformatics.
25:1754–1760. 2009. View Article : Google Scholar : PubMed/NCBI
|
|
19
|
McKenna A, Hanna M, Banks E, Sivachenko A,
Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly
M and DePristo MA: The genome analysis toolkit: A MapReduce
framework for analyzing next-generation DNA sequencing data. Genome
Res. 20:1297–1303. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Koboldt DC, Chen K, Wylie T, Larson DE,
McLellan MD, Mardis ER, Weinstock GM, Wilson RK and Ding L:
VarScan: Variant detection in massively parallel sequencing of
individual and pooled samples. Bioinformatics. 25:2283–2285. 2009.
View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Koboldt DC, Zhang Q, Larson DE, Shen D,
McLellan MD, Lin L, Miller CA, Mardis ER, Ding L and Wilson RK:
VarScan 2: Somatic mutation and copy number alteration discovery in
cancer by exome sequencing. Genome Res. 22:568–576. 2012.
View Article : Google Scholar : PubMed/NCBI
|
|
22
|
Wang K, Li M and Hakonarson H: ANNOVAR:
Functional annotation of genetic variants from high-throughput
sequencing data. Nucleic Acids Res. 38:e1642010. View Article : Google Scholar : PubMed/NCBI
|
|
23
|
Pflueger D, Terry S, Sboner A, Habegger L,
Esgueva R, Lin PC, Svensson MA, Kitabayashi N, Moss BJ, MacDonald
TY, Cao X, et al: Discovery of non-ETS gene fusions in human
prostate cancer using next-generation RNA sequencing. Genome Res.
21:56–67. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Robinson JT, Thorvaldsdóttir H, Winckler
W, Guttman M, Lander ES, Getz G and Mesirov JP: Integrative
genomics viewer. Nat Biotechnol. 29:24–26. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
25
|
Ding L, Ley TJ, Larson DE, Miller CA,
Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan
MD, et al: Clonal evolution in relapsed acute myeloid leukaemia
revealed by whole-genome sequencing. Nature. 481:506–510. 2012.
View Article : Google Scholar : PubMed/NCBI
|
|
26
|
Greenman C, Stephens P, Smith R, Dalgliesh
GL, Hunter C, Bignell G, Davies H, Teague J, Butler A, Stevens C,
et al: Patterns of somatic mutation in human cancer genomes.
Nature. 446:153–158. 2007. View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Miyazaki K, Fujita T, Ozaki T, Kato C,
Kurose Y, Sakamoto M, Kato S, Goto T, Itoyama Y, Aoki M and
Nakagawara A: NEDL1, a novel ubiquitin-protein isopeptide ligase
for dishevelled-1, targets mutant superoxide dismutase-1. J Biol
Chem. 279:11327–11335. 2004. View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Donovan P and Poronnik P: Nedd4 and
Nedd4-2: Ubiquitin ligases at work in the neuron. Int J Biochem
Cell Biol. 45:706–710. 2013. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Cui Y, He S, Xing C, Lu K, Wang J, Xing G,
Meng A, Jia S, He F and Zhang L: SCFFBXL15 regulates BMP
signalling by directing the degradation of HECT-type ubiquitin
ligase Smurf1. EMBO J. 30:2675–2689. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Zhang L, Haraguchi S, Koda T, Hashimoto K
and Nakagawara A: Muscle atrophy and motor neuron degeneration in
human NEDL1 transgenic mice. J Biomed Biotechnol. 2011:8310922011.
View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Li Y, Ozaki T, Kikuchi H, Yamamoto H,
Ohira M and Nakagawara A: A novel HECT-type E3 ubiquitin protein
ligase NEDL1 enhances the p53-mediated apoptotic cell death in its
catalytic activity-independent manner. Oncogene. 27:3700–3709.
2008. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Li Y, Zhou Z, Alimandi M and Chen C: WW
domain containing E3 ubiquitin protein ligase 1 targets the
full-length ErbB4 for ubiquitin-mediated degradation in breast
cancer. Oncogene. 28:2948–2958. 2009. View Article : Google Scholar : PubMed/NCBI
|
