1
|
Bray F, Ferlay J, Soerjomataram I, Siegel
RL, Torre LA and Jemal A: Global cancer statistics 2018: GLOBOCAN
estimates of incidence and mortality worldwide for 36 cancers in
185 countries. CA Cancer J Clin. 68:394–424. 2018. View Article : Google Scholar : PubMed/NCBI
|
2
|
Molina JR, Yang P, Cassivi SD, Schild SE
and Adjei AA: Non-small cell lung cancer: Epidemiology, risk
factors, treatment, and survivorship. Mayo Clinic Oroceedings.
83:584–594. 2008. View Article : Google Scholar
|
3
|
Miller KD, Siegel RL, Lin CC, Mariotto AB,
Kramer JL, Rowland JH, Stein KD, Alteri R and Jemal A: Cancer
treatment and survivorship statistics, 2016. CA Cancer J Clin.
66:271–289. 2016. View Article : Google Scholar : PubMed/NCBI
|
4
|
Chen Z, Fillmore CM, Hammerman PS, Kim CF
and Wong KK: Non-small-cell lung cancers: A heterogeneous set of
diseases. Nat Rev Cancer. 14:535–546. 2014. View Article : Google Scholar : PubMed/NCBI
|
5
|
Del Prete C and Azzoli CG: Non-small cell
lung cancer in the Era of personalized medicine: Molecular tests
that matter. R I Med J (2013). 103:28–32. 2020.
|
6
|
Muller IB, de Langen AJ, Giovannetti E and
Peters GJ: Anaplastic lymphoma kinase inhibition in metastatic
non-small cell lung cancer: Clinical impact of alectinib. Onco
Targets Ther. 10:4535–4541. 2017. View Article : Google Scholar : PubMed/NCBI
|
7
|
Bergethon K, Shaw AT, Ou SH, Katayama R,
Lovly CM, McDonald NT, Massion PP, Siwak-Tapp C, Gonzalez A, Fang
R, et al: ROS1 rearrangements define a unique molecular class of
lung cancers. J Clin Oncol. 30:863–870. 2012. View Article : Google Scholar : PubMed/NCBI
|
8
|
Paez JG, Janne PA, Lee JC, Tracy S,
Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, et
al: EGFR mutations in lung cancer: Correlation with clinical
response to gefitinib therapy. Science. 304:1497–1500. 2004.
View Article : Google Scholar : PubMed/NCBI
|
9
|
Comprehensive molecular characterization
of human colon and rectal cancer. Nature. 487:330–337. 2012.
View Article : Google Scholar : PubMed/NCBI
|
10
|
Ronglai S, Olshen AB and Marc L:
Integrative clustering of multiple genomic data types using a joint
latent variable model with application to breast and lung cancer
subtype analysis. Bioinformatics. 25:29062009. View Article : Google Scholar : PubMed/NCBI
|
11
|
Cancer Genome Atlas Research Network.
Electronic address, . simplewheeler@bcm.edu; Cancer
Genome Atlas Research Network: Comprehensive and integrative
genomic characterization of hepatocellular carcinoma. Cell.
169:1327–1341.e23. 2017. View Article : Google Scholar : PubMed/NCBI
|
12
|
Cancer Genome Atlas Research Network, .
Comprehensive molecular profiling of lung adenocarcinoma. Nature.
511:543–550. 2014. View Article : Google Scholar : PubMed/NCBI
|
13
|
Yue QY, Zhao W, Tan Y, Deng XL and Zhang
YH: PLCE1 inhibits apoptosis of non-small cell lung cancer via
promoting PTEN methylation. Eur Rev Med Pharmacol Sci.
23:6211–6216. 2019.PubMed/NCBI
|
14
|
Shahabi S, Kumaran V, Castillo J, Cong Z,
Nandagopal G, Mullen DJ, Alvarado A, Correa MR, Saizan A, Goel R,
et al: LINC00261 Is an epigenetically regulated tumor suppressor
essential for activation of the DNA damage response. Cancer Res.
79:3050–3062. 2019. View Article : Google Scholar : PubMed/NCBI
|
15
|
Yun J, Mi HP, Dong JS, Nam KT, Moon DB, Ju
JH, Hwang OK, Choi JS, Kim TH, Jung YS, et al: IL-32 gamma reduces
lung tumor development through upregulation of TIMP-3
overexpression and hypomethylation. Cell Death Dis. 9:3062018.
View Article : Google Scholar : PubMed/NCBI
|
16
|
Kang X, Kong F, Huang K, Li L, Li Z, Wang
X, Zhang W and Wu X: LncRNA MIR210HG promotes proliferation and
invasion of non-small cell lung cancer by upregulating methylation
of CACNA2D2 promoter via binding to DNMT1. Onco Targets Ther.
12:3779–3790. 2019. View Article : Google Scholar : PubMed/NCBI
|
17
|
Wang Y, Zhang Q, Gao Z, Xin S, Zhao Y,
Zhang K, Shi R and Bao X: A novel 4-gene signature for overall
survival prediction in lung adenocarcinoma patients with lymph node
metastasis. Cancer Cell Int. 19:1002019. View Article : Google Scholar : PubMed/NCBI
|
18
|
Liu C, Li Y, Wei M, Zhao L, Yu Y and Li G:
Identification of a novel glycolysis-related gene signature that
can predict the survival of patients with lung adenocarcinoma. Cell
Cycle. 18:568–579. 2019. View Article : Google Scholar : PubMed/NCBI
|
19
|
Songyang Y, Zhu W, Liu C, Li LL, Hu W,
Zhou Q, Zhang H, Li W and Li D: Large-scale gene expression
analysis reveals robust gene signatures for prognosis prediction in
lung adenocarcinoma. PeerJ. 7:e69802019. View Article : Google Scholar : PubMed/NCBI
|
20
|
R Core Team (2019), . R: A language and
environment for statistical computing. R Foundation for Statistical
Computing. (Vienna, Austria). URL https://www.R-project.org/.
|
21
|
Colaprico A, Silva TC, Olsen C, Garofano
L, Cava C, Garolini D, Sabedot TS, Malta TM, Pagnotta SM,
Castiglioni I, et al: TCGAbiolinks: An R/Bioconductor package for
integrative analysis of TCGA data. Nucleic Acids Res. 44:e712016.
View Article : Google Scholar : PubMed/NCBI
|
22
|
Mo Q, Wang S, Seshan VE, Olshen AB,
Schultz N, Sander C, Powers RS, Ladanyi M and Shen R: Pattern
discovery and cancer gene identification in integrated cancer
genomic data. Proc Natl Acad Sci USA. 110:4245–4250. 2013.
View Article : Google Scholar : PubMed/NCBI
|
23
|
Xu T, Duy LT, Liu L, Su N, Wang R, Sun B,
Colaprico A, Bontempi G and Li J: CancerSubtypes: An R/Bioconductor
package for molecular cancer subtype identification, validation,
and visualization. Bioinformatics. 33:3131–3133. 2017. View Article : Google Scholar : PubMed/NCBI
|
24
|
Sadanori K and Genshiro K: Bayesian
information Criteria. Information Criteria and Statistical
Modeling. Springer Series in Statistics. Springer. (New York, NY).
2008.
|
25
|
Kassambara A and Kosinski M: Survminer:
Drawing Survival Curves using ‘ggplot2’. 2018.
|
26
|
Dardis C: survMisc: Miscellaneous
functions for survival data. 2018.
|
27
|
Bolstad B: PreprocessCore: A collection of
pre-processing functions. 2018.
|
28
|
Therneau TM: A package for survival
analysis in S. 2015.
|
29
|
Simon N, Friedman J, Hastie T and
Tibshirani R: Regularization paths for Cox's proportional hazards
model via coordinate descent. J Stat Softw. 39:1–13. 2011.
View Article : Google Scholar : PubMed/NCBI
|
30
|
Frank E Harrell Jr; with contributions
from Charles Dupont and many others, . Hmisc: Harrell
Miscellaneous. R package version 4.4-0. 2020.
|
31
|
Caesar-Johnson SJ, Demchok JA, Felau I, et
al: The immune landscape of cancer. Immunity. 81:1052018.
|
32
|
Taylor AM, Shih J, Ha G, Gao GF, Zhang X,
Berger AC, Schumacher SE, Wang C, Hu H, Liu J, et al: Genomic and
functional approaches to understanding cancer aneuploidy. Cancer
Cell. 33:676–689.e3. 2018. View Article : Google Scholar : PubMed/NCBI
|
33
|
Cerami E, Gao J, Dogrusoz U, Gross BE,
Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, et
al: The cBio cancer genomics portal: An open platform for exploring
multidimensional cancer genomics data. Cancer Discov. 2:401–404.
2012. View Article : Google Scholar : PubMed/NCBI
|
34
|
Gao J, Aksoy BA, Dogrusoz U, Dresdner G,
Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, et al:
Integrative analysis of complex cancer genomics and clinical
profiles using the cBioPortal. Sci Signal. 6:pl12013. View Article : Google Scholar : PubMed/NCBI
|
35
|
Kassambara A: Ggpubr: ‘Ggplot2’ Based
Publication Ready Plots. 2018.
|
36
|
Mayakonda A and Koeffler HP: Maftools:
Efficient analysis, visualization and summarization of MAF files
from large-scale cohort based cancer studies. bioRxiv.
0526622016.doi: https://doi.org/10.1101/052662.
|
37
|
Chun YS, Pawlik TM and Vauthey JN: 8th
Edition of the AJCC cancer staging manual: Pancreas and
hepatobiliary cancers. Ann Surg Oncol. 25:845–847. 2018. View Article : Google Scholar : PubMed/NCBI
|
38
|
Cancer Genome Atlas Research Network, .
Comprehensive molecular profiling of lung adenocarcinoma. Nature.
511:543–550. 2014. View Article : Google Scholar : PubMed/NCBI
|
39
|
Wei JS, Matsuo K, Hsiung CA, Shiraishi K,
Song M, Kim HN, Wong MP, Hong YC, Hosgood HD III, Wang Z, et al:
Association between GWAS-identified lung adenocarcinoma
susceptibility loci and EGFR mutations in never-smoking Asian
women, and comparison with findings from Western populations. Hum
Mol Genet. 26:454–465. 2016.
|
40
|
Leng S, Wu G, Collins LB, Thomas CL,
Tellez CS, Jauregui AR, Picchi MA, Zhang X, Juri DE, Desai D, et
al: Implication of a chromosome 15q15.2 locus in regulating UBR1
and predisposing smokers to MGMT methylation in lung. Cancer Res.
75:3108–3117. 2015. View Article : Google Scholar : PubMed/NCBI
|
41
|
Tseng RC, Chang JW, Hsien FJ, Chang YH,
Hsiao CF, Chen JT, Chen CY, Jou YS and Wang YC: Genomewide loss of
heterozygosity and its clinical associations in non small cell lung
cancer. Int J Cancer. 117:241–247. 2005. View Article : Google Scholar : PubMed/NCBI
|
42
|
Barter MJ, Gomez R, Hyatt S, Cheung K,
Skelton AJ, Xu Y, Clark IM and Young DA: The long non-coding RNA
ROCR contributes to SOX9 expression and chondrogenic
differentiation of human mesenchymal stem cells. Development.
144:4510–4521. 2017. View Article : Google Scholar : PubMed/NCBI
|
43
|
Dai Z, Popkie AP, Zhu WG, Timmers CD,
Raval A, Tannehill-Gregg S, Morrison CD, Auer H, Kratzke RA,
Niehans G, et al: Bone morphogenetic protein 3B silencing in
non-small-cell lung cancer. Oncogene. 23:3521–3529. 2004.
View Article : Google Scholar : PubMed/NCBI
|
44
|
Lafont J, Talma S, Hopfgarten C and Murphy
CL: Hypoxia promotes the differentiated human articular chondrocyte
phenotype through SOX9-dependent and -independent pathways. J Biol
Chem. 283:4778–4786. 2008. View Article : Google Scholar : PubMed/NCBI
|
45
|
Humbert-Claude M, Duc D, Dwir D, Thieren
L, Sandström von Tobel J, Begka C, Legueux F, Velin D, Maillard MH,
Do KQ, et al: Tollip, an early regulator of the acute inflammatory
response in the substantia nigra. J Neuroinflammation. 13:3032016.
View Article : Google Scholar : PubMed/NCBI
|
46
|
Hsu HP, Lai MD, Lee JC, Yen MC, Weng TY,
Chen WC, Fang JH and Chen YL: Mucin 2 silencing promotes colon
cancer metastasis through interleukin-6 signaling. Sci Rep.
7:58232017. View Article : Google Scholar : PubMed/NCBI
|
47
|
Enss ML, Cornberg M, Wagner S, Gebert A,
Henrichs M, Eisenblätter R, Beil W, Kownatzki R and Hedrich HJ:
Proinflammatory cytokines trigger MUC gene expression and mucin
release in the intestinal cancer cell line LS180. Inflamm Res.
49:162–169. 2000. View Article : Google Scholar : PubMed/NCBI
|
48
|
Rebouissou S, Amessou M, Couchy G, Poussin
K, Imbeaud S, Pilati C, Izard T, Balabaud C, Bioulac-Sage P and
Zucman-Rossi J: Frequent in-frame somatic deletions activate gp130
in inflammatory hepatocellular tumours. Nature. 457:200–204. 2008.
View Article : Google Scholar : PubMed/NCBI
|
49
|
Lakshmanan I, Salfity S, Seshacharyulu P,
Rachagani S, Thomas A, Das S, Majhi PD, Nimmakayala RK, Vengoji R,
Lele SM, et al: MUC16 regulates TSPYL5 for lung cancer cell growth
and chemoresistance by suppressing p53. Clin Cancer Res.
23:3906–3917. 2017. View Article : Google Scholar : PubMed/NCBI
|
50
|
Liu H, Liao Y, Tang M, Wu T, Tan D, Zhang
S and Wang H: Trps1 is associated with the multidrug resistance of
lung cancer cell by regulating MGMT gene expression. Cancer Med.
7:1921–1932. 2018. View Article : Google Scholar : PubMed/NCBI
|
51
|
Shen L, Yang M, Lin Q, Zhang Z, Zhu B and
Miao C: COL11A1 is overexpressed in recurrent non-small cell lung
cancer and promotes cell proliferation, migration, invasion and
drug resistance. Oncol Rep. 36:877–885. 2016. View Article : Google Scholar : PubMed/NCBI
|
52
|
Qiu Z, Lin A, Li K, Lin W, Wang Q, Wei T,
Zhu W, Luo P and Zhang J: A novel mutation panel for predicting
etoposide resistance in small-cell lung cancer. Drug Des Devel
Ther. 13:2021–2041. 2019. View Article : Google Scholar : PubMed/NCBI
|
53
|
Teng JF, Mei QB, Zhou XG, Tang Y, Xiong R,
Qiu WQ, Pan R, Law BY, Wong VK, Yu CL, et al: Polyphyllin VI
induces caspase-1-mediated pyroptosis via the induction of
ROS/NF-κB/NLRP3/GSDMD signal axis in non-small cell lung cancer.
Cancers. 12:1932020. View Article : Google Scholar
|
54
|
Sun H and Wu YL: Dacomitinib in
non-small-cell lung cancer: A comprehensive review for clinical
application. Future Oncol. 15:2769–2777. 2019. View Article : Google Scholar : PubMed/NCBI
|
55
|
Chen H, Chong W, Wu Q, Yao Y, Mao M and
Wang X: Corrigendum: Association of LRP1B mutation with tumor
mutation burden and outcomes in melanoma and non-small cell lung
cancer patients treated with immune check-point blockades. Front
Immunol. 10:15232019. View Article : Google Scholar : PubMed/NCBI
|