Multicolor spectral karyotyping of human chromosomes

1. Jemal A, Siegel R, Ward E, et al. Cancer statistics, 2008. CA Cancer J
Clin 2008;58(2):71–96.
2. Speicher MR, Gwyn Ballard S, Ward DC. Karyotyping human chromosomes
by combinatorial multi-fluor FISH. Nat Genet 1996;12(4):
368–375.
3. Schröck E, du Manoir S, Veldman T, et al. Multicolor spectral karyotyping
of human chromosomes. Science 1996;273(5274):494–497.
4. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic
hybridization for molecular cytogenetic analysis of solid tumors. Science
1992;258(5083):818–821.
5. Heidenblad M, Lindgren D, Veltman JA, et al. Microarray analyses
reveal strong influence of DNA copy number alterations on the
transcriptional patterns in pancreatic cancer: implications for the
interpretation of genomic amplifications. Oncogene 2005;24(10):
1794–7801.
6. Hertzberg L, Betts DR, Raimondi SC, et al. Prediction of chromosomal
aneuploidy from gene expression data. Genes Chromosomes
Cancer 2007;46(1):75–86.
7. Hyman E, Kauraniemi P, Hautaniemi S, et al. Impact of DNA amplification
on gene expression patterns in breast cancer. Cancer Res
2002;62(21):6240–6245.
8. Masayesva BG, Ha P, Garrett-Mayer E, et al. Gene expression alterations
over large chromosomal regions in cancers include multiple genes unrelated
to malignant progression. Proc Natl Acad Sci U S A 2004;101(23):
8715–8720.
9. Pollack JR, Sørlie T, Perou CM, et al. Microarray analysis reveals a major
direct role of DNA copy number alteration in the transcriptional program
of human breast tumors. Proc Natl Acad Sci U S A 2002;99(20):
12963–12968.
10. Wang Q, Diskin S, Rappaport E, et al. Integrative genomics identifies
distinct molecular classes of neuroblastoma and shows that multiple
genes are targeted by regional alterations in DNA copy number. Cancer
Res 2006;66(12):6050–6062.
11. Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA
copy number variation using comparative genomic hybridization to
microarrays. Nat Genet 1998;20(2):207–211.
12. Solinas-Toldo S, Lampel S, Stilgenbauer S, et al. Matrix-based comparative
genomic hybridization: biochips to screen for genomic imbalances.
Genes Chromosomes Cancer 1997;20(4):399–407.
13. Ishkanian AS, Malloff CA, Watson SK, et al. A tiling resolution DNA
microarray with complete coverage of the human genome. Nat Genet
2004;36(3):299–303.
14. Chung YJ, Jonkers J, Kitson H, et al. A whole-genome mouse BAC
microarray with 1-Mb resolution for analysis of DNA copy number
changes by array comparative genomic hybridization. Genome Res
2004;14(1):188–196.
15. de Smith AJ, Tsalenko A, Sampas N, et al. Array CGH analysis of copy
number variation identifies 1284 new genes variant in healthy white
males: implications for association studies of complex diseases. Hum
Mol Genet 2007;16(23):2783–2794.
16. de Ståhl TD, Sandgren J, Piotrowski A, et al. Profiling of copy number
variations (CNVs) in healthy individuals from three ethnic groups
using a human genome 32 K BAC-clone-based array. Hum Mutat
2008;29(3):398–408.
17. Choma D, Daurès JP, Quantin X, et al. Aneuploidy and prognosis
of non-small-cell lung cancer: a meta-analysis of published data. Br J
Cancer 2001;85(1):14–22.
18. Whang-Peng J, Kao-Shan CS, Lee EC, et al. Specific chromosome defect
associated with human small-cell lung cancer; deletion 3p(14–23).
Science 1982;215(4529):181–182.
19. Balsara BR, Testa JR. Chromosomal imbalances in human lung cancer.
Oncogene 2002;21(45):6877–6883.
20. Berker-Karaüzüm S, Lüleci G, Ozbilim G, et al. Cytogenetic findings
in thirty lung carcinoma patients. Cancer Genet Cytogenet 1998;
100(2):114–123.
21. Petersen I, Bujard M, Petersen S, et al. Patterns of chromosomal imbalances
in adenocarcinoma and squamous cell carcinoma of the lung.
Cancer Res 1997;57(12):2331–2335.
22. Petersen I, Langreck H, Wolf G, et al. Small-cell lung cancer is characterized
by a high incidence of deletions on chromosomes 3p, 4q, 5q,
10q, 13q and 17p. Br J Cancer 1997;75(1):79–86.
23. Testa JR, Siegfried JM. Chromosome abnormalities in human nonsmall
cell lung cancer. Cancer Res 1992;52(9 Suppl):2702s–2706s.
24. Testa JR, Siegfried JM, Liu Z, et al. Cytogenetic analysis of 63 nonsmall
cell lung carcinomas: recurrent chromosome alterations amid
frequent and widespread genomic upheaval. Genes Chromosomes Cancer
1994;11(3):178–194.
25. Testa JR, Liu Z, Feder M, et al. Advances in the analysis of chromosome
alterations in human lung carcinomas. Cancer Genet Cytogenet
1997;95(1):20–32.
26. Feder M, Siegfried JM, Balshem A, et al. Clinical relevance of chromosome
abnormalities in non-small cell lung cancer. Cancer Genet
Cytogenet 1998;102(1):25–31.
27. Levin NA, Brzoska P, Gupta N, et al. Identification of frequent
novel genetic alterations in small cell lung carcinoma. Cancer Res
1994;54(19):5086–5091.
28. Levin NA, Brzoska PM, Warnock ML, et al. Identification of novel
regions of altered DNA copy number in small cell lung tumors. Genes
Chromosomes Cancer 1995;13(3):175–185.
29. Michelland S, Gazzeri S, Brambilla E, et al. Comparison of chromosomal
imbalances in neuroendocrine and non-small-cell lung carcinomas.
Cancer Genet Cytogenet 1999;114(1):22–30.
30. Ried T, Petersen I, Holtgreve-Grez H, et al. Mapping of multiple DNA
gains and losses in primary small cell lung carcinomas by comparative
genomic hybridization. Cancer Res 1994;54(7):1801–1806.
31. Schwendel A, Langreck H, Reichel M, et al. Primary small-cell lung
carcinomas and their metastases are characterized by a recurrent pattern
of genetic alterations. Int J Cancer 1997;74(1):86–93.
32. Dennis TR, Stock AD. A molecular cytogenetic study of chromosome 3
rearrangements in small cell lung cancer: consistent involvement of chromosome
band 3q13.2. Cancer Genet Cytogenet 1999;113(2):134–140.
33. Grigorova M, Lyman RC, Caldas C, et al. Chromosome abnormalities
in 10 lung cancer cell lines of the NCI-H series analyzed with spectral
karyotyping. Cancer Genet Cytogenet 2005;162(1):1–9.
34. Luk C, Tsao MS, Bayani J, et al. Molecular cytogenetic analysis of nonsmall
cell lung carcinoma by spectral karyotyping and comparative genomic
hybridization. Cancer Genet Cytogenet 2001;125(2):87–99.
35. Sy SM, Fan B, Lee TW, et al. Spectral karyotyping indicates complex
rearrangements in lung adenocarcinoma of nonsmokers. Cancer Genet
Cytogenet 2004;153(1):57–59.
36. Sy SM, Wong N, Lee TW, et al. Distinct patterns of genetic alterations
in adenocarcinoma and squamous cell carcinoma of the lung. Eur J
Cancer 2004;40(7):1082–1094.
37. Tai AL, Fang Y, Sham JS, et al. Establishment and characterization of
a human non-small cell lung cancer cell line. Oncol Rep 2005;13(6):
1029–1032.
38. Harada R, Uemura Y, Kobayashi M, et al. Establishment and characterization
of a new lung cancer cell line (MI-4) producing high
levels of granulocyte colony stimulating factor. Jpn J Cancer Res
2002;93(6):667–676.
39. Ashman JN, Brigham J, Cowen ME, et al. Chromosomal alterations
in small cell lung cancer revealed by multicolour fluorescence in situ
hybridization. Int J Cancer 2002;102(3):230–236.
40. Berrieman HK, Ashman JN, Cowen ME, et al. Chromosomal analysis
of non-small-cell lung cancer by multicolour fluorescent in situ hybridisation.
Br J Cancer 2004;90(4):900–905.
41. Gunawan B, Mirzaie M, Schulten HJ, et al. Molecular cytogenetic
analysis of two primary squamous cell carcinomas of the lung
using multicolor fluorescence in situ hybridization. Virchows Arch
2001;439(1):85–89.
42. Roschke AV, Tonon G, Gehlhaus KS, et al. Karyotypic complexity of the
NCI-60 drug-screening panel. Cancer Res 2003;63(24):8634–8647.
43. Speicher MR, Petersen S, Uhrig S, et al. Analysis of chromosomal
alterations in non-small cell lung cancer by multiplex-FISH, comparative
genomic hybridization, and multicolor bar coding. Lab Invest
2000;80(7):1031–1041.
44. Varella-Garcia M, Chen L, Powell RL, et al. Spectral karyotyping detects
chromosome damage in bronchial cells of smokers and patients
with cancer. Am J Respir Crit Care Med 2007;176(5):505–512.
45. Dang TP, Gazdar AF, Virmani AK, et al. Chromosome 19 translocation,
overexpression of Notch3, and human lung cancer. J Natl Cancer
Inst 2000;92(16):1355–1357.
46. Haruki N, Kawaguchi KS, Eichenberger S, et al. Dominant-negative
Notch3 receptor inhibits mitogen-activated protein kinase pathway and
the growth of human lung cancers. Cancer Res 2005;65(9):3555–3561.
47. Haruki N, Kawaguchi KS, Eichenberger S, et al. Cloned fusion product
from a rare t(15;19)(q13.2;p13.1) inhibit S phase in vitro. J Med
Genet 2005;42(7):558–564.
48. Coe BP, Lee EH, Chi B, et al. Gain of a region on 7p22.3, containing
MAD1L1, is the most frequent event in small-cell lung cancer cell
lines. Genes Chromosomes Cancer 2006;45(1):11–19.
49. Kim YH, Girard L, Giacomini CP, et al. Combined microarray analysis
of small cell lung cancer reveals altered apoptotic balance and distinct
expression signatures of MYC family gene amplification. Oncogene
2006;25(1):130–138.
50. Peng WX, Shibata T, Katoh H, et al. Array-based comparative genomic
hybridization analysis of high-grade neuroendocrine tumors of the
lung. Cancer Sci 2005;96(10):661–667.
51. Zhao X, Weir BA, LaFramboise T, et al. Homozygous deletions
and chromosome amplifications in human lung carcinomas revealed
by single nucleotide polymorphism array analysis. Cancer Res
2005;65(13):5561–5570.
52. Choi JS, Zheng LT, Ha E, et al. Comparative genomic hybridization
array analysis and real-time PCR reveals genomic copy number alteration
for lung adenocarcinomas. Lung 2006;184(6):355–362.
53. Choi YW, Choi JS, Zheng LT, et al. Comparative genomic hybridization
array analysis and real time PCR reveals genomic alterations in
squamous cell carcinomas of the lung. Lung Cancer 2007;55(1):43–51.
54. Dehan E, Ben-Dor A, Liao W, et al. Chromosomal aberrations and
gene expression profiles in non-small cell lung cancer. Lung Cancer
2007;56(2):175–184.
55. Garnis C, Lockwood WW, Vucic E, et al. High resolution analysis of
non-small cell lung cancer cell lines by whole genome tiling path array
CGH. Int J Cancer 2006;118(6):1556–1564.
56. Jiang F, Yin Z, Caraway NP, et al. Genomic profiles in stage I primary
non small cell lung cancer using comparative genomic hybridization
analysis of cDNA microarrays. Neoplasia 2004;6(5):623–635.
57. Kim TM, Yim SH, Lee JS, et al. Genome-wide screening of genomic
alterations and their clinicopathologic implications in non-small cell
lung cancers. Clin Cancer Res 2005;11(23):8235–8242.
58. Ma J, Gao M, Lu Y, et al. Gain of 1q25–32, 12q23–24.3, and 17q12–
22 facilitates tumorigenesis and progression of human squamous cell
lung cancer. J Pathol 2006;210(2):205–213.
59. Tonon G, Wong KK, Maulik G, et al. High-resolution genomic profiles of
human lung cancer. Proc Natl Acad Sci U S A 2005;102(27):9625–9630.
60. Weir BA, Woo MS, Getz G, et al. Characterizing the cancer genome in
lung adenocarcinoma. Nature 2007;450(7171):893–898.
61. Yakut T, Schulten HJ, Demir A, et al. Assessment of molecular events
in squamous and non-squamous cell lung carcinoma. Lung Cancer
2006;54(3):293–301.
62. Kendall J, Liu Q, Bakleh A, et al. Oncogenic cooperation and coamplification
of developmental transcription factor genes in lung cancer.
Proc Natl Acad Sci U S A 2007;104(42):16663–16668.
63. Knudson AG. Chasing the cancer demon. Annu Rev Genet 2000;34:1–19.
64. Levine AJ, Momand J, Finlay CA. The p53 tumour suppressor gene.
Nature 1991;351(6326):453–546.
65. Kishimoto Y, Murakami Y, Shiraishi M, et al. Aberrations of the p53
tumor suppressor gene in human non-small cell carcinomas of the
lung. Cancer Res 1992;52(17):4799–4804.
66. Takahashi T, Nau MM, Chiba I, et al. p53: a frequent target for genetic
abnormalities in lung cancer. Science 1989;246(4929):491–944.
67. Huang CL, Yokomise H, Miyatake A. Clinical significance of the p53
pathway and associated gene therapy in non-small cell lung cancers.
Future Oncol 2007;3(1):83–93.
68. Subramanian J, Govindan R. Lung cancer in never smokers: a review.
J Clin Oncol 2007;25(5):561–570.
69. Toyooka S, Tsuda T, Gazdar AF. The TP53 gene, tobacco exposure, and
lung cancer. Hum Mutat 2003;21(3):229–239.
70. Breuer RH, Snijders PJ, Sutedja GT, et al. Expression of the p16(INK4a)
gene product, methylation of the p16(INK4a) promoter region and
expression of the polycomb-group gene BMI-1 in squamous cell lung
carcinoma and premalignant endobronchial lesions. Lung Cancer
2005;48(3):299–306.
71. Vega FJ, Iniesta P, Caldes T, et al. p53 exon 5 mutations as a prognostic
indicator of shortened survival in non-small-cell lung cancer. Br J
Cancer 1997;76(1):44–51.
72. Berghmans T, Mascaux C, Martin B, et al. Prognostic role of p53 in stage
III non-small cell lung cancer. Anticancer Res 2005;25(3c):2385–2389.
73. Breuer RH, Snijders PJ, Sutedja TG, et al. Suprabasal p53 immunostaining
in premalignant endobronchial lesions in combination
with histology is associated with bronchial cancer. Lung Cancer
2003;40(2):165–172.
74. Mitsudomi T, Lam S, Shirakusa T, et al. Detection and sequencing of
p53 gene mutations in bronchial biopsy samples in patients with lung
cancer. Chest 1993;104(2):362–365.
75. Mitsudomi T, Oyama T, Kusano T, et al. Mutations of the p53 gene
as a predictor of poor prognosis in patients with non-small-cell lung
cancer. J Natl Cancer Inst 1993;85(24):2018–2023.
76. Ponticiello A, Barra E, Giani U, et al. P53 immunohistochemistry can
identify bronchial dysplastic lesions proceeding to lung cancer: a prospective
study. Eur Respir J 2000;15(3):547–552.
77. Higashiyama M, Doi O, Kodama K, et al. MDM2 gene amplification
and expression in non-small-cell lung cancer: immunohistochemical expression
of its protein is a favourable prognostic marker in patients without
p53 protein accumulation. Br J Cancer 1997;75(9):1302–1308.
78. Mori S, Ito G, Usami N, et al. p53 apoptotic pathway molecules are
frequently and simultaneously altered in nonsmall cell lung carcinoma.
Cancer 2004;100(8):1673–1682.
79. Stefanaki K, Rontogiannis D, Vamvouka C, et al. Immunohistochemical
detection of bcl2, p53, mdm2 and p21/waf1 proteins in small-cell lung
carcinomas. Anticancer Res 1998;18(2A):1167–1173.
80. Daniel JC, Smythe WR. The role of Bcl-2 family members in non-small
cell lung cancer. Semin Thorac Cardiovasc Surg 2004;16(1):19–27.
81. Ewen ME. The cell cycle and the retinoblastoma protein family. Cancer
Metastasis Rev 1994;13(1):45–66.
82. Sherr CJ. The INK4a/ARF network in tumour suppression. Nat Rev
Mol Cell Biol 2001;2(10):731–737.
83. Dosaka-Akita H, Cagle PT, Hiroumi H, et al. Differential retinoblastoma
and p16(INK4A) protein expression in neuroendocrine tumors
of the lung. Cancer 2000;88(3):550–556.
84. Cagle PT, el-Naggar AK, Xu HJ, et al. Differential retinoblastoma protein
expression in neuroendocrine tumors of the lung. Potential diagnostic
implications. Am J Pathol 1997;150(2):393–400.
85. Xu HJ, Hu SX, Cagle PT, et al. Absence of retinoblastoma protein
expression in primary non-small cell lung carcinomas. Cancer Res
1991;51(10):2735–2739.
86. Wikenheiser-Brokamp KA. Retinoblastoma regulatory pathway in
lung cancer. Curr Mol Med 2006;6(7):783–793.
87. Goldstein NS. Analysis of stage I lung carcinoma patients including
p53 and Rb protein. Ann Thorac Surg 2000;69(5):1648–1649.
88. Xu HJ, Quinlan DC, Davidson AG, et al. Altered retinoblastoma protein
expression and prognosis in early-stage non-small-cell lung carcinoma.
J Natl Cancer Inst 1994;86(9):695–699.
89. Chen JT, Chen YC, Chen CY, et al. Loss of p16 and/or pRb protein
expression in NSCLC. An immunohistochemical and prognostic study.
Lung Cancer 2001;31(2–3):163–170.
90. Hommura F, aka-Akita H, Kinoshita I, et al. Predictive value of expression
of p16INK4A, retinoblastoma and p53 proteins for the prognosis
of non-small-cell lung cancers. Br J Cancer 1999;81(4):696–701.
91. Gazzeri S, Gouyer V, Vour’ch C, et al. Mechanisms of p16INK4A inactivation
in non small-cell lung cancers. Oncogene 1998;16(4):497–504.
92. Gorgoulis VG, Zacharatos P, Kotsinas A, et al. Alterations of the p16-
pRb pathway and the chromosome locus 9p21–22 in non-small-cell
lung carcinomas: relationship with p53 and MDM2 protein expression.
Am J Pathol 1998;153(6):1749–1765.
93. Sanchez-Cespedes M, Decker PA, et al. Increased loss of chromosome
9p21 but not p16 inactivation in primary non-small cell lung cancer
from smokers. Cancer Res 2001;61(5):2092–2096.
94. Singhal S, Vachani A, ntin-Ozerkis D, et al. Prognostic implications
of cell cycle, apoptosis, and angiogenesis biomarkers in non-small cell
lung cancer: a review. Clin Cancer Res 2005;11(11):3974–3986.
95. Wiest JS, Franklin WA, Drabkin H, et al. Genetic markers for early
detection of lung cancer and outcome measures for response to chemoprevention.
J Cell Biochem Suppl 1997;28–29:64–73.
96. Yanagawa N, Tamura G, Oizumi H, et al. Frequent epigenetic silencing
of the p16 gene in non-small cell lung cancers of tobacco smokers. Jpn
J Cancer Res 2002;93(10):1107–1113.
97. Belinsky SA, Nikula KJ, Palmisano WA, et al. Aberrant methylation
of p16(INK4a) is an early event in lung cancer and a potential biomarker
for early diagnosis. Proc Natl Acad Sci U S A 1998;95(20):
11891–11896.
98. Brambilla E, Constantin B, Drabkin H, et al. Semaphorin SEMA3F
localization in malignant human lung and cell lines: A suggested role in
cell adhesion and cell migration. Am J Pathol 2000;156(3):939–950.
99. Niklinski J, Niklinska W, Chyczewski L, et al. Molecular genetic abnormalities
in premalignant lung lesions: biological and clinical implications.
Eur J Cancer Prev 2001;10(3):213–226.
100. Wang J, Lee JJ, Wang L, et al. Value of p16INK4a and RASSF1A promoter
hypermethylation in prognosis of patients with resectable nonsmall
cell lung cancer. Clin Cancer Res 2004;10(18 Pt 1):6119–6125.
101. Brock MV, Hooker CM, Ota-Machida E, et al. DNA methylation
markers and early recurrence in stage I lung cancer. N Engl J Med
2008;358(11):1118–1128.
102. Braithwaite KL, Rabbitts PH. Multi-step evolution of lung cancer.
Semin Cancer Biol 1999;9(4):255–65.
103. Kok K, Naylor SL, Buys CH. Deletions of the short arm of chromosome
3 in solid tumors and the search for suppressor genes. Adv Cancer
Res 1997;71:27–92.
104. Croce CM, Sozzi G, Huebner K. Role of FHIT in human cancer.
J Clin Oncol 1999;17(5):1618–1624.
105. Garinis GA, Gorgoulis VG, Mariatos G, et al. Association of allelic
loss at the FHIT locus and p53 alterations with tumour kinetics and
chromosomal instability in non-small cell lung carcinomas (NSCLCs).
J Pathol 2001;193(1):55–65.
106. Sard L, Accornero P, Tornielli S, et al. The tumor-suppressor gene
FHIT is involved in the regulation of apoptosis and in cell cycle control.
Proc Natl Acad Sci U S A 1999;96(15):8489–8492.
107. Sozzi G, Pastorino U, Moiraghi L, et al. Loss of FHIT function in lung cancer
and preinvasive bronchial lesions. Cancer Res 1998;58(22):5032–5037.
108. Burbee DG, Forgacs E, Zochbauer-Muller S, et al. Epigenetic inactivation
of RASSF1A in lung and breast cancers and malignant phenotype
suppression. J Natl Cancer Inst 2001;93(9):691–699.
109. Chen H, Suzuki M, Nakamura Y, et al. Aberrant methylation of
RASGRF2 and RASSF1A in human non-small cell lung cancer. Oncol
Rep 2006;15(5):1281–1285.
110. Dammann R, Schagdarsurengin U, Seidel C, et al. The tumor suppressor
RASSF1A in human carcinogenesis: an update. Histol Histopathol
2005;20(2):645–663.
111. Kaira K, Sunaga N, Tomizawa Y, et al. Epigenetic inactivation of the RASeffector
gene RASSF2 in lung cancers. Int J Oncol 2007;31(1):169–173.
112. Feng Q, Hawes SE, Stern JE, et al. DNA methylation in tumor and
matched normal tissues from non-small cell lung cancer patients.
Cancer Epidemiol Biomarkers Prev 2008;17(3):645–654.
113. Ji L, Roth JA. Tumor suppressor FUS1 signaling pathway. J Thorac
Oncol 2008;3(4):327–330.
114. Potiron VA, Roche J, Drabkin HA. Semaphorins and their receptors in
lung cancer. Cancer Lett 2009;273(1):1–14.
115. Ito M, Ito G, Kondo M, Uchiyama M, et al. Frequent inactivation
of RASSF1A, BLU, and SEMA3B on 3p21.3 by promoter hypermethylation
and allele loss in non-small cell lung cancer. Cancer Lett
2005;225(1):131–139.
116. Kuroki T, Trapasso F, Yendamuri S, et al. Allelic loss on chromosome
3p21.3 and promoter hypermethylation of semaphorin 3B in nonsmall
cell lung cancer. Cancer Res 2003;63(12):3352–3355.
117. Lantuejoul S, Constantin B, Drabkin H, et al. Expression of VEGF,
semaphorin SEMA3F, and their common receptors neuropilins NP1
and NP2 in preinvasive bronchial lesions, lung tumours, and cell lines.
J Pathol 2003;200(3):336–347.
118. Futamura M, Kamino H, Miyamoto Y, et al. Possible role of semaphorin
3F, a candidate tumor suppressor gene at 3p21.3, in p53-regulated
tumor angiogenesis suppression. Cancer Res 2007;67(4):1451–1460.
119. Ochi K, Mori T, Toyama Y, et al. Identification of semaphorin3B as a
direct target of p53. Neoplasia 2002;4(1):82–87.
120. Wang YC, Lu YP, Tseng RC, et al. Inactivation of hMLH1 and hMSH2
by promoter methylation in primary non-small cell lung tumors and
matched sputum samples. J Clin Invest 2003;111(6):887–95.
121. Seng TJ, Currey N, Cooper WA, et al. DLEC1 and MLH1 promoter
methylation are associated with poor prognosis in non-small cell lung
carcinoma. Br J Cancer 2008;99(2):375–382.
122. Alvarez S, Germain P, Alvarez R, et al. Structure, function and modulation
of retinoic acid receptor beta, a tumor suppressor. Int J Biochem
Cell Biol 2007;39(7–8):1406–1415.
123. Xu XC. Tumor-suppressive activity of retinoic acid receptor-beta in
cancer. Cancer Lett 2007;253(1):14–24.
124. Virmani AK, Rathi A, Zöchbauer-Müller S, et al. Promoter methylation
and silencing of the retinoic acid receptor-beta gene in lung carcinomas.
J Natl Cancer Inst 2000;92(16):1303–1307.
125. Katayama H, Hiraki A, Fujiwara K, et al. Aberrant promoter methylation
profile in pleural fluid DNA and clinicopathological factors in patients with
non-small cell lung cancer. Asian Pac J Cancer Prev 2007;8(2):221–224.
126. Kim YT, Park SJ, Lee SH, et al. Prognostic implication of aberrant
promoter hypermethylation of CpG islands in adenocarcinoma of the
lung. J Thorac Cardiovasc Surg 2005;130(5):1378.
127. Bogos K, Renyi-Vamos F, Kovacs G, et al. Role of retinoic receptors in
lung carcinogenesis. J Exp Clin Cancer Res 2008;27(1):18.
128. Kim JS, Lee H, Kim H, et al. Promoter methylation of retinoic acid
receptor beta 2 and the development of second primary lung cancers in
non-small-cell lung cancer. J Clin Oncol 2004;22(17):3443–3450.
129. Bunn PA Jr, Franklin W. Epidermal growth factor receptor expression,
signal pathway, and inhibitors in non-small cell lung cancer. Semin
Oncol 2002;29(5 Suppl 14):38–44.
130. Zajac-Kaye M. Myc oncogene: a key component in cell cycle regulation
and its implication for lung cancer. Lung Cancer 2001;34(Suppl 2):
S43–S46.
131. Molina JR, Adjei AA. The Ras/Raf/MAPK pathway. J Thorac Oncol
2006;1(1):7–9.
132. Karamouzis MV, Konstantinopoulos PA, Papavassiliou AG. The role of
STATs in lung carcinogenesis: an emerging target for novel therapeutics.
J Mol Med 2007;85(5):427–436.
133. Angulo B, Suarez-Gauthier A, Lopez-Rios F, et al. Expression signatures
in lung cancer reveal a profile for EGFR-mutant tumours and identify
selective PIK3CA overexpression by gene amplification. J Pathol
2008;214(3):347–356.
134. Massion PP, Taflan PM, Shyr Y, et al. Early involvement of the phosphatidylinositol
3-kinase/Akt pathway in lung cancer progression. Am
J Respir Crit Care Med 2004;170(10):1088–1094.
135. Gautschi O, Ratschiller D, Gugger M, et al. Cyclin D1 in non-small
cell lung cancer: a key driver of malignant transformation. Lung Cancer
2007;55(1):1–14.
136. Thomadaki H, Scorilas A. BCL2 family of apoptosis-related genes:
functions and clinical implications in cancer. Crit Rev Clin Lab Sci
2006;43(1):1–67.
137. Zinkel S, Gross A, Yang E. BCL2 family in DNA damage and cell cycle
control. Cell Death Differ 2006;13(8):1351–1359.
138. Lockwood WW, Chari R, Coe BP, et al. DNA amplification is a ubiquitous
mechanism of oncogene activation in lung and other cancers.
Oncogene 2008;27(33):4615–4624.
139. Hirsch FR, Varella-Garcia M, Bunn PA Jr, et al. Epidermal growth
factor receptor in non-small-cell lung carcinomas: correlation between
gene copy number and protein expression and impact on prognosis.
J Clin Oncol 2003;21(20):3798–3807.
140. Hirsch FR, Varella-Garcia M, Cappuzzo F, et al. Combination of
EGFR gene copy number and protein expression predicts outcome
for advanced non-small-cell lung cancer patients treated with gefitinib.
Ann Oncol 2007;18(4):752–760.
141. Franklin WA, Veve R, Hirsch FR, et al. Epidermal growth factor receptor
family in lung cancer and premalignancy. Semin Oncol 2002;29
(1 Suppl 4):3–14.
142. Merrick DT, Kittelson J, Winterhalder R, et al. Analysis of c-ErbB1/
epidermal growth factor receptor and c-ErbB2/HER-2 expression in
bronchial dysplasia: evaluation of potential targets for chemoprevention
of lung cancer. Clin Cancer Res 2006;12(7 Pt 1):2281–2288.
143. Sharma SV, Bell DW, Settleman J, et al. Epidermal growth factor receptor
mutations in lung cancer. Nat Rev Cancer 2007;7(3):169–181.
144. Endo K, Konishi A, Sasaki H, et al. Epidermal growth factor receptor
gene mutation in non-small cell lung cancer using highly sensitive and
fast TaqMan PCR assay. Lung Cancer 2005;50(3):375–384.
145. Kosaka T, Yatabe Y, Endoh H, et al. Mutations of the epidermal growth
factor receptor gene in lung cancer: biological and clinical implications.
Cancer Res 2004;64(24):8919–8923.
146. Paez JG, Janne PA, Lee JC, et al. EGFR mutations in lung cancer:
correlation with clinical response to gefitinib therapy. Science
2004;304(5676):1497–1500.
147. Shigematsu H, Lin L, Takahashi T, et al. Clinical and biological features
associated with epidermal growth factor receptor gene mutations
in lung cancers. J Natl Cancer Inst 2005;97(5):339–346.
148. Tokumo M, Toyooka S, Kiura K, et al. The relationship between epidermal
growth factor receptor mutations and clinicopathologic features in
non-small cell lung cancers. Clin Cancer Res 2005;11(3):1167–1173.
149. Pao W, Miller V, Zakowski M, et al. EGF receptor gene mutations are
common in lung cancers from “never smokers” and are associated with
sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A
2004;101(36):13306–13311.
150. Marchetti A, Martella C, Felicioni L, et al. EGFR mutations in nonsmall-
cell lung cancer: analysis of a large series of cases and development
of a rapid and sensitive method for diagnostic screening with
potential implications on pharmacologic treatment. J Clin Oncol
2005;23(4):857–865.
151. Lynch TJ, Bell DW, Sordella R, et al. Activating mutations in the epidermal
growth factor receptor underlying responsiveness of non-small-cell
lung cancer to gefitinib. N Engl J Med 2004;350(21):2129–2139.
152. Cappuzzo F, Hirsch FR, Rossi E, et al. Epidermal growth factor receptor
gene and protein and gefitinib sensitivity in non-small-cell lung
cancer. J Natl Cancer Inst 2005;97(9):643–655.
153. Felip E, Rojo F, Reck M, et al. A phase II pharmacodynamic study
of erlotinib in patients with advanced non-small cell lung cancer previously
treated with platinum-based chemotherapy. Clin Cancer Res
2008;14(12):3867–3874.
154. Hirsch FR, Herbst RS, Olsen C, et al. Increased EGFR gene copy
number detected by fluorescent in situ hybridization predicts outcome
in non-small-cell lung cancer patients treated with cetuximab and chemotherapy.
J Clin Oncol 2008;26(20):3351–3357.
155. Zhu CQ, da Cunha SG, Ding K, et al. Role of KRAS and EGFR
as biomarkers of response to erlotinib in National Cancer Institute of
Canada Clinical Trials Group Study BR.21. J Clin Oncol 2008;26(26):
4268–4275.
156. Sone T, Kasahara K, Kimura H, et al. Comparative analysis of epidermal
growth factor receptor mutations and gene amplification as predictors
of gefitinib efficacy in Japanese patients with nonsmall cell lung
cancer. Cancer 2007;109(9):1836–1844.
157. Varella-Garcia M. Stratification of non-small cell lung cancer patients
for therapy with epidermal growth factor receptor inhibitors:
the EGFR fluorescence in situ hybridization assay. Diagn Pathol
2006;1:19.
158. Kanematsu T, Yano S, Uehara H, et al. Phosphorylation, but not
overexpression, of epidermal growth factor receptor is associated
with poor prognosis of non-small cell lung cancer patients. Oncol Res
2003;13(5):289–298.
159. Kobayashi N, Toyooka S, Ichimura K, et al. Non-BAC component but
not epidermal growth factor receptor gene mutation is associated with
poor outcomes in small adenocarcinoma of the lung. J Thorac Oncol
2008;3(7):704–710.
160. Shepherd FA, Tsao MS. Unraveling the mystery of prognostic and predictive
factors in epidermal growth factor receptor therapy. J Clin Oncol
2006;24(7):1219–1220.
161. Cappuzzo F. EGFR FISH versus mutation: different tests, different
end-points. Lung Cancer 2008;60(2):160–165.
162. Mitsudomi T, Kosaka T, Endoh H, et al. Mutations of the epidermal
growth factor receptor gene predict prolonged survival after gefitinib
treatment in patients with non-small-cell lung cancer with postoperative
recurrence. J Clin Oncol 2005;23(11):2513–2520.
163. Hirsch FR, Varella-Garcia M, McCoy J, et al. Increased epidermal
growth factor receptor gene copy number detected by fluorescence
in situ hybridization associates with increased sensitivity to gefitinib
in patients with bronchioloalveolar carcinoma subtypes: a Southwest
Oncology Group Study. J Clin Oncol 2005;23(28):6838–6845.
164. Hirsch FR, Varella-Garcia M, Bunn PA Jr, et al. Molecular predictors of
outcome with gefitinib in a phase III placebo-controlled study in advanced
non-small-cell lung cancer. J Clin Oncol 2006;24(31):5034–5042.
165. Janne PA, Johnson BE. Effect of epidermal growth factor receptor
tyrosine kinase domain mutations on the outcome of patients with
non-small cell lung cancer treated with epidermal growth factor receptor
tyrosine kinase inhibitors. Clin Cancer Res 2006;12(14 Pt 2):
4416s–4420s.
166. Mitsudomi T, Yatabe Y. Mutations of the epidermal growth factor receptor
gene and related genes as determinants of epidermal growth factor
receptor tyrosine kinase inhibitors sensitivity in lung cancer. Cancer
Sci 2007;98(12):1817–1824.
167. Pastorino U, Sozzi G, Miozzo M, et al. Genetic changes in lung cancer.
J Cell Biochem Suppl 1993;17F:237–248.
168. Korrapati V, Gaffney M, Larsson LG, et al. Effect of HER2/neu expression
on survival in non-small-cell lung cancer. Clin Lung Cancer
2001;2(3):216–219.
169. Saad RS, Liu Y, Han H, Landreneau RJ, et al. Prognostic significance
of HER2/neu, p53, and vascular endothelial growth factor expression
in early stage conventional adenocarcinoma and bronchioloalveolar
carcinoma of the lung. Mod Pathol 2004;17(10):1235–1242.
170. Szelachowska J, Jelen M, Kornafel J. Prognostic significance of intracellular
laminin and Her2/neu overexpression in non-small cell lung
cancer. Anticancer Res 2006;26(5B):3871–3876.
171. Cappuzzo F, Varella-Garcia M, Shigematsu H, et al. Increased HER2
gene copy number is associated with response to gefitinib therapy in
epidermal growth factor receptor-positive non-small-cell lung cancer
patients. J Clin Oncol 2005;23(22):5007–5018.
172. Hirsch FR, Varella-Garcia M, Franklin WA, et al. Evaluation of HER-
2/neu gene amplification and protein expression in non-small cell lung
carcinomas. Br J Cancer 2002;86(9):1449–1456.
173. Heinmoller P, Gross C, Beyser K, et al. HER2 status in non-small cell
lung cancer: results from patient screening for enrollment to a phase II
study of herceptin. Clin Cancer Res 2003;9(14):5238–5243.
174. Ugocsai K, Mandoky L, Tiszlavicz L, et al. Investigation of HER2 overexpression
in non-small cell lung cancer. Anticancer Res 2005;25(4):
3061–3066.
175. Pellegrini C, Falleni M, Marchetti A, et al. HER-2/Neu alterations in
non-small cell lung cancer: a comprehensive evaluation by real time
reverse transcription-PCR, fluorescence in situ hybridization, and immunohistochemistry.
Clin Cancer Res 2003;9(10 Pt 1):3645–3652.
176. Mounawar M, Mukeria A, Le CF, et al. Patterns of EGFR, HER2, TP53,
and KRAS mutations of p14arf expression in non-small cell lung cancers
in relation to smoking history. Cancer Res 2007;67(12):5667–5672.
177. Shigematsu H, Takahashi T, Nomura M, et al. Somatic mutations
of the HER2 kinase domain in lung adenocarcinomas. Cancer Res
2005;65(5):1642–1646.
178. Cappuzzo F, Bemis L, Varella-Garcia M. HER2 mutation and response
to trastuzumab therapy in non-small-cell lung cancer. N Engl J Med
2006;354(24):2619–2621.
179. Sithanandam G, Anderson LM. The ERBB3 receptor in cancer and
cancer gene therapy. Cancer Gene Ther 2008;15(7):413–48.
180. Hilbe W, Dirnhofer S, Oberwasserlechner F, et al. Immunohistochemical
typing of non-small cell lung cancer on cryostat sections: correlation
with clinical parameters and prognosis. J Clin Pathol 2003;56(10):
736–741.
181. Lai WW, Chen FF, Wu MH, et al. Immunohistochemical analysis of
epidermal growth factor receptor family members in stage I non-small
cell lung cancer. Ann Thorac Surg 2001;72(6):1868–1876.
182. Cappuzzo F, Toschi L, Domenichini I, et al. HER3 genomic gain and
sensitivity to gefitinib in advanced non-small-cell lung cancer patients.
Br J Cancer 2005;93(12):1334–1340.
183. Carpenter G. ErbB-4: mechanism of action and biology. Exp Cell Res
2003;284(1):66–77.
184. Soung YH, Lee JW, Kim SY, et al. Somatic mutations of the ERBB4 kinase
domain in human cancers. Int J Cancer 2006;118(6):1426–1429.
185. Kranenburg O. The KRAS oncogene: past, present, and future. Biochim
Biophys Acta 2005;1756(2):81–82.
186. Aviel-Ronen S, Blackhall FH, Shepherd FA, et al. K-ras mutations in nonsmall-
cell lung carcinoma: a review. Clin Lung Cancer 2006;8(1):30–38.
187. Hilbe W, Dlaska M, Duba HC, et al. Automated real-time PCR to
determine K-ras codon 12 mutations in non-small cell lung cancer:
comparison with immunohistochemistry and clinico-pathological features.
Int J Oncol 2003;23(4):1121–1126.
188. Marks JL, Broderick S, Zhou Q, et al. Prognostic and therapeutic implications
of EGFR and KRAS mutations in resected lung adenocarcinoma.
J Thorac Oncol 2008;3(2):111–116.
189. Sekido Y, Fong KM, Minna JD. Molecular genetics of lung cancer.
Annu Rev Med 2003;54:73–87.
190. Finberg KE, Sequist LV, Joshi VA, et al. Mucinous differentiation correlates
with absence of EGFR mutation and presence of KRAS mutation
in lung adenocarcinomas with bronchioloalveolar features. J Mol
Diagn 2007;9(3):320–326.
191. Shibata T, Hanada S, Kokubu A, et al. Gene expression profiling of
epidermal growth factor receptor/KRAS pathway activation in lung
adenocarcinoma. Cancer Sci 2007;98(7):985–991.
192. Mascaux C, Iannino N, Martin B, et al. The role of RAS oncogene in
survival of patients with lung cancer: a systematic review of the literature
with meta-analysis. Br J Cancer 2005;92(1):131–139.
193. Bonomi PD, Buckingham L, Coon J. Selecting patients for treatment
with epidermal growth factor tyrosine kinase inhibitors. Clin Cancer
Res 2007;13(15 Pt 2):S4606–S4612.
194. Endoh H, Yatabe Y, Kosaka T, et al. PTEN and PIK3CA expression is
associated with prolonged survival after gefitinib treatment in EGFRmutated
lung cancer patients. J Thorac Oncol 2006;1(7):629–634.
195. Massarelli E, Varella-Garcia M, Tang X, et al. KRAS mutation is an important
predictor of resistance to therapy with epidermal growth factor
receptor tyrosine kinase inhibitors in non-small-cell lung cancer. Clin
Cancer Res 2007;13(10):2890–2896.
196. Pao W, Wang TY, Riely GJ, et al. KRAS mutations and primary resistance
of lung adenocarcinomas to gefitinib or erlotinib. PLoS Med
2005;2(1):E17.
197. Shigematsu H, Gazdar AF. Somatic mutations of epidermal growth
factor receptor signaling pathway in lung cancers. Int J Cancer
2006;118(2):257–262.
198. Ueda M, Toji E, Nunobiki O, et al. Mutational analysis of the BRAF
gene in human tumor cells. Hum Cell 2008;21(2):13–17.
199. Dang CV, O’Donnell KA, Zeller KI, et al. The c-Myc target gene network.
Semin Cancer Biol 2006;16(4):253–264.
200. O’Donnell KA, Wentzel EA, Zeller KI, et al. c-Myc-regulated micro-
RNAs modulate E2F1 expression. Nature 2005;435(7043):839–843.
201. Knoepfler PS, Zhang XY, Cheng PF, et al. Myc influences global chromatin
structure. EMBO J 2006;25(12):2723–2734.
202. Dominguez-Sola D, Ying CY, Grandori C, Ruggiero L, et al. Nontranscriptional
control of DNA replication by c-Myc. Nature 2007;
448(7152):445–451.
203. Bergh JC. Gene amplification in human lung cancer. The myc family
genes and other proto-oncogenes and growth factor genes. Am Rev
Respir Dis 1990;142(6 Pt 2):S20–S26.
204. Brennan J, O’Connor T, Makuch RW, et al. Myc family DNA amplification
in 107 tumors and tumor cell lines from patients with small
cell lung cancer treated with different combination chemotherapy regimens.
Cancer Res 1991;51(6):1708–1712.
205. Kubokura H, Tenjin T, Akiyama H, et al. Relations of the c-myc gene
and chromosome 8 in non-small cell lung cancer: analysis by fluorescence
in situ hybridization. Ann Thorac Cardiovasc Surg 2001;7(4):197–203.
206. Toker A, Newton AC. Cellular signaling: pivoting around PDK-1. Cell
2000;103(2):185–188.
207. Li J, Yen C, Liaw D, et al. PTEN, a putative protein tyrosine phosphatase
gene mutated in human brain, breast, and prostate cancer. Science
1997;275(5308):1943–1947.
208. Cardone MH, Roy N, Stennicke HR, et al. Regulation of cell death protease
caspase-9 by phosphorylation. Science 1998;282(5392):1318–1321.
209. Di CA, Pandolfi PP. The multiple roles of PTEN in tumor suppression.
Cell 2000;100(4):387–390.
210. Mayo LD, Donner DB. The PTEN, Mdm2, p53 tumor suppressoroncoprotein
network. Trends Biochem Sci 2002;27(9):462–467.
211. Brognard J, Clark AS, Ni Y, et al. Akt/protein kinase B is constitutively
active in non-small cell lung cancer cells and promotes cellular
survival and resistance to chemotherapy and radiation. Cancer Res
2001;61(10):3986–3997.
212. Lee HY. Molecular mechanisms of deguelin-induced apoptosis in
transformed human bronchial epithelial cells. Biochem Pharmacol
2004;68(6):1119–1124.
213. Cappuzzo F, Magrini E, Ceresoli GL, et al. Akt phosphorylation and
gefitinib efficacy in patients with advanced non-small-cell lung cancer.
J Natl Cancer Inst 2004;96(15):1133–1141.
214. Kimura S, Hara Y, Pineau T, et al. The T/ebp null mouse: thyroid-specific
enhancer-binding protein is essential for the organogenesis of the thyroid,
lung, ventral forebrain, and pituitary. Genes Dev 1996;10(1):60–69.
215. Berghmans T, Mascaux C, Haller A, et al. EGFR, TTF-1 and Mdm2
expression in stage III non-small cell lung cancer: a positive association.
Lung Cancer 2008;62(1):35–44.
216. Berghmans T, Paesmans M, Mascaux C, et al. Thyroid transcription
factor 1—a new prognostic factor in lung cancer: a meta-analysis. Ann
Oncol 2006;17(11):1673–1676.
217. Kwei KA, Kim YH, Girard L, et al. Genomic profiling identifies TITF1
as a lineage-specific oncogene amplified in lung cancer. Oncogene 2008;
27(25):3635–3640.
218. Petitjean A, Hainaut P, Caron de FC. TP63 gene in stress response and
carcinogenesis: a broader role than expected. Bull Cancer 2006;93(12):
E126–E135.
219. Cipriani NA, Abidoye OO, Vokes E, et al. MET as a target for treatment
of chest tumors. Lung Cancer 2009;63(2):169–179.
220. Ma PC, Kijima T, Maulik G, et al. c-MET mutational analysis in small
cell lung cancer: novel juxtamembrane domain mutations regulating
cytoskeletal functions. Cancer Res 2003;63(19):6272–6281.
221. Ma PC, Jagadeeswaran R, Jagadeesh S, et al. Functional expression
and mutations of c-Met and its therapeutic inhibition with SU11274
and small interfering RNA in non-small cell lung cancer. Cancer Res
2005;65(4):1479–1488.
222. Lutterbach B, Zeng Q, Davis LJ, et al. Lung cancer cell lines harboring
MET gene amplification are dependent on Met for growth and
survival. Cancer Res 2007;67(5):2081–2088.
223. Bean J, Brennan C, Shih JY, et al. MET amplification occurs with or
without T790M mutations in EGFR mutant lung tumors with acquired
resistance to gefitinib or erlotinib. Proc Natl Acad Sci U S A
2007;104(52):20932–20937.
224. Engelman JA, Zejnullahu K, Mitsudomi T, et al. MET amplification
leads to gefitinib resistance in lung cancer by activating ERBB3 signaling.
Science 2007;316(5827):1039–1043.
225. Gazdar AF, Shigematsu H, Herz J, et al. Mutations and addiction
to EGFR: the Achilles ‘heal’ of lung cancers? Trends Mol Med
2004;10(10):481–486.
226. Weinstein IB. Cancer. Addiction to oncogenes—the Achilles heal of
cancer. Science 2002;297(5578):63–64.
227. Weinstein IB, Joe A. Oncogene addiction. Cancer Res 2008;68(9):
3077–3080.
228. Felsher DW. Oncogene addiction versus oncogene amnesia: perhaps
more than just a bad habit? Cancer Res 2008;68(9):3081–3086.
229. Mitelman F, Johansson B, Mertens F. Fusion genes and rearranged
genes as a linear function of chromosome aberrations in cancer. Nat
Genet 2004;36(4):331–334.
230. Mitelman F, Johansson B, Mertens F. The impact of translocations and
gene fusions on cancer causation. Nat Rev Cancer 2007;7(4):233–245.
231. Kumar-Sinha C, Tomlins SA, Chinnaiyan AM. Recurrent gene fusions
in prostate cancer. Nat Rev Cancer 2008;8(7):497–511.
232. Tomlins SA, Rhodes DR, Perner S, et al. Recurrent fusion of
TMPRSS2 and ETS transcription factor genes in prostate cancer.
Science 2005;310(5748):644–648.
233. Tomlins SA, Mehra R, Rhodes DR, et al. TMPRSS2:ETV4 gene fusions
define a third molecular subtype of prostate cancer. Cancer Res
2006;66(7):3396–3400.
234. Tomlins SA, Laxman B, Dhanasekaran SM, et al. Distinct classes of
chromosomal rearrangements create oncogenic ETS gene fusions in
prostate cancer. Nature 2007;448(7153):595–599.
235. Demichelis F, Rubin MA. TMPRSS2-ETS fusion prostate cancer: biological
and clinical implications. J Clin Pathol 2007;60(11):1185–1186.
236. Yoshimoto M, Joshua AM, Cunha IW, et al. Absence of TMPRSS2:
ERG fusions and PTEN losses in prostate cancer is associated with a
favorable outcome. Mod Pathol 2008 21(12):1451–1460.
237. Saramaki OR, Harjula AE, Martikainen PM, et al. TMPRSS2:ERG
fusion identifies a subgroup of prostate cancers with a favorable prognosis.
Clin Cancer Res 2008;14(11):3395–3400.
238. Soda M, Choi YL, Enomoto M, et al. Identification of the transforming
EML4-ALK fusion gene in non-small-cell lung cancer. Nature
2007;448(7153):561–566.
239. Choi YL, Takeuchi K, Soda M, et al. Identification of novel isoforms
of the EML4-ALK transforming gene in non-small cell lung cancer.
Cancer Res 2008;68(13):4971–4976.
240. Perner S, Wagner PL, Demichelis F, et al. EML4-ALK fusion lung cancer:
a rare acquired event. Neoplasia 2008;10(3):298–302.
241. Inamura K, Takeuchi K, Togashi Y, et al. EML4-ALK fusion is linked
to histological characteristics in a subset of lung cancers. J Thorac Oncol
2008;3(1):13–17.
242. Koivunen JP, Mermel C, Zejnullahu K, et al. EML4-ALK fusion gene
and efficacy of an ALK kinase inhibitor in lung cancer. Clin Cancer Res
2008;14(13):4275–4283.
243. Shinmura K, Kageyama S, Tao H, et al. EML4-ALK fusion transcripts,
but no NPM-, TPM3-, CLTC-, ATIC-, or TFG-ALK fusion transcripts,
in non-small cell lung carcinomas. Lung Cancer 2008;61(2):163–169.
244. Perner S, Rubin MA. A variant TMPRSS2 isoform and ERG fusion
product in prostate cancer with implications for molecular diagnosis.
Mod Pathol 2008;21(8):1056–1057.
245. Perner S, Rubin MA. A variant TMPRSS2 isoform and ERG fusion
product in prostate cancer with implications for molecular diagnosis.
Mod Pathol 2008;21(8):1056–1057.
246. Lagos-Quintana M, Rauhut R, Lendeckel W, et al. Identification of
novel genes coding for small expressed RNAs. Science 2001;294(5543):
853–858.
247. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene
lin-4 encodes small RNAs with antisense complementarity to lin-14.
Cell 1993;75(5):843–854.
248. Lau NC, Lim LP, Weinstein EG, et al. An abundant class of tiny RNAs
with probable regulatory roles in Caenorhabditis elegans. Science
2001;294(5543):858–862.
249. Scott GK, Goga A, Bhaumik D, et al. Coordinate suppression of
ERBB2 and ERBB3 by enforced expression of micro-RNA miR-125a
or miR-125b. J Biol Chem 2007;282(2):1479–1486.
250. John B, Enright AJ, Aravin A, et al. Human microRNA targets. PLoS
Biol 2004;2(11):e363.
251. He L, Hannon GJ. MicroRNAs: small RNAs with a big role in gene
regulation. Nat Rev Genet 2004;5(7):522–531.
252. Ambros V. The functions of animal microRNAs. Nature 2004;
431(7006):350–355.
253. Lim LP, Lau NC, Garrett-Engele P, et al. Microarray analysis shows
that some microRNAs downregulate large numbers of target mRNAs.
Nature 2005;433(7027):769–773.
254. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function.
Cell 2004;116(2):281–297.
255. Lewis BP, Shih IH, Jones-Rhoades MW, et al. Prediction of mammalian
microRNA targets. Cell 2003;115(7):787–798.
256. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked
by adenosines, indicates that thousands of human genes are microRNA
targets. Cell 2005;120(1):15–20.
257. Krek A, Grun D, Poy MN, et al. Combinatorial microRNA target predictions.
Nat Genet 2005;37(5):495–500.
258. Kiriakidou M, Nelson PT, Kouranov A, et al. A combined computational-
experimental approach predicts human microRNA targets.
Genes Dev 2004;18(10):1165–1178.
259. Volinia S, Calin GA, Liu CG, et al. A microRNA expression signature
of human solid tumors defines cancer gene targets. Proc Natl Acad Sci
U S A 2006;103(7):2257–2261.
260. Calin GA, Sevignani C, Dumitru CD, et al. Human microRNA genes
are frequently located at fragile sites and genomic regions involved in
cancers. Proc Natl Acad Sci U S A 2004;101(9):2999–3004.
261. Lu J, Getz G, Miska EA, et al. MicroRNA expression profiles classify
human cancers. Nature 2005;435(7043):834–838.
262. Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular
profiles in lung cancer diagnosis and prognosis. Cancer Cell
2006;9(3):189–198.
263. Takamizawa J, Konishi H, Yanagisawa K, et al. Reduced expression of
the let-7 microRNAs in human lung cancers in association with shortened
postoperative survival. Cancer Res 2004;64(11):3753–3756.
264. Johnson SM, Grosshans H, Shingara J, et al. RAS is regulated by the
let-7 microRNA family. Cell 2005;120(5):635–647.
265. Kumar MS, Lu J, Mercer KL, et al. Impaired microRNA processing
enhances cellular transformation and tumorigenesis. Nat Genet
2007;39(5):673–677.
266. Weiss GJ, Bemis LT, Nakajima E, et al. EGFR regulation by microRNA
in lung cancer: correlation with clinical response and survival
to gefitinib and EGFR expression in cell lines. Ann Oncol 2008;19(6):
1053–1059.
267. Hayashita Y, Osada H, Tatematsu Y, et al. A polycistronic microRNA
cluster, miR-17-92, is overexpressed in human lung cancers and en