publication . Article . 2017

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex

Hong yan Zhong; Yong qun Zhang; Zhao min Deng; Yun hong Wu; Ping Liao; Lin Liu; Wen hai Qiu;
Open Access English
  • Published: 01 May 2017 Journal: PeerJ (issn: 2167-8359, Copyright policy)
  • Publisher: PeerJ Inc.
Abstract
<jats:sec> <jats:title>Background</jats:title> <jats:p>Molecularly targeted therapies improved survival status of some patients with lung adenocarcinoma, which accounts for 40% of all lung cancers, and in-depth study of gene alterations is important for the personalized treatment.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>The legacy archive data of clinical information and genomic variations under the project TCGA Lung Adenocarcinoma were downloaded from the GDC Data Portal using R package TCGAbiolinks. The significantly aberrant copy number variants segments were figured out using GAIA. After annotation, the genes involving CNV we...
Subjects
free text keywords: Lung adenocarcinoma, Genomic variation, CNV, Mutations, PI3K, Medicine, R, Genetics, Oncology, Respiratory Medicine, Medical Genetics, Adenocarcinoma, medicine.disease, Copy-number variation, Lung cancer, PIK3C2B, Protein family, Cancer, SNP, Biology, Cancer research, Mutation, medicine.disease_cause
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24 references, page 1 of 2

Campbell, JD, Alexandrov, A, Kim, J, Wala, J, Berger, AH, Pedamallu, CS, Shukla, SA, Guo, G, Brooks, AN, Murray, BA, Imielinski, M, Hu, X, Ling, S, Akbani, R, Rosenberg, M, Cibulskis, C, Ramachandran, A, Collisson, EA, Kwiatkowski, DJ, Lawrence, MS, Weinstein, JN, Verhaak, RG, Wu, CJ, Hammerman, PS, Cherniack, AD, Getz, G, Artyomov, MN, Schreiber, R, Govindan, R, Meyerso, M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nature Genetics. 2016; 48: 607-616 [OpenAIRE] [PubMed] [DOI]

Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014; 511: 543-550 [OpenAIRE] [PubMed] [DOI]

Colaprico, A, Silva, TC, Olsen, C, Garofano, L, Cava, C, Garolini, D, Sabedot, TS, Malta, TM, Pagnotta, SM, Castiglioni, I, Ceccarelli, M, Bontempi, G, Noushmehr, H. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Research. 2016; 44: e71 [OpenAIRE] [PubMed] [DOI]

Ding, L, Getz, G, Wheeler, DA, Mardis, ER, McLellan, MD, Cibulskis, K, Sougnez, C, Greulich, H, Muzny, DM, Morgan, MB, Fulton, L, Fulton, RS, Zhang, Q, Wendl, MC, Lawrence, MS, Larson, DE, Chen, K, Dooling, DJ, Sabo, A, Hawes, AC, Shen, H, Jhangiani, SN, Lewis, LR, Hall, O, Zhu, Y, Mathew, T, Ren, Y, Yao, J, Scherer, SE, Clerc, K, Metcalf, GA, Ng, B, Milosavljevic, A, Gonzalez-Garay, ML, Osborne, JR, Meyer, R, Shi, X, Tang, Y, Koboldt, DC, Lin, L, Abbott, R, Miner, TL, Pohl, C, Fewell, G, Haipek, C, Schmidt, H, Dunford-Shore, BH, Kraja, A, Crosby, SD, Sawyer, CS, Vickery, T, Sander, S, Robinson, J, Winckler, W, Baldwin, J, Chirieac, LR, Dutt, A, Fennell, T, Hanna, M, Johnson, BE, Onofrio, RC, Thomas, RK, Tonon, G, Weir, BA, Zhao, X, Ziaugra, L, Zody, MC, Giordano, T, Orringer, MB, Roth, JA, Spitz, MR, Wistuba, II, Ozenberger, B, Good, PJ, Chang, AC, Beer, DG, Watson, MA, Ladanyi, M, Broderick, S, Yoshizawa, A, Travis, WD, Pao, W, Province, MA, Weinstock, GM, Varmus, HE, Gabriel, SB, Lander, ES, Gibbs, RA, Meyerson, M, Wilson, RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008; 455: 1069-1075 [OpenAIRE] [PubMed] [DOI]

Durinck, S, Spellman, PT, Birney, E, Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols. 2009; 4: 1184-1191 [OpenAIRE] [PubMed] [DOI]

Gao, J, Aksoy, BA, Dogrusoz, U, Dresdner, G, Gross, B, Sumer, SO, Sun, Y, Jacobsen, A, Sinha, R, Larsson, E, Cerami, E, Sander, C, Schultz, N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling. 2013; 6

Giudice, FS, Squarize, CH. The determinants of head and neck cancer: unmasking the PI3K pathway mutations. Journal of Carcinogenesis & Mutagenesis. 2013; Suppl 5: 1-3

Grivennikov, SI, Greten, FR, Karin, M. Immunity, inflammation, and cancer. Cell. 2010; 140: 883-899 [OpenAIRE] [PubMed] [DOI]

Gu, Z. 2016

Gu, Z, Gu, L, Eils, R, Schlesner, M, Brors, B. Circlize implements and enhances circular visualization in R. Bioinformatics. 2014; 30: 2811-2812 [OpenAIRE] [PubMed] [DOI]

Huang, DW, Sherman, BT, Lempicki, RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research. 2009a; 37: 1-13 [OpenAIRE] [PubMed] [DOI]

Huang, DW, Sherman, BT, Lempicki, RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2009b; 4: 44-57 [PubMed]

Huber, W, Carey, VJ, Gentleman, R, Anders, S, Carlson, M, Carvalho, BS, Bravo, HC, Davis, S, Gatto, L, Girke, T, Gottardo, R, Hahne, F, Hansen, KD, Irizarry, RA, Lawrence, M, Love, MI, MacDonald, J, Obenchain, V, Oles, AK, Pages, H, Reyes, A, Shannon, P, Smyth, GK, Tenenbaum, D, Waldron, L, Morgan, M. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015; 12: 115-121 [OpenAIRE] [PubMed] [DOI]

Imielinski, M, Berger, AH, Hammerman, PS, Hernandez, B, Pugh, TJ, Hodis, E, Cho, J, Suh, J, Capelletti, M, Sivachenko, A, Sougnez, C, Auclair, D, Lawrence, MS, Stojanov, P, Cibulskis, K, Choi, K, De Waal, L, Sharifnia, T, Brooks, A, Greulich, H, Banerji, S, Zander, T, Seidel, D, Leenders, F, Ansen, S, Ludwig, C, Engel-Riedel, W, Stoelben, E, Wolf, J, Goparju, C, Thompson, K, Winckler, W, Kwiatkowski, D, Johnson, BE, Janne, PA, Miller, VA, Pao, W, Travis, WD, Pass, HI, Gabriel, SB, Lander, ES, Thomas, RK, Garraway, LA, Getz, G, Meyerson, M. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 2012; 150: 1107-1120 [OpenAIRE] [PubMed] [DOI]

Krzywinski, M, Schein, J, Birol, I, Connors, J, Gascoyne, R, Horsman, D, Jones, SJ, Marra, MA. Circos: an information aesthetic for comparative genomics. Genome Research. 2009; 19: 1639-1645 [OpenAIRE] [PubMed] [DOI]

24 references, page 1 of 2
Abstract
<jats:sec> <jats:title>Background</jats:title> <jats:p>Molecularly targeted therapies improved survival status of some patients with lung adenocarcinoma, which accounts for 40% of all lung cancers, and in-depth study of gene alterations is important for the personalized treatment.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>The legacy archive data of clinical information and genomic variations under the project TCGA Lung Adenocarcinoma were downloaded from the GDC Data Portal using R package TCGAbiolinks. The significantly aberrant copy number variants segments were figured out using GAIA. After annotation, the genes involving CNV we...
Subjects
free text keywords: Lung adenocarcinoma, Genomic variation, CNV, Mutations, PI3K, Medicine, R, Genetics, Oncology, Respiratory Medicine, Medical Genetics, Adenocarcinoma, medicine.disease, Copy-number variation, Lung cancer, PIK3C2B, Protein family, Cancer, SNP, Biology, Cancer research, Mutation, medicine.disease_cause
Related Organizations
Download fromView all 3 versions
PeerJ
Article . 2017
PeerJ
Article . 2017
Provider: Crossref
PeerJ
Article
Provider: UnpayWall
24 references, page 1 of 2

Campbell, JD, Alexandrov, A, Kim, J, Wala, J, Berger, AH, Pedamallu, CS, Shukla, SA, Guo, G, Brooks, AN, Murray, BA, Imielinski, M, Hu, X, Ling, S, Akbani, R, Rosenberg, M, Cibulskis, C, Ramachandran, A, Collisson, EA, Kwiatkowski, DJ, Lawrence, MS, Weinstein, JN, Verhaak, RG, Wu, CJ, Hammerman, PS, Cherniack, AD, Getz, G, Artyomov, MN, Schreiber, R, Govindan, R, Meyerso, M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nature Genetics. 2016; 48: 607-616 [OpenAIRE] [PubMed] [DOI]

Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014; 511: 543-550 [OpenAIRE] [PubMed] [DOI]

Colaprico, A, Silva, TC, Olsen, C, Garofano, L, Cava, C, Garolini, D, Sabedot, TS, Malta, TM, Pagnotta, SM, Castiglioni, I, Ceccarelli, M, Bontempi, G, Noushmehr, H. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Research. 2016; 44: e71 [OpenAIRE] [PubMed] [DOI]

Ding, L, Getz, G, Wheeler, DA, Mardis, ER, McLellan, MD, Cibulskis, K, Sougnez, C, Greulich, H, Muzny, DM, Morgan, MB, Fulton, L, Fulton, RS, Zhang, Q, Wendl, MC, Lawrence, MS, Larson, DE, Chen, K, Dooling, DJ, Sabo, A, Hawes, AC, Shen, H, Jhangiani, SN, Lewis, LR, Hall, O, Zhu, Y, Mathew, T, Ren, Y, Yao, J, Scherer, SE, Clerc, K, Metcalf, GA, Ng, B, Milosavljevic, A, Gonzalez-Garay, ML, Osborne, JR, Meyer, R, Shi, X, Tang, Y, Koboldt, DC, Lin, L, Abbott, R, Miner, TL, Pohl, C, Fewell, G, Haipek, C, Schmidt, H, Dunford-Shore, BH, Kraja, A, Crosby, SD, Sawyer, CS, Vickery, T, Sander, S, Robinson, J, Winckler, W, Baldwin, J, Chirieac, LR, Dutt, A, Fennell, T, Hanna, M, Johnson, BE, Onofrio, RC, Thomas, RK, Tonon, G, Weir, BA, Zhao, X, Ziaugra, L, Zody, MC, Giordano, T, Orringer, MB, Roth, JA, Spitz, MR, Wistuba, II, Ozenberger, B, Good, PJ, Chang, AC, Beer, DG, Watson, MA, Ladanyi, M, Broderick, S, Yoshizawa, A, Travis, WD, Pao, W, Province, MA, Weinstock, GM, Varmus, HE, Gabriel, SB, Lander, ES, Gibbs, RA, Meyerson, M, Wilson, RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008; 455: 1069-1075 [OpenAIRE] [PubMed] [DOI]

Durinck, S, Spellman, PT, Birney, E, Huber, W. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt. Nature Protocols. 2009; 4: 1184-1191 [OpenAIRE] [PubMed] [DOI]

Gao, J, Aksoy, BA, Dogrusoz, U, Dresdner, G, Gross, B, Sumer, SO, Sun, Y, Jacobsen, A, Sinha, R, Larsson, E, Cerami, E, Sander, C, Schultz, N. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science Signaling. 2013; 6

Giudice, FS, Squarize, CH. The determinants of head and neck cancer: unmasking the PI3K pathway mutations. Journal of Carcinogenesis & Mutagenesis. 2013; Suppl 5: 1-3

Grivennikov, SI, Greten, FR, Karin, M. Immunity, inflammation, and cancer. Cell. 2010; 140: 883-899 [OpenAIRE] [PubMed] [DOI]

Gu, Z. 2016

Gu, Z, Gu, L, Eils, R, Schlesner, M, Brors, B. Circlize implements and enhances circular visualization in R. Bioinformatics. 2014; 30: 2811-2812 [OpenAIRE] [PubMed] [DOI]

Huang, DW, Sherman, BT, Lempicki, RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research. 2009a; 37: 1-13 [OpenAIRE] [PubMed] [DOI]

Huang, DW, Sherman, BT, Lempicki, RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols. 2009b; 4: 44-57 [PubMed]

Huber, W, Carey, VJ, Gentleman, R, Anders, S, Carlson, M, Carvalho, BS, Bravo, HC, Davis, S, Gatto, L, Girke, T, Gottardo, R, Hahne, F, Hansen, KD, Irizarry, RA, Lawrence, M, Love, MI, MacDonald, J, Obenchain, V, Oles, AK, Pages, H, Reyes, A, Shannon, P, Smyth, GK, Tenenbaum, D, Waldron, L, Morgan, M. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 2015; 12: 115-121 [OpenAIRE] [PubMed] [DOI]

Imielinski, M, Berger, AH, Hammerman, PS, Hernandez, B, Pugh, TJ, Hodis, E, Cho, J, Suh, J, Capelletti, M, Sivachenko, A, Sougnez, C, Auclair, D, Lawrence, MS, Stojanov, P, Cibulskis, K, Choi, K, De Waal, L, Sharifnia, T, Brooks, A, Greulich, H, Banerji, S, Zander, T, Seidel, D, Leenders, F, Ansen, S, Ludwig, C, Engel-Riedel, W, Stoelben, E, Wolf, J, Goparju, C, Thompson, K, Winckler, W, Kwiatkowski, D, Johnson, BE, Janne, PA, Miller, VA, Pao, W, Travis, WD, Pass, HI, Gabriel, SB, Lander, ES, Thomas, RK, Garraway, LA, Getz, G, Meyerson, M. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 2012; 150: 1107-1120 [OpenAIRE] [PubMed] [DOI]

Krzywinski, M, Schein, J, Birol, I, Connors, J, Gascoyne, R, Horsman, D, Jones, SJ, Marra, MA. Circos: an information aesthetic for comparative genomics. Genome Research. 2009; 19: 1639-1645 [OpenAIRE] [PubMed] [DOI]

24 references, page 1 of 2
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