publication . Article . Other literature type . 2018

Erratum: The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma (Cell Reports (2018) 23(1) (313–326.e5) (S2211124718304364) (10.1016/j.celrep.2018.03.075))

Christopher J. Ricketts; Aguirre A. De Cubas; Huihui Fan; Christof C. Smith; Martin Lang; Ed Reznik; Reanne Bowlby; Ewan A. Gibb; Rehan Akbani; Rameen Beroukhim; ...
Open Access English
  • Published: 01 Jan 2018 Journal: Cell Reports (issn: 2211-1247, Copyright policy)
  • Publisher: Elsevier
Abstract
Graphical abstract In Brief Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtypespecific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes.
Subjects
Medical Subject Headings: urologic and male genital diseasesneoplasmsfemale genital diseases and pregnancy complications
free text keywords: Biology (General), QH301-705.5, General Biochemistry, Genetics and Molecular Biology, 610 Medicine & health, Article, Science & Technology, Life Sciences & Biomedicine, Cell Biology, SOMATIC POINT MUTATIONS, SEQUENCING DATA, RNA-SEQ, CLASS DISCOVERY, MESSENGER-RNA, KIDNEY CANCER, GENETIC-BASIS, EXPRESSION, BREAST, DNA, CDKN2A, DNA hypermethylation, PanCanAtlas, TCGA, chromatin remodeling, chromophobe renal cell carcinoma, clear cell renal cell carcinoma, immune signature, papillary renal cell carcinoma, Cancer Genome Atlas Research Network, CDKN2A; chromatin remodeling; chromophobe renal cell carcinoma; clear cell renal cell carcinoma; DNA hypermethylation; immune signature; PanCanAtlas; papillary renal cell carcinoma; TCGA; Biochemistry, Genetics and Molecular Biology (all), 610 Medicine & health, Biochemistry, Genetics and Molecular Biology (all), Biomarkers, Tumor, Carcinoma, Renal Cell, Cyclin-Dependent Kinase Inhibitor p16, Humans, Kidney Neoplasms, Metabolic Networks and Pathways, Nuclear Proteins, PTEN Phosphohydrolase, Phenotype, Survival Analysis, Transcription Factors, Tumor Suppressor Proteins, Ubiquitin Thiolesterase, Genome, Human, Somatic point mutations; sequencing data; RNA-SEQ; lass discovery; messenger-RNA; kidney cancer; genetic-basis; expression; breast; DNA, Settore MED/27 - Neurochirurgia, Oncology, medicine.medical_specialty, medicine, Regret, business.industry, business, Cancer genome, Cell, medicine.anatomical_structure, Renal cell carcinoma, medicine.disease, Internal medicine, Chromophobe cell, BAP1, Cancer research, Papillary renal cell carcinomas, Biology, PBRM1
Funded by
NIH| TCGA Data Analysis Center at Berkeley
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24CA143799-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| UCSC-Buck Inst. Genome Data Analysis Center for TCGA Research Network (GDAC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24CA143858-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| The USC-JHU Cancer Epigenome Characterization Center
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143882-05S2
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Genome Characterization Center (GCC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143867-05S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143848-02S1
  • Funding stream: NATIONAL CANCER INSTITUTE
62 references, page 1 of 5

Aine, M, Eriksson, P, Liedberg, F, Sjödahl, G, Höglund, M. Biological determinants of bladder cancer gene expression subtypes. Sci Rep. 2015; 5: 10957 [OpenAIRE] [PubMed]

Beck, AH, Espinosa, I, Edris, B, Li, R, Montgomery, K, Zhu, S, Varma, S, Marinelli, RJ, van de Rijn, M, West, RB. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res. 2009; 15: 778-787 [OpenAIRE] [PubMed]

Bindea, G, Mlecnik, B, Tosolini, M, Kirilovsky, A, Waldner, M, Obenauf, AC, Angell, H, Fredriksen, T, Lafontaine, L, Berger, A. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013; 39: 782-795 [PubMed]

Bolotin, DA, Shugay, M, Mamedov, IZ, Putintseva, EV, Turchaninova, MA, Zvyagin, IV, Britanova, OV, Chudakov, DM. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013; 10: 813-814 [OpenAIRE] [PubMed]

Calabrese, C, Simone, D, Diroma, MA, Santorsola, M, Guttà, C, Gasparre, G, Picardi, E, Pesole, G, Attimonelli, M. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014; 30: 3115-3117 [OpenAIRE] [PubMed]

Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013; 499: 43-49 [OpenAIRE] [PubMed]

Linehan, WM, Spellman, PT, Ricketts, CJ, Creighton, CJ, Fei, SS, Davis, C, Wheeler, DA, Murray, BA, Schmidt, L, Vocke, CD. Comprehensive molecular characterization of papillary renal-cell carcinoma. N Engl J Med. 2016; 374: 135-145 [OpenAIRE] [PubMed]

Casuscelli, J, Weinhold, N, Gundem, G, Wang, L, Zabor, EC, Drill, E, Wang, PI, Nanjangud, GJ, Redzematovic, A, Nargund, AM. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma. JCI Insight. 2017; 2: 2

Chen, F, Zhang, Y, Şenbabaoglu, Y, Ciriello, G, Yang, L, Reznik, E, Shuch, B, Micevic, G, De Velasco, G, Shinbrot, E. Multilevel genomics-based taxonomy of renal cell carcinoma. Cell Rep. 2016; 14: 2476-2489 [OpenAIRE] [PubMed]

Chu, A, Robertson, G, Brooks, D, Mungall, AJ, Birol, I, Coope, R, Ma, Y, Jones, S, Marra, MA. Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res. 2016; 44: e3 [OpenAIRE] [PubMed]

Cibulskis, K, Lawrence, MS, Carter, SL, Sivachenko, A, Jaffe, D, Sougnez, C, Gabriel, S, Meyerson, M, Lander, ES, Getz, G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013; 31: 213-219 [OpenAIRE] [PubMed]

Davis, CF, Ricketts, CJ, Wang, M, Yang, L, Cherniack, AD, Shen, H, Buhay, C, Kang, H, Kim, SC, Fahey, CC. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014; 26: 319-330 [OpenAIRE] [PubMed]

Dobin, A, Davis, CA, Schlesinger, F, Drenkow, J, Zaleski, C, Jha, S, Batut, P, Chaisson, M, Gingeras, TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29: 15-21 [OpenAIRE] [PubMed]

Edgar, RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004; 5: 113 [OpenAIRE] [PubMed]

Fan, C, Prat, A, Parker, JS, Liu, Y, Carey, LA, Troester, MA, Perou, CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics. 2011; 4: 3 [OpenAIRE] [PubMed]

62 references, page 1 of 5
Abstract
Graphical abstract In Brief Ricketts et al. find distinctive features of each RCC subtype, providing the foundation for development of subtypespecific therapeutic and management strategies. Somatic alteration of BAP1, PBRM1, and metabolic pathways correlates with subtype-specific decreased survival, while CDKN2A alteration, DNA hypermethylation, and Th2 immune signature correlate with decreased survival within all subtypes.
Subjects
Medical Subject Headings: urologic and male genital diseasesneoplasmsfemale genital diseases and pregnancy complications
free text keywords: Biology (General), QH301-705.5, General Biochemistry, Genetics and Molecular Biology, 610 Medicine & health, Article, Science & Technology, Life Sciences & Biomedicine, Cell Biology, SOMATIC POINT MUTATIONS, SEQUENCING DATA, RNA-SEQ, CLASS DISCOVERY, MESSENGER-RNA, KIDNEY CANCER, GENETIC-BASIS, EXPRESSION, BREAST, DNA, CDKN2A, DNA hypermethylation, PanCanAtlas, TCGA, chromatin remodeling, chromophobe renal cell carcinoma, clear cell renal cell carcinoma, immune signature, papillary renal cell carcinoma, Cancer Genome Atlas Research Network, CDKN2A; chromatin remodeling; chromophobe renal cell carcinoma; clear cell renal cell carcinoma; DNA hypermethylation; immune signature; PanCanAtlas; papillary renal cell carcinoma; TCGA; Biochemistry, Genetics and Molecular Biology (all), 610 Medicine & health, Biochemistry, Genetics and Molecular Biology (all), Biomarkers, Tumor, Carcinoma, Renal Cell, Cyclin-Dependent Kinase Inhibitor p16, Humans, Kidney Neoplasms, Metabolic Networks and Pathways, Nuclear Proteins, PTEN Phosphohydrolase, Phenotype, Survival Analysis, Transcription Factors, Tumor Suppressor Proteins, Ubiquitin Thiolesterase, Genome, Human, Somatic point mutations; sequencing data; RNA-SEQ; lass discovery; messenger-RNA; kidney cancer; genetic-basis; expression; breast; DNA, Settore MED/27 - Neurochirurgia, Oncology, medicine.medical_specialty, medicine, Regret, business.industry, business, Cancer genome, Cell, medicine.anatomical_structure, Renal cell carcinoma, medicine.disease, Internal medicine, Chromophobe cell, BAP1, Cancer research, Papillary renal cell carcinomas, Biology, PBRM1
Funded by
NIH| TCGA Data Analysis Center at Berkeley
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24CA143799-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| UCSC-Buck Inst. Genome Data Analysis Center for TCGA Research Network (GDAC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24CA143858-04
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| The USC-JHU Cancer Epigenome Characterization Center
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143882-05S2
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Genome Characterization Center (GCC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143867-05S1
  • Funding stream: NATIONAL CANCER INSTITUTE
,
NIH| Gene Expression Patterns in Human Tumors Identified Using Transcript Sequencing
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 3U24CA143848-02S1
  • Funding stream: NATIONAL CANCER INSTITUTE
62 references, page 1 of 5

Aine, M, Eriksson, P, Liedberg, F, Sjödahl, G, Höglund, M. Biological determinants of bladder cancer gene expression subtypes. Sci Rep. 2015; 5: 10957 [OpenAIRE] [PubMed]

Beck, AH, Espinosa, I, Edris, B, Li, R, Montgomery, K, Zhu, S, Varma, S, Marinelli, RJ, van de Rijn, M, West, RB. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res. 2009; 15: 778-787 [OpenAIRE] [PubMed]

Bindea, G, Mlecnik, B, Tosolini, M, Kirilovsky, A, Waldner, M, Obenauf, AC, Angell, H, Fredriksen, T, Lafontaine, L, Berger, A. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013; 39: 782-795 [PubMed]

Bolotin, DA, Shugay, M, Mamedov, IZ, Putintseva, EV, Turchaninova, MA, Zvyagin, IV, Britanova, OV, Chudakov, DM. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013; 10: 813-814 [OpenAIRE] [PubMed]

Calabrese, C, Simone, D, Diroma, MA, Santorsola, M, Guttà, C, Gasparre, G, Picardi, E, Pesole, G, Attimonelli, M. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014; 30: 3115-3117 [OpenAIRE] [PubMed]

Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013; 499: 43-49 [OpenAIRE] [PubMed]

Linehan, WM, Spellman, PT, Ricketts, CJ, Creighton, CJ, Fei, SS, Davis, C, Wheeler, DA, Murray, BA, Schmidt, L, Vocke, CD. Comprehensive molecular characterization of papillary renal-cell carcinoma. N Engl J Med. 2016; 374: 135-145 [OpenAIRE] [PubMed]

Casuscelli, J, Weinhold, N, Gundem, G, Wang, L, Zabor, EC, Drill, E, Wang, PI, Nanjangud, GJ, Redzematovic, A, Nargund, AM. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma. JCI Insight. 2017; 2: 2

Chen, F, Zhang, Y, Şenbabaoglu, Y, Ciriello, G, Yang, L, Reznik, E, Shuch, B, Micevic, G, De Velasco, G, Shinbrot, E. Multilevel genomics-based taxonomy of renal cell carcinoma. Cell Rep. 2016; 14: 2476-2489 [OpenAIRE] [PubMed]

Chu, A, Robertson, G, Brooks, D, Mungall, AJ, Birol, I, Coope, R, Ma, Y, Jones, S, Marra, MA. Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res. 2016; 44: e3 [OpenAIRE] [PubMed]

Cibulskis, K, Lawrence, MS, Carter, SL, Sivachenko, A, Jaffe, D, Sougnez, C, Gabriel, S, Meyerson, M, Lander, ES, Getz, G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013; 31: 213-219 [OpenAIRE] [PubMed]

Davis, CF, Ricketts, CJ, Wang, M, Yang, L, Cherniack, AD, Shen, H, Buhay, C, Kang, H, Kim, SC, Fahey, CC. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014; 26: 319-330 [OpenAIRE] [PubMed]

Dobin, A, Davis, CA, Schlesinger, F, Drenkow, J, Zaleski, C, Jha, S, Batut, P, Chaisson, M, Gingeras, TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013; 29: 15-21 [OpenAIRE] [PubMed]

Edgar, RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004; 5: 113 [OpenAIRE] [PubMed]

Fan, C, Prat, A, Parker, JS, Liu, Y, Carey, LA, Troester, MA, Perou, CM. Building prognostic models for breast cancer patients using clinical variables and hundreds of gene expression signatures. BMC Med Genomics. 2011; 4: 3 [OpenAIRE] [PubMed]

62 references, page 1 of 5
Any information missing or wrong?Report an Issue