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hepatocellular_carcinoma [2019/10/18 16:19] – [Data] adminhepatocellular_carcinoma [2020/03/18 18:45] – [Related work] admin
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   - Sequencing was completed by Beckman Coulter using [[http://www.illumina.com/products/truseq_rna_library_prep_kit_v2.html|TruSeq RNA Library Preparation Kit v2]] which is an unstranded protocol.   - Sequencing was completed by Beckman Coulter using [[http://www.illumina.com/products/truseq_rna_library_prep_kit_v2.html|TruSeq RNA Library Preparation Kit v2]] which is an unstranded protocol.
   - Jielei provided TruSeq {{:illumina_stranded_rnaseq_mapping.pdf|Stranded}}  RNA-Seq data from 8 mice in August 2017 (See ~/proj/hcc/data/TPT1/readme.txt), which was analyzed using TruSeq Stranded RNA-Seq.   - Jielei provided TruSeq {{:illumina_stranded_rnaseq_mapping.pdf|Stranded}}  RNA-Seq data from 8 mice in August 2017 (See ~/proj/hcc/data/TPT1/readme.txt), which was analyzed using TruSeq Stranded RNA-Seq.
-  - Gao, Qiang, et al. "Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma." //[[https://www.sciencedirect.com/science/article/pii/S0092867419310037|Cell//]]// 179.2 (2019): 561-577. \\  "The data of WES, transcriptome sequencing, proteome, and phosphoproteome are available in [[https://www.biosino.org/node|NODE]] (accession # [[https://www.biosino.org/node/experiment/detail/OEX001697|OEP000321]]).+  - Gao, Qiang, et al. "Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma." //[[https://www.sciencedirect.com/science/article/pii/S0092867419310037|Cell//]]// 179.2 (2019): 561-577. \\ "The data of WES, transcriptome sequencing, proteome, and phosphoproteome are available in [[https://www.biosino.org/node|NODE]] (accession # [[https://www.biosino.org/node/experiment/detail/OEX001697|OEP000321]]). Survival data (~5 years of followup) were included in Table S1.
  
  
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   - Ching, Travers, Sijia Huang, and Lana X. Garmire. "Power analysis and sample size estimation for RNA-Seq differential expression." //[[http://rnajournal.cshlp.org/content/early/2014/09/22/rna.046011.114|rna]]//20.11 (2014): 1684-1696.   - Ching, Travers, Sijia Huang, and Lana X. Garmire. "Power analysis and sample size estimation for RNA-Seq differential expression." //[[http://rnajournal.cshlp.org/content/early/2014/09/22/rna.046011.114|rna]]//20.11 (2014): 1684-1696.
   - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://www.cell.com/cell/abstract/S0092-8674(17)30639-6?innerTabgraphical_S0092867417306396|Cell]], 2017 [{{:ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}}  ]. TCGA's HCC data and subtyping using DNA copy number, DNA methylation, mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples.   - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, [[http://www.cell.com/cell/abstract/S0092-8674(17)30639-6?innerTabgraphical_S0092867417306396|Cell]], 2017 [{{:ally-copmprehensive_and_integrative_genomic_char_of_hcc-cell-2017.pdf|pdf}}  ]. TCGA's HCC data and subtyping using DNA copy number, DNA methylation, mRNA expression, miRNA expression and RPPA (protein expression). Links to the MDACC dataset with 100 HCC samples.
-  - Subramaniam, Somasundaram, Robin K. Kelley, and Alan P. Venook. "A review of hepatocellular carcinoma (HCC) staging systems." [[http://cco.amegroups.com/article/view/2528/3943|Chinese clinical oncology]] 2.4 (2013). +  - Subramaniam, Somasundaram, Robin K. Kelley, and Alan P. Venook. "A review of hepatocellular carcinoma (HCC) staging systems." [[http://cco.amegroups.com/article/view/2528/3943|Chinese clinical oncology]] 2.4 (2013).​​​ 
- +  Alexandrov, Ludmil B., et al. "The repertoire of mutational signatures in human cancer." [[https://www.nature.com/articles/s41586-020-1943-3#Sec17|Nature]] 578.7793 (2020): 94-101. \\  Analyzed WGS and WXS data of thousands of tumors available from TCGA and PCAWG consortia. 
-----+  Dr. Sukeshi Arora's {{:sukeshi_arora_hcc_update_3.18.20.pptx|slides}}  presented in the HCC meeting on 2020-04-18, which summarizes statistics on the prognosis, the current clinical practice, and response to different treatments.