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hepatocellular_carcinoma [2019/10/18 19:19]
admin [Data]
hepatocellular_carcinoma [2020/03/18 20:45] (current)
admin [Related work]
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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.