Readings

• Sean Davis - Resources for Interpreting Variants in Precision Genomic Oncology Applications

• Ben Busby - Bioinformatics Overview
• Introduction to Kidney cancer
  • 20160109 “Molecular Genetics for the Practicing Physician” - Gabriel G. Malouf - Relates Kidney Physiology to Gene Expression to Therapeutic Targets in 31 slides - pdf
  • 20171103 Papillary RCC - Laurence Albiges - Key point is slide 5: "No increase in Overall survival after a decade."
  • 201712 - “Recommendations for the Management of Rare Kidney Cancers” - pdf - authored by Rarekidneycancer.org members - includes pRCC clinical trials list.
  • 20151105 “Papillary Kidney Carcinoma” - This page is the Web Entry point to pRCC TCGA (The Cancer Genome Atlas) data.
  • 20180305 “Papillary Renal Cell Carcinoma Transcriptome Meta-Analysis” - Michael Edwards - 15 minute Youtube introduction. video metaanalysis presentation
• James Hsieh
  • 20170309 ​Renal cell carcinoma - pdf - General Introduction to all types of Kidney Cancer
  • 20160114 "Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma" - pdf - Marston Linehan et. al. - Molecular characterization based on TCGA.
  • 20180403 The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma - pdf
  • 20180412 - Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal - pdf
  • 20161110 Phase II Trial and Correlative Genomic Analysis of Everolimus Plus Bevacizumab in Advanced Non-Clear Cell Renal Cell Carcinoma. - pdf - Dr. Hsieh's current therapeutic approach to pRcc
  • 20160315 Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma. - pdf
  • 20191031 Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma - pdf
  • 201512 A river model to map convergent cancer evolution and guide therapy in RCC - pdf
• Ryan Leung
  • Building Genomic Analysis Pipelines in a Hackathon Setting
  • Cytogenetic and Molecular Tumor Profiling for Type 1 and Type 2 PRCC
  • Papillary renal cell carcinoma Prognostic value of morphological subtypes in a clinicopathologic study of 43 cases
  • MET Is a Potential Target across All Papillary Renal Cell Carcinomas, Result from a Large Molecular Study of pRCC with CGH Array and Matching Gene Expression Array
  • First-line treatment with sunitinib for type 1 and type 2 locally advanced or metastatic papillary renal cell carcinoma, a phase II study (SUPAP) by the French Genitourinary Group (GETUG)
  • Off‐label drug use in oncology a systematic review of literature
  • The Cancer Genome Atlas Pan-Cancer analysis project
  • Patterns of somatic mutation in human cancer genomes
  • A comprehensive catalogue of somatic mutations from a human cancer genome
  • Mutational heterogeneity in cancer and the search for new cancer-associated genes
  • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
  • Cancer-Specific High-Throughput Annotation of Somatic Mutations, Computational Prediction of Driver Missense Mutations
  • Overcome tumor heterogeneity-imposed therapeutic barriers through convergent genomic biomarker discovery: A braided cancer river model of kidney cancer
  • Gene set enrichment analysis, A knowledge-based approach for interpreting genome-wide expression profiles
  • Neoantigens in cancer immunotherapy
  • An Immunogenic Personal Neoantigen Vaccine for Melanoma Patients
  • In Silico HLA Typing Using Standard RNA-Seq Sequence Reads
  • Best practices for bioinformatic characterization of neoantigens for clinical utility