Fri, May 18, 2018 · 10:00

We are excited to announce the second computational cancer genomics event in SVAI's Collaborative Research Series. This event will focus on papillary renal-cell carcinoma type 1 (p1RCC), in partnership with RareKidneyCancer.org, Salesforce, Google, NIH, and NCBI.

We will invite 150 researchers, engineers and enthusiasts to join us at Salesforce in San Francisco for an intense weekend of exploration in computational biomedicine. Interdisciplinary teams will work to further understand, develop potential interventions and advance the standard of care for p1RCC. In addition to sequencing a patient for this event, we will use genomic datasets for p1RCC through the NIH's Cancer Genome Atlas.

https://sv.ai/papillary-renal-cell-carcinoma 

What to expect

BACKGROUND

Papillary renal-cell carcinoma, accounts for between 15 to 20% of all kidney cancers. It occurs in the cells lining the small tubules in the kidney that filter waste from the blood and make urine. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist. 

PURPOSE

  • Advance papillary renal-cell carcinoma research.
  • Contribute to real, ongoing patient case.
  • Create interdisciplinary opportunities for computer scientists and biologists.
  • Learn and develop skills in AI/ML, computational biology and cancer genomics.
  • Build an open community for collaborative biomedicine discovery. 

KEYNOTE

Dr. James Hsieh, MD, PhD, one of North America’s foremost Kidney cancer experts, will be providing the keynote address. Dr. Hsieh is a professor at Washington University's School of Medicine. His research spans Kidney cancer metabolomics, Genomics, Epigenetics, Therapeutics, Precision Medicine, drug development and more.

INVITED RESEARCH PRESENTATION

Clemson University has been working on Translating gene-chemical molecular signature interactions between six tumor subtypes, and will present their findings for:

  1. Identifying TCGA gene expression signatures that are common and unique between Kidney Chromophobe (KICH), Kidney Renal Clear Cell Carcinoma (KIRC), Kidney Renal Papillary Cell Carcinoma (KIRP), Glioblastoma Multiforme (GBM), and Skin Cutaneous Melanoma (SKCM). 
  2. Molecular signatures that are relevant when sub-grouped into tumor stage or male/female samples.
  3. Approved drugs or relevant chemicals that interact with PRRC signatures as possible therapeutics. 

DATASETS

  1. SVAI facilitated sequencing for one p1RCC patient (paid for by UCSF Health): RNA and DNA Whole Genome Sequencing for Tumor and Blood samples, sequenced at 90x using a BGISEQ-500. The data will be available as .bam and .vcf files.
  2. NIH Cancer Genome Atlas (TCGA) for data for Papillary Renal Cell Carcinoma which includes: RNA-Seq gene expression, identifiable germ-line mutations and some clinical information:

    Cases (291)

    Genes (12,063)

    Mutations (25,723)