cssi-occpr (Agenda)


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WELCOME (10:00 a.m. – 10:30 a.m.)
10:00 a.m. - 10:15 a.m. Opening Remarks
James H. Doroshow, M.D.
Deputy Director for Clinical and Translational Research, National Cancer Institute, NIH
Director, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH
10:15 a.m. -10:30 a.m. State of CPTAC (Status Report)
Henry Rodriguez, Ph.D., M.B.A.
National Cancer Institute, NIH
SESSION I - Tumor Characterization (10:30 a.m. - 12:00 p.m.)
10:30 a.m. -11:00 a.m. Integrated Proteogenomic Characterization Across Major Histological Types of Pediatric Brain Cancer (CPTAC partnership with the Gabriella Miller Kids First Pediatric Research Program)
Francesca Petralia, Ph.D., Icahn School of Medicine at Mount Sinai (Mt Sinai)
11:00 a.m. -11:30 a.m. Proteogenomic Analysis of Head & Neck Cancer
Bing Zhang, Ph.D., Baylor College of Medicine (BCM)
11:30 a.m. - 12:00 p.m. Proteogenomics Refines Breast Cancer Molecular Subtypes and Therapeutic Targets
Michael Gillette, M.D., Ph.D., Broad Institute
12:00 p.m. - 12:30 p.m Lunch and poster viewing
SESSION II - Tumor Characterization (12:30 p.m. - 2:00 p.m.)
12:30 p.m. - 1:00 p.m. Glycoproteomic Characterization of Human High-Grade Serous Ovarian Cancer
Hui Zhang, Ph.D., Johns Hopkins School of Medicine
1:00 p.m. - 1:30 p.m. Global and Phosphoproteomic Analysis of Acute Myeloid Leukemia
(Partnership with BEAT AML Master Clinical Trial)

Elie Traer M.D., Ph.D., Oregon Health & Science University
1:30 p.m. - 2:00 p.m. Progress towards clinical implementation of targeted MRM mass spec-based proteomic assays
Jeff Whiteaker, Ph.D., Fred Hutchinson Cancer Research Center
2:00 p.m. - 2:15 p.m. Break
SESSION III - Data Analysis Tool (2:15 p.m. - 6:10 p.m.)
2:15 p.m. - 2:35 p.m. CPTAC Analysis Tools Catalog (BCM)
2:35 p.m. - 2:55 p.m. The CPTAC Python API (Brigham Young University)
Live Demo - Proteomic/Proteogenomic Tools
2:55 p.m. - 3:15 p.m. PANOPLY: A cloud-based pipeline for automated proteogenomic data analysis (Broad)
3:15 p.m. - 3:35 p.m. ProTrack: An Interactive Multi-Omics Data Browser for Proteogenomic Studies (Mt Sinai)
3:35 p.m. - 3:55 p.m. Deep learning-based peptide retention time prediction and its applications (BCM)
3:55 p.m. - 4:15 p.m. COSMO: A precision FDA-CPTAC sample labelling challenge project (Mt Sinai/BCM)
4:15 p.m. - 4:35 p.m. DreamAI: A CPTAC-Dream Imputation challenge project (Mt Sinai/ New York Uni (NYU))
4:35 p.m. - 4:50 p.m. Break
Live Demo - Genomic/Imaging Tools
4:50 p.m. - 5:10 p.m. CPTAC genomic pipeline organization, tracking, and management (Washington Uni in St. Louis)
5:10 p.m. - 5:30 p.m. CNVEX tool for CNV analysis (Uni of Michigan)
5:30 p.m. - 5:50 p.m. Interpreting pathways to discover cancer driver genes with Moonlight (Uni of Miami/BCM)
5:50 p.m. - 6:10 p.m. Predicting Cancer Subtypes and Molecular Features from Histopathology Images (NYU)
6:10 p.m. Adjourn