The Clinical Proteomic Tumor Analysis Consortium

(CPTAC 3.0) STEERING COMMITTEE Meeting

 

<scientific & Programmatic updates>

May 1-3, 2018

 

National Institutes of Health

Neuroscience Center (NSC) building

6001 Executive Blvd, Rockville, MD 20852

ROOMS A/b/c/d/e

 

Agenda

 

DAY 1 - Tuesday , May 1

 

 

8:00 am               Registration

8:30 am               NCI Welcome and Overview

              Ned Sharpless, M.D. Director, NCI, NIH

              Henry Rodriruez, Ph.D., M.B.A., Director, Office of Cancer Clinical Proteomics Rsearch, NCI, NIH

 

8:30 am               Translational Program (partnership with NCI-Sponsored Clinical Trials)

              Proteogenomic Translational Research Center (PTRC) Session

 

One unified presentation from each disease group with a max of two presenters  (30 min + 15 for Q&A total/disease)

PTRC Teams Milestone Updates

Preclinical/Clinical Research Arm

Target Identification and Assay Aevelopement

Pilot Project Update

 

Moderator: Mehdi Mesri, Ph.D., NCI

 

8:30               Acute Myeloid Leukemia Team (OHSU & PNNL)

Karin Rodland, Ph.D., Pacific Northwest National Laboratory

Brian Druker, M.D., Oregon Health & Science University

 

9:15               Breast Cancer Team (Baylor & Broad)

                            Matthew Ellis, Ph.D., M.B., B.Chir., F.R.C.P., Baylor College of Medicine

                            Steven Carr, Ph.D., Broad Institute

 

10:00               Ovarian Cancer Team (FHCRC & UAB)

Michael Birrer, M.D., Ph.D., University of Alabama at Birmingham Comprehensive Cancer Center

Amanda Paulovich, M.D., Ph.D., Fred Hutchinson Cancer Research Center

 

10:45 am                             Break

 

 

11:00 am                             Retrospective vs Prospective Samples

 

Respective CPTAC 2.0 cancer type centers (BCM: colon; PNNL/JHU: ovarian; and Broad/FHCRC: breast) to present data on biology stemming from retrospective vs. prospective collection procedures. This will assist NCI program to assess prospective fresh-frozen tumor samples versus retrospective (non-CPTAC protocol) fresh-frozen tumor samples.

 

Moderator: Emily Boja, Ph.D., NCI

 

11:00               Breast Cancer:                             D.R. Mani, Ph.D., Broad Institute

11:20               Ovarian Cancer:               Karin Rodland, Ph.D., Pacific Northwest National Laboratory

                                                        Hui Zhang, Ph.D., Johns Hopkins University

11:40               Colon Canecr:                             Bing Zhang, Ph.D., Baylor College of Medicine

 

12:00               Lessons from CPTAC DREAM Challenge: Adopting New Algorithm? & Missing Value Imputation.

David Fenyo, Ph.D., NYU School of Medicine

                                                        Pei Wang, Ph.D., Ican School of Medicine at Mount Sinai

 

12:15 pm               12:15               Lunch

              1:00               Poster viewing

 

 

 

             

 

1:45               Data Jamboree: Proteogenomic Data Analysis Centers (PGDACs)

              This session is for PGDAC groups to convene and focus on the details of data analysis particulary on Endometrial, Kideny and Lung Adeno cancers.  This session will discuss issues, bottlenecks, timelines, tools, coordination, approaches etc.

The Data Jamboree group will create a short slide presentation integrating main points/relevant approaches discussed, and one representative from that group will provide update (20 min + 10 for Q&A) at the main meeting in the morning of Day 2.

 

4:45                     NCI Proteome Data Commons (PDC)

Chris Kinsinger, Ph.D., NCI

Mike MacCoss, Ph.D. ,University of Washington

 

5:15 pm               Adjourn

 

 

DAY 2 - Wednesday , May 2

 

 

 

 

8:30    Single Data Jamboree report back from Day 1 (20 min + 10 for Q&A)

                          Presenter: TBD

 

 

9:00 am               Breakout sessions: Disease & Tool/Software Training Centric

             

Topics to be decided by science and data teams in March/ April .

Diease related topics may include : Six Disease WGs action items, sample collection;  tumor heterogeneity; LMD/core/bulk analysis; small scale proteomics; new PTM analyses; preparing for pan-can study, etc.

Software training topics may include : mature or nearly mature packages such as FireCloud and Docker modules; CPTAC ToolNet, WebGestalt, etc.

 

Two of the breakouts will be selected to present in the afternoon of Day 2.  Selection should be driven by topics/projects having broad impact across CPTAC sites.

 

12:00 pm               12:00               Lunch

              12:45               Poster viewing

 

 

             

1:30 pm               Treatment Naïve Tumor Characterion Program

 

 

                                          Endometrial Cancer Program

 

Moderators: Bing Zhang, Ph.D., Baylor College of Medicine

              David Fenyo, Ph.D., NYU School of Medicine

 

 

1:30               Introduction to Proteogenomic Needs , Data Generation (PNNL PCC Team), Data Analyses (Oversight PGDACs – Baylor & NYU): Updates and Completion Timelines

Presenters TBD

 

 

 

 

 

Kidney Cancer Program

 

Moderators: Pei Wang, Ph.D., Ican School of Medicine at Mount Sinai

              Alexey Nesvizhskii, Ph.D., University of Michigan

 

2:15               Introduction to Proteogenomic Needs, Data Generation (JHU PCC Team), Data Analyses (Oversight PGDACs – Mt. Sinai & UMich): Updates and Completion Timeline

Presenters TBD

 

 

3:00 pm                             3:00               Break

                                          3:15               Poster viewing

 

Lung Adenocarcinoma Program

 

Moderators: D.R. Mani, Ph.D., Broad Institute,

Alexey Nesvizhskii, Ph.D., University of Michigan

 

3:45               Introduction to Proteogenomic Needs, Data Generation (Broad PCC Team), Data Analyses (Oversight PGDACs – Broad & UMich): Updates and Completion Timeline

Presenters TBD

 

 

 

 

 

 

Moderator: Chris Kinsinger, Ph.D. , NCI

 

4:30               Sample Accrual Report back (20 min presentation + 10 Q&A). 

Sample accrual presentation and discussion to be done as pre-work via e-mail and teleconference. Sample collection head to distribute a spreadsheet and any necessary text explanations on sample collection progress for each disease area and any associated issues in advance of the meeting. 

 

5:00               Selected breakout report: (20 min + 10 for Q&A)

Presenters TBD

 

5:30               Selected breakout report: (20 min + 10 for Q&A)

Presenters TBD

 

 

6:00 pm               Adjourn

 

 

 

 

 

 

 

DAY 3 - Thursday , May 3

 

 

 

             

Moderator: Tara Hiltke, Ph.D. , NCI

 

8:30               CPTAC Data Coordinating Center (DCC)

                                                        Update on Data Upload, Assay Portal Progress and Timelines, and CDAP

Karen Ketchum, Ph.D., ESAC Inc.

Nathan Edwards, Ph.D. , Georgetown University

 

8:50               QC Metrics/TMT overlabeling

Steve Stein , Ph.D. , National Institute of Standards and Technology

 

9:10               NCI’s Cancer Imaging Program Update

                                                        Brenda Fevrier-Sullivan, Cancer Imaging Program, NCI

 

9:20               Program Performance and Evaluation

Christine Burgess, Ph.D., Clarivate Analytics

 

 

 

 

 

 

9:30               Open discussion and interaction on topics that have arisen in prior 2 days, including: activities that could integrate work being done in PCCs, PGDACs and PTRCs; interdependencies; challenges; manuscripts that could be developed.

             

10:30 am                                           Break

 

10:45               Small group breakouts on topics defined by the science teams

              Topics TBD

 

11:45               Two selected report backs

              Topics TBD               0:15 am               Pilot Projects Updates from PCCs (Yr 1 and Yr 2 sy

 

1:00 pm                             Adjourn