Notes from the March 30-31 Meeting of the IOM Committee on the Use of Omics-Based Markers in Clinical Trials

This web page is designed to hold files from the second meeting of the IOM Committee examining the use of Omics-based signatures in clinical trials. Some case studies related to the formation of this committee are presented in the manuscript Deriving Chemosensitivity from Cell Lines: Forensic Bioinformatics and Reproducible Research in High-Throughput Biology by Keith A. Baggerly and Kevin R. Coombes (the main page is here) and Subsequent Reports (available here).

Session Description and Agenda

The March 30-31 meeting of the IOM Omics committee was largely devoted to a series of presentations from outside experts dealing with
1. basic science,
2. case studies, and
3. the relative roles of investigators, journals, institutions and agencies.

The full agenda for the meeting sessions open to the public is here.

MP3 Files of Individual Presentations

MP3 files of the talks from March 30 are given below in the order in which they were presented at the meeting.

1. Session Introduction (by Gil Omenn, chair), Larry Kessler overview of scientific bases for omics tests,
Ned Calogne on lessons from the Evaluation of Genomic Applications in Practice and Prevention (EGAPP). 49 min, 24 sec; 45.2 Mb
2. Rich Simon on the Use of Archived Tissues in the Development and validation of Prognostic and Predictive Biomarkers. 33 min, 2 sec; 30.2 Mb
3. Chuck Perou on Analytical variation of tests and cross-platform test validation. 33 min, 24 sec; 30.6 Mb
4. Sumithra Mandrekar on Clinical trial design and discussion of the four talks in this session. 1 hr, 16 min, 48 sec; 70.3 Mb
5. Peter Pronovost on Institutional Responsibility, and discussion. 47 min, 50 sec; 43.8 Mb
6. Laura van't Veer on MammaPrint. 44 min, 9 sec; 40.4 Mb
7. Steve Shak on Oncotype Dx, and discussion of the two talks in this session. 1 hr, 12 min, 1 sec; 65.9 Mb
8. Joseph Nevins on the Duke University Case Study, a Principal Investigator's Perspective, and discussion. 1 hr, 25 min, 19 sec; 78.1 Mb
9. Journal Editors Panel and Discussion: Cathy DeAngelis (JAMA), Veronique Kiermer (Nature family), Katrina Kelner (Science family). 1 hr, 13 min, 18 sec; 67.1 MB
10. Scott Zeger on roles of authors and principal investigators, and Panel on Institutional Responsibilities (Albert Reece, Harold Paz, and Scott Zeger) with Discussion. 1 hr, 25 min, 12 sec; 78.0 Mb

An MP3 file of the talk from March 31 (ours) is given below.

Keith Baggerly on Forensic Bioinformatics, mostly focused on the Duke case, with discussion. 2 hr, 44 min, 59 sec; 151 Mb

Files Supplied to the IOM

We supplied the IOM with several files pertaining to our own presentation on "Forensic Bioinformatics":
Slides of our presentation (with the color background turned off)
A more detailed written summary, with references
A zip file of supplementary files, including
3 files for JCO (letter submitted, acknowledgment of receipt, and the rejection)
3 files for Lancet Oncology (letter submitted, a figure, and the rejection)
5 files for Nat Med (letter submitted, a figure, acknowledgment of receipt, the request to share with Potti and Nevins, and the rejection)
3 files for Victoria Stodden's course on reproducible research (a flyer, guidelines for students, and the syllabus)
Baggerly notes from ENAR.

Duke also supplied a "historical perspective" to accompany Joe Nevins' presentation.

Other files may eventually appear on the IOM's web page for this session.