U.S. Department of Health and Human Services
The Human Proteome September 26-27, 2011

The Human Proteome - A Scientific Opportunity for Transforming Diagnostics, Therapeutics, and Healthcare

9/26/2011 7:00 AM
9/27/2011 7:00 AM
 
No
For questions concerning program content, contact:
Dr. Salvatore Sechi
Director, Proteomic Program 
Director, Diabetes Systems Biology Program
Division of Diabetes, Endocrinology, and Metabolic Diseases
National Institute of Diabetes and Digestive and Kidney Diseases 
6707 Democracy Boulevard Room 797 
Bethesda, MD 20892-5460 
Telephone:  (301) 594-8814
Fax:  (301) 480-3503
Email:  sechi@nih.gov

For questions concerning logistical information or registration, contact:  
Michelle Watson
Senior Conference Manager
The Scientific Consulting Group, Inc. 
656 Quince Orchard Road, Suite 210
Gaithersburg, MD 20878
Telephone:  (301) 670-4990
Fax:  (301) 670-3815
E-mail:  mwatson@scgcorp.com
Bethesda
 

Event Details

Purpose: 

There have been several discussions about the Human Proteome Project and the way that it could extend and build on the success of the Human Genome Project. The fact that proteins are the major components of biological networks and molecular machines, and that proteins are the target for the large majority of drugs available today, strongly indicates that a deeper knowledge of the human proteome and the development of the technologies needed for analyzing large subsets of proteins in a clinical setting could transform the way that we do diagnostics and could substantially enhance the overall health care enterprise.
 
Several efforts to enhance proteomics technologies have been made in recent years, including the NIH Common Fund-supported Technology Centers for Networks and Pathways program and Protein Capture programs, the Human Protein Atlas Project, the Human Multiple Reaction Monitoring (MRM) Atlas, and the HUPO Human Proteome Project. The best course of action, however, for capitalizing on recent technology developments is not clear. There are indeed many possible opportunities to synergize with these efforts. 
 
Briefly, the main goal of this NIH Workshop is to articulate ways in which members of the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. If ongoing needs for dedicated funds are identified, a white paper will be developed to articulate these needs. This will be shared with the Institutes and Centers of the NIH for their consideration. The principal purpose of this Workshop is to provide a forum for the community to consider best use of recent technological advances to move the field forward.

Organizers:

Salvatore Sechi
Maureen Beanan (NIAID),
Laurie Nadler (NIMH),
Pothur Srinivas (NHLBI)

Workshop Chairs:  

Daniel Chan, Johns Hopkins University School of Medicine
Mark Gerstein, Yale University
Matthias Mann, Max-Planck Institute of Biochemistry
Gil Omenn, University of Michigan
Marc Vidal, Harvard University
​​​

Agenda

Monday, September 26, 2011

8:00 - 8:15 a.m. Welcome and Workshop Introduction
Mary Perry, Program Director, NIH, OD
Salvatore Sechi, Program Director, NIDDK, NIH
8:15 a.m. - 2:30 p.m. Proteomics in Systems Biology
 

Subsession 1:  

Protein Networks 

Chair:  Marc Vidal, Dana-Farber Cancer Institute

8:15 - 8:35 a.m. Marc Vidal, Dana-Farber Cancer Institute
8:35 - 8:55 a.m. Suzanne Gaudet, Dana-Farber Cancer Institute
8:55 - 9:15 a.m. Kara Dolinski, Lewis-Sigler Institute for Integrative Genomics
 

Subsession 2:  

Integrating Proteomics with Other Omics 

Chair: Mark Gerstein, Yale University

9:15 - 9:35 a.m. Mark Gerstein, Yale University
9:35 - 9:55 a.m. Rolf Apweiler, EMBL Outstation European Bioinformatics Institute (EBI)
9:55 - 10:15 a.m. Joel Bader, The Johns Hopkins University
10:15 - 10:35 a.m. Robert Gerszten, Massachusetts General Hospital
10:35 - 10:55 a.m. Zhiping Weng, University of Massachusetts Medical School
10:55 - 11:15 a.m. BREAK
 

Subsession 3:  

Quantitative Proteomics by Exploratory and Targeted Methodologies 

Chair:  Mathias Mann, Max Planck Institute of Biochemistry

11:15 - 11:35 a.m. Mathias Mann, Max Planck Institute of Biochemistry
11:35 - 11:55 a.m. Forest White, The David H. Koch Institute for Integrative Cancer Research
11:55a.m. - 12:15 p.m. Josh Coon, University of Wisconsin-Madison
12:15 - 12:35 p.m. Rob Moritz, Institute for Systems Biology
12:35 - 1:40 p.m. LUNCH
1:40 - 2:40 p.m.
Panel Discussion 
John Quackenbush, Dana-Farber Cancer Institute; Akilesh Pandey, The Johns Hopkins University; Peipei Ping, University of California, Los Angeles; Steve Bryant, National Center for Biotechnology Information, NIH, Stephen Barnes, University of Alabama at Birmingham
2:40 - 6:10 p.m. Translating Proteomics
 

Subsession 1:

Proteomic Technologies in a Clinical Setting

Chair: Daniel Chan, The Johns Hopkins University School of Medicine

2:40 - 3:00 p.m. Daniel Chan, The Johns Hopkins University School of Medicine
3:00 - 3:20 p.m. Barry Dowell, Abbott Laboratories
3:20 - 3:40 p.m. Darryl Palmer-Toy, Southern California Permanente Medical Group
3:40 - 4:00 p.m. Maria Chan, U.S. Food and Drug Administration
4:00 - 4:20 p.m. BREAK
 

Subsession 2:

Study Design and Statistical Challenges in Clinical Proteomics

Chair: Gil Omenn, University of Michigan

 
4:20 - 4:40 p.m.
Gil Omenn, University of Michigan
4:40 - 5:00 p.m. Steven Skates, Harvard University Medical School
5:00 - 5:20 p.m. Lisa McShane, National Cancer Institute
5:20 - 6:10 p.m.
Brainstorming on Ideas Discussed

Tuesday, September 27, 2011

8:00 - 9:00 a.m. General Discussion
Additional feedback from the participants to the chairs
9:00 - 11:30 a.m. Chairs and Organizers Meeting 
Chairs Meet to Write Report and Finalize Ideas

Directions/Travel

​Meeting Location:

Hyatt Regency Bethesda Hotel
One Bethesda Metro Center
7400 Wisconsin Avenue
Bethesda, MD  20814 
Telephone:  (301) 657-1234 or (800) 233-1234

Hotel Accommodations:

A block of sleeping rooms has been reserved at the Hyatt Regency Bethesda, Bethesda, MD, for out-of-town guests attending the The Human Proteome - A Scientific Opportunity for Transforming Diagnostics, Therapeutics, and Healthcare on September 26-27, 2011.
 
The Hyatt Regency Bethesda has rooms reserved for guests arriving on Sunday, September 25, 2011, and departing on Tuesday, September 27, 2011. The room rate is $211 plus tax per night. You will be responsible for the room cost and your incidental charges upon checkout.
 
Hyatt Regency Bethesda by Friday, August 26, 2011, at (301) 657-1234 or 1 (800) 233-1234, NIDDK�s Human Proteome Workshop when making your sleeping room reservations. For online registrations, please use the meeting code HPTW at the following link:  https://resweb.passkey.com/go/HPTW  . Please be certain that the hotel provides you with a confirmation number. After August 26, 2011, the hotel will accept reservations on a space-available basis at the prevailing hotel rate. When making a reservation, please provide your room and bedding preferences. The hotel will assign specific room types at check-in, based on availability. Please be advised that requests are not guaranteed. Check-in time is at 3:00 p.m., and check-out time is 12:00 noon.
 
If for any reason you need to cancel your hotel reservation, please do so 48 hours in advance of your check-in date.

Additional Information

The Scientific Consulting Group, Inc. (SCG) is providing the logistical support for this meeting. The above information should help you with your planning. If you have any questions, please contact Michelle Watson of SCG by telephone at 301-670-4990 or by email at mwatson@scgcorp.com.

Directions

From Points North

From I-95: Take I-95 South to I-495 (Capital Beltway) West toward Silver Spring. Take Exit 34 (Wisconsin Avenue/Route 355). Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.
 
From I-270: Take I-270 South to I-495 (Capital Beltway) East toward Washington, DC. Stay in one of the three left lanes. Follow signs for 355 South, a left-lane exit, onto Wisconsin Avenue. Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.

From Points South

Take I-95 North to I-495 (Capital Beltway) toward Tysons Corner/Rockville. Follow I-495 for 20 miles. At the I-495/I-270 split, stay to the right on I-495. Take Exit 34 (Wisconsin Avenue/Route 355). Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.
 
From Baltimore/Washington International Thurgood Marshall Airport (BWI)
Take Route 195 West to Exit 4 (I-95 South). From I-95 take I-495 (Capital Beltway) West toward Silver Spring. Take Exit 34 (Wisconsin Avenue/Route 355). Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.
 
From Washington Dulles International Airport
Take the Dulles Access Road for approximately 13 miles to Exit 18. Move to the right on the Dulles Toll Road (Route 267); get off at Exit 18. Stay to the left on the ramp for Bethesda/Baltimore and proceed toward Bethesda on I-495 (Capital Beltway) for approximately 9 miles. At the I-495/I-270 split, stay to the right on I-495. Take Exit 34 (Wisconsin Avenue/Route 355 South). Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.
 
From Ronald Reagan National Airport
Take the George Washington Parkway North to I-495 (Capital Beltway) and follow the signs to Maryland. At the I-495/I-270 split, stay to the right on I-495. Take Exit 34 (Wisconsin Avenue/Route 355). Follow Route 355 South for approximately 3 miles and the Hyatt Regency Bethesda will be on the right, on the corner of Wisconsin Avenue and Old Georgetown Road.

METRO INFORMATION

The Metro System is clean, reliable, and safe. It operates from 5:30 a.m. to 12:00 midnight Monday through Thursday; 5:00 a.m. to 2:00 a.m. on Fridays; 8:00 a.m. to 2:00 a.m. on Saturdays; and 8:00 a.m. to 12:00 midnight on Sundays. Each passenger must buy a farecard to travel in the system. Guides for purchasing farecards are posted on the vending machines in each station. Each Metro car features a complete color-coded map. Station attendants on duty at each station can provide additional information on request.
 
From Union Station or downtown Washington (main Metro Lines into the city converge at Metro Center Station and Gallery Place Station), take the Metro Red Line toward Shady Grove or Grosvenor. Exit at the Bethesda Metro Station. The Hyatt is directly above the Bethesda Metro Station.

SHUTTLES

SuperShuttle offers service to most hotels from Ronald Reagan National Airport, Washington Dulles International Airport, and Baltimore/Washington International Thurgood Marshall Airport. The shuttle leaves on an as-needed basis between the hours of 5:30 a.m. and 11:00 p.m. During other times, arrange for a shuttle by calling 800-258-3826< from the airport.

TAXIS

The taxi fare is approximately $45-$55 from Ronald Reagan Washington National Airport, approximately $55-$65 from Washington Dulles International Airport, and approximately $65-$75 from Baltimore/Washington International Thurgood Marshall Airport.  Fares may differ during peak travel hours.

MARC TRAINS  

From BWI Airport, take the MARC train on the Penn Line to Union Station. Take the Metro Red Line toward Grosvenor or Shady Grove and exit at the Bethesda Metro Station. The hotel is directly above the Bethesda Metro Station.

PARKING INFORMATION

Self-parking at the hotel is $15 per day/overnight. Valet parking is $20 per day/overnight.

Minutes

​Minutes are currently unavailable.

Attendees

​​Attendees are currently unavailable.

Abstracts

PUBLICATIONS

Development and Application of a Biomarker Discovery through Verification Pipeline to Cardiovascular Disease. 
Nat Biotechnol. 2011 Jun 19;29(7):635-43. doi: 10.1038/nbt.1899.
 
Collecting and organizing systematic sets of protein data.
Nat Rev Mol Cell Biol. 2006 Nov;7(11):803-12.  
 
Ongoing and future developments at the Universal Protein Resource. 
Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. Epub 2010 Nov 4.
 
PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637.
 
Gene inactivation and its implications for annotation in the era of personal genomics.
Genes Dev. 2011 Jan 1;25(1):1-10.
 
Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum.
Science. 2011 May 6;332(6030):687-96.
 
Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions.
Protein Sci. 2011 Oct;20(10):1745-54. doi: 10.1002/pro.710. Epub 2011 Sep 15.
 
Conducting the metabolic syndrome orchestra. 
Nat Genet. 2011 Jun;43(6):506-8.  
 
Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast.
Nature. 2008 Oct 30;455(7217):1251-4. Epub 2008 Sep 28.
 
Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria. 
Mol Cell Proteomics. 2011 Feb;10(2):M110.000117.
 
In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry.
J Proteome Res. 2011 May 6;10(5):2286-99. Epub 2011 Apr 14.
 
A high-confidence human plasma proteome reference set with estimated concentrations in peptideatlas. 
Mol Cell Proteomics 2011 Sep;10(9):M110.006353.
 
A community standard format for the representation of protein affinity reagents.
Mol Cell Proteomics. 2010 Jan;9(1):1-10.
 
Big data: The future of biocuration. 
Nature. 2008 Sep 4;455(7209):47-50.
 
Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution. 
Molecular Cell Proteomic 2009 Oct;8(10):2339-49. Epub 2009 Jul 13.
 
Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20274-9. Epub 2007 Dec 12.
 
Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. 
Clinical Chemistry 2009;55:1108-17. Epub 2009 Apr 16.
 
Selected reaction monitoring for quantitative proteomics: a tutorial.
Mol Syst Biol. 2008;4:222. Epub 2008 Oct 14.
 
The human proteome project: current state and future direction.
Mol Cell Proteomics. 2011 Jul;10(7):M111.009993.
 
Enhanced levels of both membrane-bound and soluble forms of IgM Fc receptor in patients with chronic lymphocytic leukemia.
Blood. 2011 Sep 9.
 
A bioinformatics workflow for variant peptide detection in shotgun proteomics.
Mol Cell Proteomics. 2011 May;10(5):M110.006536. Epub 2011 Mar 9.
 
REporting recommendations for tumor MARKer prognostic studies (REMARK).
Breast Cancer Res Treat. 2006 Nov;100(2):229-35. Epub 2006 Aug 24.
 
Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. 
Cancer Res 2010; 70 (9):3440-3449.
 
Serine protease PrtA from Streptococcus pneumoniae plays a role in the killing of S. pneumoniae by apolactoferrin.
Infect Immun. 2011 Jun;79(6):2440-50. Epub 2011 Mar 21.
 
Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome.
J Proteome Res. 2011 Feb 4;10(2):637-45. Epub 2011 Jan 5.
 
Mass spectrometry in high-throughput proteomics: ready for the big time.
Nat Methods. 2010 Sep;7(9):681-5.
 
Census for proteome quantification.
Curr Protoc Bioinformatics. 2010 Mar; Chapter 13: Unit 13.12.1-11.
 
Dynamic networks from hierarchical bayesian graph clustering.
PLoS One. 2010 Jan 11;5(1):e8118.
 
Pivotal evaluation of the accuracy of a biomarker used for classification or prediction: standards for study design.
J Natl Cancer Inst. 2008 Oct 15;100(20):1432-8. Epub 2008 Oct 7.
 
Proteomic and phosphoproteomic comparison of human ES and iPS cells - Nature Methods in press (online only)  (PDF, 135KB)
 
Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics.
Cell. 2009 Aug 21;138(4):795-806. Epub 2009 Aug 6.
 
High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.
Nat Methods. 2010 Jan;7(1):43-6. Epub 2009 Dec 6.
 
ConceptGen: a gene set enrichment and gene set relation mapping tool. 
Bioinformatics 2010; 26:456-463.  
 
Tissue localization and solubilities of ?A-crystallin and its numerous C-terminal truncation products in pre- and postcataractous ICR/f rat lenses.
Invest Ophthalmol Vis Sci. 2010 Oct;51(10):5153-61. Epub 2010 Apr 30.
 
Global quantification of mammalian gene expression control.
Nature. 2011 May 19;473(7347):337-42.
 
A checklist for evaluating reports of expression profiling for treatment selection.
Clin Adv Hematol Oncol. 2006 Mar;4(3):219-24.
 
A prospective, multicenter, National Cancer Institute Early Detection Research Network study of [-2]proPSA: improving prostate cancer detection and correlating with cancer aggressiveness. 
Cancer Epidemiol Biomarkers Prev. 2010 May;19(5):1193-200.
 
Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis.
Nature. 2009 May 21;459(7245):428-32. Epub 2009 Apr 12.
 
The BioGRID Interaction Database: 2011 update
Nucleic Acids Res. 2011 Jan;39(Database issue):D698-704. Epub 2010 Nov 11
 
Towards a knowledge-based Human Protein Atlas.
Nat Biotechnol. 2010 Dec;28(12):1248-50
 
The Proteomics Identifications database: 2010 update.
Nucleic Acids Res. 2010 Jan;38(Database issue):D736-42. Epub 2009 Nov 11
 
A probabilistic disease-gene finder for personal genomes.
Genome Res. 2011 Sep;21(9):1529-42. Epub 2011 Jun 23.
 
Next-generation sequencing to generate interactome datasets.
Nat Methods. 2011 Jun;8(6):478-80. Epub 2011 Apr 24.
 
The Road from Discovery to Clinical Diagnostics: Lessons Learned from the First FDA-Cleared In Vitro Diagnostic Multivariate Index Assay of Proteomic Biomarkers. 
Cancer Epidemiology, Biomarkers & Prevention, 19 (12): 2995-2999, 2010.

Program Concepts

Location

Line
  • Hyatt Regency
  • One Bethesda Metro Center
  • MD 20814
Webinar

Contacts

Line
For questions concerning program content, contact:
Dr. Salvatore Sechi
Director, Proteomic Program 
Director, Diabetes Systems Biology Program
Division of Diabetes, Endocrinology, and Metabolic Diseases
National Institute of Diabetes and Digestive and Kidney Diseases 
6707 Democracy Boulevard Room 797 
Bethesda, MD 20892-5460 
Telephone:  (301) 594-8814
Fax:  (301) 480-3503
Email:  sechi@nih.gov

For questions concerning logistical information or registration, contact:  
Michelle Watson
Senior Conference Manager
The Scientific Consulting Group, Inc. 
656 Quince Orchard Road, Suite 210
Gaithersburg, MD 20878
Telephone:  (301) 670-4990
Fax:  (301) 670-3815
E-mail:  mwatson@scgcorp.com