Genomics (GRG)

Mission

The goal of the Genomics Research Group is to provide both academic and industrial scientists useful information and guidance in the use of various microarray, next gen sequencing and other genomic platforms and applications in their research. The main focus of the GRG is to promote communication and cooperation among core laboratories providing microarray and data analysis services. In addition, the GRG is charged with conducting studies to help assess technological advancements and provide information about these technologies to all interested parties. Information developed and communicated by the GRG should be used to help laboratories evaluate their performance and achieve the highest quality results possible from the use of genomic technologies. In order to accomplish these goals the GRG will also strive to provide ways for sharing information relevant to the administration of facility laboratories that provide microarray technologies as a shared resource.

Current Membership

John M. Ashton - (Co-Chair) - University of Rochester

Jin Jen - (Co-Chair) Mayo Clinic

Sarah A. Boswell - Harvard Medical School

Sridar Chittur SUNY Albany
Catharine A. Fournier ETH Zurich Functional Genomics Center

Kate Hall, Stowers Institute for Medical Research

Christopher E. Mason - Weill Cornell Medical College
Hubert Rehrauer
 - ETH Zurich Functional Genomics Center
Natalia Reyero-Vinas
 - Mississippi State University

Robert Steen  - Harvard Medical School

Chris Lytle (EB Liaison) Dartmouth

Studies

1) GRG 2012 Study: Elucidating the effects of the Deepwater Horizon oil spill on the Atlantic oyster using global transcriptome analysis
    - View Document (96K)
2) MARG 2011 Study: evaluation of the sensitivity and specificity of miRNA profiling on QPCR, microarray, and next-gen sequencing platforms
3) MARG 2008 Study
    - View Announcement (8K)
4) 2007 MARG Research Project Powerpoint Presentation
    - View Document (2,623K)
5) 2004 RESEARCH PROJECT PROTOCOLS
    - Ambion- MessageAmp II aRNA kit (48K)
    - Enzo BioArray RNA Amplification labeling system (126K)
    - Nugen Ovation Biotin system (27K)
    - AffymetrixTwo-cycles labeling Assay (140K)
    - Standard protocol 

Activities

1) 2012: MARG changes name to GRG to reflect the expansion of the technology focus areas
2) 2010 MARG session - microRNA Profiling: Platform Comparison; microRNA Synthetic Reference Project
    - View Presentation (pdf) 
3) 2010 MARG session: MARG Activities and New Wiki Discussion Forum
    - View Document (909K)
4) MARG wiki link - technology discussion forum
    - View Document 
5) 2008 MARG Talk
    - 2008 MARG Talk 
6) 2007 MARG Educational Session
    - View Document (6,826K)
7) At the national ABRF meeting the MARG convened a roundtable to discuss data comparability among commercial microarray platforms. A distinguished acadmic panel asked questions of bioinformaticists representing the microarray industry leaders. The discussion centered around 10 questions created by the academic panel and also addressed questions and comments from the meeting participants. Below are the transcripts from this meeting.
    - View Document (117K)
    - View Document (63K)

Electronic Posters

1) 2012 - GRG Study Poster: Effects of the Deepwater Horizon Oil Spill on the Atlantic Oysters
    - View Document (7,214K)
2) 2008 MARG Survey Poster
    - 2008 MARG Survey Poster 
    - Survey Summary 
3) 2009 MARG Study Poster - microRNA Profiling
    - View Document (620K)
4) 2007 MARG Research Project Poster
    - View Document (2,193K)
5) Evaluation of Small Sample Nucleic Acid Amplification Technologies for Gene Expression Profiling. For more information and requests for the slide presentation please email Herber Auer at [email protected]
    - View Document (50K)
6) Taking the Pulse of the Microarray Field: The Microarray Survey 2005. For more information and requests for the slide presentation please email [email protected]
    - View Document (204K)
7) Comparing GeneChip Data Generated in Different Laboratories (Reid et al.)
    - View Document (224K)
8) A Current Profile of Microarray Laboratories: The Microarray Survey 2003
    - View Document (418K)
9) Microarray Variability Study 2002
    - View Document (1,486K)
10) Estimation and Reduction of the Bias Caused by RNA Degradation in Microarray Analysis
    - View Document (71K)
11) A Current Profile of Microarray Laboratories: The Microarray Survey 2001
    - View Document (106K)
12) The State of the Art of Microarray Analysis: The Microarray Survey 1999
    - View Document (184K)

Links

MARG wiki - technology discussion forum
    - MARG wiki 
Microarray Information Resource
    - View Link 

Membership History

Member NameOrganizationDetails
Mr Jason P Affourtit The Jackson Laboratory  Member: 03/04 - 09/04
Herbert Auer IRB Barcelona  Chair: 02/05 - 02/06
Member: 03/04 - 02/05
Don Baldwin MicroPath ID Diagnostics Member: 2015 - 2017
Dr. Yongde Bao Univ of Virginia Sch of Med  Ad hoc: 01/99 - 01/00
Ad hoc: 03/01 - 04/02
Sean Blake Global Biologics LLC  Member: 06/12 - 03/13
Dr Andrew I Brooks UMDNJ/Rutgers  Chair: 05/02 - 03/04
Member: 03/01 - 03/02
Ad hoc: 02/05 - 02/06
Co-Chair: 03/04 - 02/05
Andrew Crenshaw Broad Institute  Member: 01/11 - 01/13
Dr Nancy D Denslow Univ of Florida-Gainesville  EB Liaison: 02/05 - 03/09
Jaime Gill   Member: 06/03 - 03/04
Chandi A. Griffin Bionovo, Inc  Member: 01/99 - 02/01
Member: 04/02 - 02/05
Ad hoc: 02/05 - 02/07
Co-Chair: 03/01 - 03/02
George S. Grills Cornell University  Chair: 07/99 - 03/00
Member: 01/99 - 07/99
Ad hoc: 03/01 - 03/07
Co-Chair: 03/00 - 03/01
Dr Christina A Harrington Oregon Health & Science Univesity  MemberCo-Chair: 07/07 - 09/11
Dr. Susan Hester US Environmental Protection Agency  emeritus: 04/04 - 03/09
Dr Dumitru A. Iacobas Albert Einstein Coll of Med  Member: 03/01 - 06/03
Ad hoc: 06/03 - 03/04
Ad hoc: 08/04 - 08/04
Kevin A. Johnson The Jackson Laboratory  Member: 03/01 - 06/03
Ad hoc: 06/03 - 06/04
Mrs. Cassie Keener moved - no address  Member: 06/03 - 03/04
Jelena Kühn-Georgijevic ETH Zurich Functional Genomics Center Member: 2015 - 2017
Dr Greg Khitrov Mount Sinai Medical Center  Member: 06/04 - 05/06
Dr. Kevin L. Knudtson Univ of Iowa  ChairCo-Chair: 03/01 - 04/02
Member: 05/02 - 02/05
Ad hoc: 02/05 - 02/07
Ad hoc: 01/00 - 03/01
Dr Shawn E Levy Vanderbilt University  Member: 11/02 - 03/04
Dr Kathryn S Lilley University of Cambridge  Member: 01/99 - 01/00
Ad hoc: 01/00 - 04/02
EB Liason: 03/04 - 02/05
Mr. Aldo B Massimi Albert Einstein College of Medicine  Member: 08/99 - 02/02
Ad hoc: 02/02 - 09/08
Paul T Morrison MBCF @ Dana-Farber Cancer Institute  EB Liason: 01/99 - 01/00
Dr. Norma J. Nowak SUNY Buffalo and RPCI  Member: 07/02 - 03/04
Anoja G Perera Stowers Institute for Medical Research  MemberEb Liaison: 09/12 - 04/14
Dr. Steven Potter Children's Hospital Medical Center  Member: 07/07 - 03/09
Dr Marco F Ramoni Harvard Medical School  Member: 08/04 - 02/05
Dr. Laura H Reid Expression Analysis, Inc.  Memberretired: 05/05 - 03/08
Caprice Rosato Oregon State Univ  Member: 06/12 - 01/13
Member: 10/06 - 05/07
Nalini Raghavachari  NIH MEMBER:  - 3/15
Laurey Steinke University of Nebraska Medical Center  EB Liason: 01/00 - 03/01
Theodore W Thannhauser USDA/Agricultural Research Service  EB Liason: 03/01 - 03/04
Dr. Jay P. Tiesman Procter & Gamble  Member: 06/04 - 01/09
James Van Ee Cornell University  Ad hoc: 01/99 - 04/01
Agnes Viale Memorial Sloan Kettering Cancer Ctr.  Member: 03/01 - 03/04
Member: 04/04 - 12/07
Dr. Wei Wang Cornell University  Member: 09/10 - 09/11

Publications

  1. A current profile of microarray laboratories: results of the 2000-2001 ABRF Microarray Research Group survey of laboratories using microarray technologies. J. Biomol. Tech. 2000; 11(4):225.
    Grills GS, Griffin C, Massimi A, Lilley K, Knudtson K, VanEe JI.
  2. A profile of microarray laboratories. Proceedings of the Northwest Microarray Conference 2000.
    Grills GS, Griffin C, Lilley K, Massimi A, Bao Y, VanEe JI.
  3. A Userís-Eye View of the Affymetrix Gene Expression System: The Early Days. J. Biomol. Tech. 1999; 10(2), 105.
    Sandmeyer, S.
  4. A Userís-Eye View of the Affymetrix Gene Expression System: The Early Days. J. Biomolecular Techniques 10(2), 105 (abstract). 1999
    Sandmeyer, S.
  5. DNA Arrays: Technologies, Applications, and Data Analysis. J. Biomol. Tech. 2000; 11(1), 35 (abstract).
    Bumgarner, R.
  6. DNA Arrays: Technologies, Applications, and Data Analysis. J. Biomolecular Techniques 11(1), 35 (abstract). 2000
    Bumgarner, R.
  7. Factors contributing to variability in DNA microarray results: the ABRF Microarray Research Group 2002 study. J. Biomol. Tech. 2002; 108.
    Knudtson KL, Griffin C, Brooks A, Iacobas A, Johnson K, Khitrov G, Lilley K, Massimi A, Viale A, Zhang W, Bao Y, Grills GS, Thaler H, Cox C.
  8. Implementation of a Custom cDNA Microarray Facility at AECOM. J. Biomolecular Techniques 10(2), 105 (abstract). 1999
    Massimi, A.
  9. Implementation of a Custom cDNA Microarray Facility at AECOM. J. Biomol. Tech. 1999; 10(2), 105.
    Massimi, A.
  10. Microarrays in a Shared Facility - Practical and Scientific Experiences from the Huntsman Cancer Institute. J. Biomolecular Techniques 10(2), 105 (abstract). 1999
    Albertson, H.
  11. Microarrays in a Shared Facility - Practical and Scientific Experiences from the Huntsman Cancer Institute. J. Biomol. Tech. 1999; 10(2), 105 (abstract)
    Albertson, H.
  12. Problems and Pleasures of Implementing Microarray Technologies. J. Biomolecular Techniques 10(2), 105 (abstract). 1999
    Grills, G.
  13. Problems and pleasures of implementing microarray technologies. J. Biomol. Tech. 1999; 10(2):105
    Grills, GS
  14. The state of the art of microarray analysis: a profile of microarray laboratories. J. Biomol. Tech. 2000; 11(1):30.
    Grills GS, Griffin C, Heck D, Lilley K, Massimi A, Sandmeyer S, Bao Y, VanEe JI.
  15. The State of the Art of Microarray Analysis: A Profile of MicroarrayLaboratories.J. Biomolecular Techniques11(1), 30 (abstract). 2000
    Grills, G., Griffin, C., Heck, D., Lilley, K., Massimi, A., Sandmeyer, S., Bao, Y., and J.I. Van Ee
  16. The state of the art of microarray research: results of the ABRF Microarray Research Group studies. 12th International Genome Sequencing and Analysis Conference 2000; 10.
    Grills GS, Burngarner R, Delrow J, Lilley K, Massimi A, Bao Y, Knudtson K, VanEe JI, Griffin C.
  17. The State of the Art of Microarray Research: Results of the ABRF Microarray Research Group Studies.Microb. Comp. Genomics. 2000
    Grills, G., Bumgarner, R., Delrow, J., Lilley, K. Massimi, A., Bao, Y., Knudtson, K., VanEe, J. and C. Griffin