Genomic Variation Research Group (GVRG)
| Current Members | Studies | Activities | Electronic Posters | Publications | Links | Membership History |


The GVRG is a dedicated group of ABRF members who have a wide range of expertise in the analysis of genomic variation. We aspire to stay current with new technologies and learn more about instrumentation for genomic investigation. The groups experience includes, but is not limited, to fragment analysis, SNP analysis, mutation discovery, copy number variation, DNA methylation and allelic expression in a research and clinical setting.

It is our mission to:
  • Promote and support shared resource facilities, research laboratories and individual researchers in the research and development of methods, applications, and instrumentation applicable to the analysis of genomic variation.
  • Provide a forum for discussion and evaluation of newly emerging technologies and their associations to the analysis of genomic variation
  • Allow members to exchange technical information and to provide a mechanism for pooling resources to assess critical technical problems pertaining to the analysis of genomic variation.
  • Work closely with and exchange information with other research groups within the ABRF that may be utilizing similar platforms, applications, or analysis tools.
  • Provide a mechanism for evaluation of genotyping applications through research studies.

Current Membership
Sean Blake - Global Biologics LLC
Dr. Charles Nicolet - Univ. of Southern California
George S. Grills (EB Liaison) - Cornell University

Studies
1) GVRG 2011 Study
    - View Document (3,058K)
2) GVRG 2010 Study
    - View presentation (1,209K)
3) GVRG 2009 Study
    - View Document (1,817K)
4) FARG 2006 Survey Announcement
    - View Document (25K)
5) FARG 2005 Study
    - View Study Announcement
6) FARG 2004 Study
    - View Study Announcement (61K)
    - View Study Poster (3,064K)

Activities
1) The Fragment Analysis Research Group presented the results of its 1999 study at the annual ABRF meeting: ABRF'99: Bioinformatics and Biomolecular Technologies: Linking Genomes, Proteomes and Biochemistry,March 19 - 22, 1999, Durham, NC
2) The Fragment Analysis Research Group presented the results of its 2000 study at the annual ABRF meeting: ABRF 2000: From Singular to Global Analyses of Biological Systems
3) 2000 FARG Study poster was presented at DNA 2000:International Symposium on the State-of-the-Art in Genetic Analysis, Boston, MA June 1-3, 2000.
4) The Fragment Analysis Research Group presented the final results of its 2000 study at the ABRF Session at the 12th International Genome Sequencing and Analysis Conference, Miami, Florida, October 24 - 27, 2000.
    - View pdf (2,471K)
5) The Fragment Analysis Research Group presented the results of its 2001 study at the annual ABRF meeting: ABRF2001: The New Biology: Technologies for Resolving Macromolecular Communications. In addition to the Research Group report, a panel discussion on running Real Time Quantitative PCR as a core facility function was held. Participants: P.S. Adams, S. Bobin, J. Hawes, T. Hunter, K. Knudsen, and T. Thannhauser.
6) The Fragment Analysis Research Group presented a Tutorial at ABRF 2001: Practical Considerations for PCR and Electrophoresis in a Genotyping Core Facility
    - View pdf (Part I: PCR and Electrophoresis)
    - View pdf (Part II: Setup and Analysis)
7) 2001 FARG Study poster was presented at the ABRF Workshop at the 13th International Genome Sequencing and Analysis Conference, San Diego, California, October 24 - 27, 2001.
8) The Fragment Analysis Research Group presented the results of its 2002 study at the annual ABRF meeting: ABRF2002: Biomolecular Technologies: Tools for Discovery in Proteomics and Genomics, March 9-12, 2002, Austin, Texas. In addition, factors important in PCR multiplexing were presented.
    - View pdf (2,005K)
9) The Fragment Analysis Research Group presented a Tutorial at ABRF 2002: Using Databases to Determine Genetic Markers For Genotyping
    - View HTML
10) The 2003 Fragment Analysis Research Group survey of core facilities offering genotyping/fragment analysis as a service is now available. "Current Trends in Methodology and Instrumentation used in the Analysis of Genetic Variability in DNA Fragments."
    - View .pdf
11) The Fragment Analysis Research Group presented a Tutorial at ABRF 2003: Detecting Multiple SNPs Using Automated DNA Sequencers. An overview of Single Base Extension was followed by more detailed information on one of the currently available techniques, SNaPshot.
    - 2003 Tutorial, Part 1, Single Base Extension (2,664K)
    - 2003 Tutorial, Part 2, ABI SNaPshot (295K)
12) A poster outlining the findings from the FARG 2003 study was presented at the Albany Conference on Biotechnology in the Capital Region: Drug Discovery meeting held at the Rensselaerville Conference Center, Rensselaerville, NY, September 19-20, 2003, by FARG member Bob Keefe.
13) FARG members presented the results of the 2004 Study--Comparison of Genotyping Results Across Instrument Platform using a Mock Forensic Investigation-- to the participants of the ABRF 2004: Integrating Technologies in Proteomics and Genomics, Feb 28 -Mar 2, 2004 in Portland, OR.
    - View presentation (6,045K)
14) FARG presented Round Tables at the ABRF2004. Each round table was introduced with a short tutorial on Gene Mapper and Chromagna (invited speaker: M. Miller, National Cancer Institute) and on Non-Sequencing Method for Detecting Unknown SNPs (invited speaker: T. Yeung, Fox Chase Cancer Center), followed by an open floor for questions and discussion.
    - View T. Yeung presentation (1,805K)
15) The Fragment Analysis Research Group presented the results of its 2005-6 study at the annual ABRF meeting. FARG 2006 SURVEY: A Comparative Study of Methodology and Instrumentation Uses of Laboratories Performing DNA Fragment Analysis
    - View Slides (1,079K)

Electronic Posters
1) FARG 1999 Study: Fragment Analysis; A Changing Field and a New Research Group
    - View pdf
2) FARG 2000 Study: The Effects on Mobility of Various Protocols, Reagents and Equipment Used in Fragment Analysis: Preliminary Results from the Association of Biomolecular Resource Facilities (ABRF) Fragment Analysis Research Group (FARG) 2000 Study
    - View HTML
3) FARG 2000 Study: The Effects on Mobility of Various Protocols, Reagents and Equipment Used in Fragment Analysis: Final Results from the Association of Biomolecular Resource Facilities (ABRF) Fragment Analysis Research Group (FARG) 2000 Study
    - View pdf (2,468K)
4) FARG 2001 Study : Enhancing Automated Allele Calling by Tailing Dinucleotide Repeat Markers to Eliminate Non-Template Driven Nucleotide Addition Seen with Taq Polymerase
    - View pdf
5) FARG 2002 Study: Comparing Laboratory Protocols for Multiplexing Markers in a DNA Fragment Analysis Application.
    - View pdf (641K)
6) FARG 2003 Study: The Fragment Analysis Research Group survey of ABRF genotyping/fragment analysis laboratories for 2003. "Current Trends in Methodology and Instrumentation used in the Analysis of Genetic Variability in DNA Fragments."
    - View .pdf (2,653K)
7) FARG 2004 Study: Comparison of Genotyping Results Across Instrument Platform using a Mock Forensic Investigation
    - View Document (3,064K)
8) FARG 2005: Evaluation of STR-PCR Fragment Analysis Platforms for Mixed Cell Monitoring
    - View Document (394K)
9) FARG 2006 Survey: A Comparative Study of the Methodology and Instrumentation Trends of Laboratories Performing DNA Genotyping
    - View Document (461K)
10) Fragment Analysis Results from the Joint-RG Genotyping Pilot Study: The FARG 2007 Poster
    - View Document (824K)
11) Defining the demographics of the Genotyping Laboratory. Results from the FARG 2008 Survey.
    - View Document (596K)
12) A Review of Heterozygous Bases Detected in S.Cerevisiae Using Multiple Next-Gen Sequencing Platforms
    - Poster 2009
    - Poster update 2010 (149K)
13) GVRG 2010 Study: Analysis of copy number variation in C. elegans using next-generation sequencing
    - Poster 2010
14) GVRG 2011 Study Poster: Evaluation of Whole Genome Amplification (WGA) Technologies for Genotyping
    - View Document (1,308K)

Publications
1) Bartley, D.A., L.W. Ballard, Y. Bao, D.A. Bintzler, G. Grills, L. Kasch, L.Petukhova. (1999). Fragment Analysis: A Changing Field and a New Research Group. Results from the ABRF Fragment Analysis Research Group 1999 Survey ABRF 99: Bioinformatics and Biomolecular Technologies: Linking Genomes, Proteomes and Biochemistry, Journal of Biomolecular Techniques 10(2), 99 (abstract).
2) Bartley, D.A., P.S. Adams, L.W. Ballard, Y. Bao, D.A. Bintzler, G. Grills, L. Kasch, P. Morrison, L.Petukhova and C.E. Terrell. (2000). The Effects On Mobility Of Various Protocols, Reagents And Equipment Used In Fragment Analysis. ABRF 2000: From Singular to Global Analyses of Biological Systems, Journal of Biomolecular Techniques 11(1),00 (abstract).
3) Bartley, D.A., P.S. Adams, L.W. Ballard, Y. Bao, D.A. Bintzler, L. Kasch, L.Petukhova, C.E. Terrell and G. Grills. (2000). PreliminaryStudy Results of the Effects on Mobility of Various Protocols, Reagents and Equipment Used in Fragment Analysis. DNA 2000: International Symposium on the State-of-the-Art in Genetic Analysis, Boston, MA June 1-3, 2000. (abstract).
4) Bintzler, D.A. , P.S. Adams, L.W. Ballard, Y. Bao, D. Bartley, L. Kasch, L. O. Petukhova, C. Rosato and C.E. Terrell . (2000). Fragment Analysis Research Group (FARG) STUDY 2001: Enhancing Automated Allele Calling by Tailing Dinucleotide Repeat Markers to Eliminate Non-Template Driven Nucleotide Addition Seen with Taq Polymerase. ABRF 2001: The New Biology:Technologies for Resolving Macromolecular Communications, Journal of Biomolecular Techniques 11(4), 00 (abstract).
5) Bintzler,D. A., P. S. Adams, Y. Bao, D. Bartley, L. Kasch, R. Keefe, L. Petukhova, C. Rosato. (2002) FARG 2002 Study: Comparing Laboratory Protocols for Multiplexing Markers in a DNA Fragment Analysis Application. Journal of Biomolecular Techniques 12(4), 01 (abstract)
6) Ballard, L.W., P.S. Adams, Y. Bao, D. Bartley, D.A.Bintzler, L. Kasch, L. O. Petukhova and C. Rosato. (2002). Strategies for Genotyping: Effectiveness of Tailing Primers to Increase Accuracy in Short Tandem Repeat Determinations. Journal of Biomolecular Techniques 13:20-29

Membership History
Member Name Organization Details
Pamela Scott Adams Trudeau Institute  Member: 01/99 - 03/02
Ad hoc: 03/02 - 03/04
Linda Ballard University of Utah  Member: 01/97 - 01/01
Dr. Yongde Bao Univ of Virginia Sch of Med  Member: 01/97 - 03/04
Duane Bartley John Hopkins Univ  Chair: 12/97 - 03/00
Member: 03/00 - 03/02
Member: 01/97 - 12/97
Mr. Doug Bintzler Univ of Cincinnati  Chair: 03/00 - 02/03
Member: 01/97 - 03/00
Assistant Chair: 02/03 - 02/06
Nathan J. Bivens University of Missouri  Member: 05/07 - 02/09
Stephen A Bobin Norris Cotton Cancer Center, Dartmouth Medical School  Member: 08/03 - 02/05
Mrs Alison C Brown Harvard Partners Center for Genetics and Genomics  Member: 06/06 - 02/09
Casey Dagnall NCI / SAIC-Frederick  Member: 02/09 - 08/10
Michelle M Detwiler Roswell Park Cancer Institute  EB Liaison: 04/07 - 02/09
Helaman Escobar Eurofins-MWG|Operon Biotechnologies  Member: 08/08 - 03/11
Joe Forrester Univ of Missouri  Member: 02/03 - 02/09
George S. Grills Cornell University  Ad hoc: 01/98 - 01/00
Amy A. Hutchinson NCI/SAIC-Frederick  Member: 04/08 - 09/10
Dr Karen R Jonscher University of Colorado Denver  EB Liason: 02/09 - 03/11
Laura Kasch Johns Hopkins Hosp  Member: 01/97 - 03/02
Robert G. Keefe Wadsworth Center/NYS DOH  Member: 01/01 - 02/03
Ad hoc: 02/03 - 03/04
Brewster F Kingham University of Delaware  Chair: 03/09 - 02/10
Member: 04/06 - 03/08
Ad hoc: 03/10 - 03/11
co-chair: 03/08 - 02/09
Prof Don Kristt Rabin Medical CTR-Tissue Typing Laboratory  MemberAd hoc: 02/05 - 02/08
Dr Kathryn S Lilley University of Cambridge  EB Liason: 03/04 - 03/05
Dr. Mark O. Lively Wake Forest Univ. Sch. of Med.  Ad hocEB Liason: 01/01 - 01/02
Christian H Lytle Dartmouth College  Chair: 02/06 - 02/09
Paul T Morrison MBCF @ Dana-Farber Cancer Institute  Ad hocEB Liason: 01/97 - 01/99
Aaron Noll Stowers Institute For Medical Research  Member: 06/09 - 03/10
Lynn O. Petukhova Rockefeller University  Member: 01/97 - 08/03
Margaret Robertson   Ad hocEB liason: 02/03 - 03/04
Ad hocEB Liaison: 03/05 - 04/07
Caprice Rosato Oregon State Univ  Chair: 02/03 - 03/04
Member: 01/00 - 02/03
Brian W Sanderson Ambion  Chair: 03/10 - 08/10
Member: 03/08 - 02/09
Ad hoc: 09/10 - 03/11
chair in training: 03/09 - 02/10
Rebecca Scholl Brigham Young University  Member: 02/01 - 02/04
Ad hoc: 02/04 - 02/05
Dr Katia Sol-Church AI duPont Hospital for Children  Member: 05/02 - 03/04
Assistant Chair: 02/06 - 04/07
Cynthia S. Spittle Wyeth Research  Member: 07/08 - 06/09
Laurey Steinke University of Nebraska Medical Center  Ad hocEB Liason: 01/00 - 01/01
Tom Stelick Cornell Univ  Member: 08/03 - 04/05
Kristine Swiderek ZymoGenetics  Ad hocEB: 02/02 - 02/03
Robert A Welch NCI Core Genotyping Facility (CGF)  MemberChair in training: 04/06 - 02/08
Glenis J. Wiebe University of Alberta  Member: 05/07 - 02/08

Links
Generally Useful Links for Fragment Analysis
    - NCBI
    - NIST Biotechnology Division