DNA Sequencing Research Group (DSRG)
| Current Members | Studies | Activities | Electronic Posters | Publications | Membership History |

Our mission is to:
  • Promote and encourage communication and cooperation among member laboratories that carry out DNA sequencing.
  • Conduct studies to assess the capabilities of DNA sequencing laboratories and disseminate the findings of these while they are still accurate and relevant.
  • Provide materials that help member laboratories evaluate their performance and that promote excellence in DNA sequencing.
  • Provide a mechanism for sharing of information relevant to the organization, administration and financial management of DNA sequencing laboratories.

Sequencing Woes? Search the DSRG Sequencing Troubleshooting Web Resource!
Please visit the site at www.abrf.org/index.cfm/stwr.home

ABRF 2011
The DSRG presentations from the annual meeting are now available - see below

Current Membership
Dr Robert H Lyons (Chair) - Univ of Michigan
Marie Adams - UW-Biotechnology Center
Dr. Deborah S. Grove - Penn State University/Huck Institutes of the Life Sciences
Dr Joanna S Hamilton - Dartmouth Medical School
Dr Stuart Levine - MIT BioMicro Center
Dr. Charles Nicolet - Univ. of Southern California
Mr Ariel Paulson - Stowers Institute for Medical Research
Savita Shanker - University of Florida
Dr Jyothi Thimmapuram - Purdue University
Ms Chris Wright - W.M. Keck Center
Anoja G Perera (EB Liaison) - Stowers Institute for Medical Research

Studies
1) ABRF NGS Study ---- The immediate goal of the study is to objectively assess the technical performance of different next-generation sequencing technologies for RNA analyses, and to evaluate the pros and cons of various data analysis methods. The ultimate goal is to create a publicly available tool for assessment of data from these instruments as compared to an established set of sequencing data from a standardized protocol. The study was initially organized in 2011, and is a joint study with GVRG, NARG, and MARG. Currently the study is being done entirely with current members of the Research groups listed above.
2) DSRG Study 2010: Metagenomics --- A Study of various methodologies used in metagenomic experiments performed on Next Generation DNA sequencing systems. The methodologies include DNA extraction/purification, various platforms, and varying analysis methods. This study is ongoing with an expected completion in 2012, and being done in its entirety by members of DSRG.
    - View Presentation about progress, 2011 [pdf]
    - View Poster about progress, 2011 [pdf]
3) DSRG Study 2009: DNA Capture, Phase II --- Comparison of Commercially Available Target Enrichment Methods for Next Generation Sequencing with the Illumina Platform : Phase II - Solution Capture Methods. This study is complete with an expected publication date of 2012.
    - View Presentation on Progress, 2011 [pdf]

Activities
1) Next Generation Sequencing Software for Data Management, Analysis, and Visualization. Session Organizer: Kip Bodi, Tufts University School of Medicine,
    - View "Tools NextGen Analysis" by K, Bodi [pdf]
2) ABRF2011 Workshop: Current State and Future of Capillary Electrophoresis and Sanger Sequencing. Session Organizer: Jan Kieleczawa
    - View "Storage of plasmids" by J. Kieleczawa [pdf]
    - View "A roboitc Microcycler" by M. Zianni [pdf]
3) ABRF2010 Workshop Session: Next Generation DNA Sequencing I - Sample Prep/Workflow
    - View "SOLiD Sequencing" by D. Grove (pdf)
    - View "Illumina Sequencing" by R. Steen (pdf) (1,263K)
    - View "454 Sequencing" by S. Singh (pdf) (6,595K)
4) ABRF 2006 Satellite Meeting
    - View "DNA Sequencing Core Management" (pdf)
    - View "Commercial LIMS - dnaTools" (pdf)
    - View "In-house & Commercial LIMS: 4D, Finch" (pdf)
    - View "Comparison of Different LIMS" (pdf)
    - View "Failure Mode Analysis - HT Pipeline" (pdf)
    - View "Tips and Tweaks" (pdf)
    - View "Bisulfite Sequencing" (pdf)
    - View "CSCE" (pdf)
    - View "EcoTilling" (pdf)
    - View "BAC Fingerprinting" (pdf)
    - View "DNA Footprinting" (pdf)

Electronic Posters
1) 2011 DSRG Study PhaseII: Comparison of Custom Target Enrichment Methods; Agilent vs. Nimblegen. Kip Bodi, Genomics Core Director, Tufts University School of Medicine
    - View Poster [pdf] (1,505K)
2) 2011 DSRG Study: Comparison of Custom Target Enrichment Methods; Agilent vs. Nimblegen Anoja Perera, Stowers Institute for Medical Research Molecular Biology Facility
    - View Presentation (pdf)
3) 2011 DSRG Study: A Methodology Study for Metagenomics Using Next Generation Sequencers. Sushmita Singh, BioMedical Genomics Center, University of Minnesota
    - View Presentation (pdf)
4) 2011 DSRG study: A Methodology Study for Metagenomics using Next Generation Sequencers. Deb Grove, Pennsylvania State University
    - View Poster (pdf)
5) 2010 DSRG Study: Comparison of Commercially Available Target Enrichment Methods for Next Generation Sequencing with the Illumina Platform (Phase I)
    - View Presentation(pdf; 1Mb) (1,008K)
6) 2010 DSRG Study: Multi-Centre Genome Sequencing and Analysis of the Dutch Elm Disease Fungus using the Roche/454 Titanium System
    - View Presentation (pdf:9Mb)
    - View Movie of Bubbles (avi; 5MB)
7) 2009 NGS Survey Results
    - View Poster
    - View Presentation (464K)
8) 2008 Study: DSRG Difficult Template Sequencing Study
    - View Presentation(pdf)
    - View Poster (pdf) (233K)
9) 2007 Pilot Study: A Comparison of Variant Screening Strategies - DNA Sequencing and SNaPshot
    - View Poster (pdf)
10) 2006 Survey: DNA Sequencing Research Group: General Survey of DNA Sequencing Facilities
    - View Poster (pdf)
    - View Presentation (pdf)
    - View RG Presentation on Web Resource (pdf)
11) 2005 Resource: DSRG 2005 - DNA Sequencing Troubleshooting Guide
    - View Poster (pdf)
12) 2004 Resource: DSRG 2004 - A Web-Based User-Interactive DNA Sequencing Troubleshooting Resource.
    - View Poster (pdf)
13) 2003 Study - Part 2: Evaluation of Standardized Methods in the Analysis of Difficult DNA Repeat Sequences: A Follow Up to the ABRF 2003 Sequencing Survey.
    - View Poster (pdf) (338K)
14) 2003 Study: DNA Sequencing Research Group - Difficult Repeat Sequence Study 2003.
    - View Poster (pdf)
15) 2003 Survey: DNA Sequencing Research Group - General Survey 2003.
    - View Poster (pdf) (186K)
16) 2002 Study: DNA Sequencing Research Group (DSRG) - Single Nucleotide Polymorphism (SNP) Study Results.
    - View Poster (pdf)
17) 2001 Study: Effects of different DNA sequencing methods evaluated using a web based quality control resource: the ABRF DNA Sequence Research Group 2001 standard template study.
    - View Poster (pdf) (548K)
18) 2000/2001 Study: Update on the Continuation of the DNA Sequencing Research Group 2000 Study: An Evaluation of the Methods Used to Sequence and Isolate Bacterial Artificial Chromosomes.
    - View Poster (pdf)
19) 2000 Study: Preliminary Results from the DNA Sequencing Research Group (DSRG) 2000 Study: An Evaluation of Methods Used to Sequence and Isolate Bacterial Aritificial Chromosomes (BACS).
    - View Poster (pdf)
20) 2000 Survey: Summary of the Composition and Configuration of the Average DNA Sequencing Core Laboratory.
    - View Poster (pdf)
    - View Poster (html)
21) 1999 Study: Analysis of the Effects of Different DNA Sequencing Methods on Accuracy, Quality and Expansion of a Web-Based Sequencing Resource: Results of the ABRF DNA Sequencing Group 1999 Study.
    - View Second Poster (11/5/99) (pdf)
    - View First Poster (06/15/99) (html)
22) 1998 Study: Analysis of the Effects of Different DNA Sequencing Methods on Sequencing Quality, Creation of a Quality Control Resource, and Assessment of the Current State of the Art.
    - View Preliminary Results Poster (html)
    - View Final Poster (html)
23) 1997 Study: 2nd Annual ABRF DNA Sequence Research Committee Study: Effects of DMSO, Thermocycling and Editing on a Template with a 72% GC Rich Area.
    - View Poster (html)
24) 1996 Study: DNA Sequencing of a Moderately Difficult Template: Evaluation of Results from a Thermus thermophilus Unknown Test Sample.
    - View Poster (html)

Publications
1) Adams, P.S., D. Bintzler, K. Bodi, K. Dewar, D.S. Grove, J. Kieleczawa, R.H. Lyons, A.C. Noll, S. Singh, R. Steen, M. Zianni, A. G. Perera. (2010) Comparison of Commercially Available Target Enrichment Methods for Next Generation Sequencing with Illumina Platform J Biomol Tech. September; 21(3 Suppl): S17. (abstract)
2) Kieleczawa, J. (2010) LIMS Primer J Biomol Tech. 2010 September; 21(3 Suppl): S8. (abstract)
3) Kieleczawa, J., Adam, D., Bintzler, D., Detwiler, M., Needleman, D., Schweitzer, P., Singh, S., Steen, R., and Zianni, M. (2009) Identification of Optimal Protocols for Sequencing Difficult Templates: Results of the 2008 ABRF DNA Sequencing Research Group Difficult Template Study 2008. J Biomol Tech. April; 20(2): 116–127.
4) Wiebe, G.J., Pershad, R., Adam, D., Escobar, H., Lin, H., Knudtson, K.L., Needleman, D.S., Schweitzer, P.A., and T. Thannhauser (2005). DNA Sequencing Research Group Presentation and Open Discussion: The Development and Launch of the Web-based DNA Sequencing Troubleshooting Resource. ABRF 2005: Biomolecular Technologies: Discovery to Hypothesis. Journal of Biomolecular Techniques 16(1), 73 (abstract).
5) Lin, H., Adam, D., Escobar, H., Needleman, D., Knudtson, K., Pershad, R., Schweitzer, P.A., Thannhauser, T. and G. Wiebe (2005). DNA Sequencing Research Group: DNA Sequencing Troubleshooting Guide. ABRF 2005: Biomolecular Technologies: Discovery to Hypothesis. Journal of Biomolecular Techniques 16(1), 74 (abstract).
6) Lin, H., Escobar, H., Hawes, J.W., Needleman, D.S., Hunter, T., Jackson-Machelski, E., Knudtson, K.L., Pershad, R., Robertson, M. and G.J. Wiebe (2004). DSRG-2004 - a web-based, user-interactive DNA sequencing troubleshooting resource. ABRF 2004: Integrating Technologies in Proteomics and Genomics. Journal of Biomolecular Techniques 15(1), 12 (abstract).
7) Pershad, R., Lyons, R., and G. Grills (2004). Data tracking and quality control in high throughput DNA sequencing: the ABRF DNA Sequencing Research Group (DSRG) 2004 applied technology and informatics tutorial. ABRF 2004: Integrating Technologies in Proteomics and Genomics. Journal of Biomolecular Techniques 15(1), 82 (abstract).
8) Escobar, H., Hawes, J.W., Lin, H., Needleman, D.S., Hunter, T., Jackson-Machelski, E., Knudtson, K.L., Pershad, R., Robertson, M. and G.J. Wiebe (2004). DNA Sequencing Research Group (DSRG) presentation and open discussion: a web-based DNA sequencing troubleshooting resource. ABRF 2004: Integrating Technologies in Proteomics and Genomics. Journal of Biomolecular Techniques 15(1), 84 (abstract).
9) Wiebe, G.J., Pershad, R., Escobar, H., Hawes, J.W., Hunter, T., Jackson-Machelski, E., Knudtson, K.L., Robertson, M. and T.W. Thannhauser (2003). DNA Sequencing Research Group (DSRG) 2003 - A general survey of core DNA sequencing facilities. Journal of Biomolecular Techniques 14(3), 231-237 (research group committee report).
    - View PDF (166K)
10) Hawes, J.W., Grills, G.S., Jackson-Machelski, E., Escobar, H., Hunter, T., Knudtson, K.L., Pershad, R., Spicer, D., and T.W. Thannhauser (2003). DSRG 2003 study: evaluation of methods for analysis of difficult DNA repeat sequences. ABRF 2003: Translating Biology Using Proteomics and Functional Genomics. Journal of Biomolecular Techniques 14(1), 55 (abstract).
11) Pershad, R., Hawes, J., Hunter, T., Jackson-Machelski, E., Knudtson, K., Escobar, H., Spicer, D., Grills, G., and T. Thannhauser (2003). The state of the art of DNA sequencing laboratories. ABRF 2003: Translating Biology Using Proteomics and Functional Genomics. Journal of Biomolecular Techniques 14(1), 55 (abstract).
12) Hunter, T.C., Escobar, H., Grills, G., Hawes, J., Jackson-Machelski, E., Knudtson, K., Pershad, R., and T. Thannhauser (2003). DNA Sequencing Research Group roundtable discussion. ABRF 2003: Translating Biology Using Proteomics and Functional Genomics. Journal of Biomolecular Techniques 14(1), 105 (abstract).
13) Jackson-Machelski, E., Hunter, T.C., Leviten, D., Pershad, R., and D. Spicer (2001). DNA Sequencing Roundtable Discussion. ABRF 2002: Biomolecular Technologies: Tools for Discovery in Proteomics and Genomics. Journal of Biomolecular Techniques 12(4), 91 (abstract).
14) Leviten, D., Hawes, J., Hunter, T., Jackson-Machelski, E., Pershad, R., Spicer, D., Bartley, D., Knudtson, K.L., Grills, G., Robertson, M., VanEe, J., and T. Thannhauser (2001). DNA Sequencing Research Group (DSRG) single nucleotide polymorphism (SNP) study 2002 results. ABRF 2002: Biomolecular Technologies: Tools for Discovery in Proteomics and Genomics. Journal of Biomolecular Techniques 12(4), 135 (abstract).
15) Hawes, J., Bartley, D., Hunter, T.C., Jackson-Machelski, E., Leviten, D., Pershad, R., Robertson, M., and D. Spicer (2001). DNA Sequencing Research Group (DSRG) 2001-2002 General Survey: A snapshot of the composition and configuration of the current DNA sequencing core facility. ABRF 2002: Biomolecular Technologies: Tools for Discovery in Proteomics and Genomics. Journal of Biomolecular Techniques 12(4), 139 (abstract).
16) Thannhauser, T., Hall, L.S., Hawes, J., Hunter, T., Jackson-Machelski, E. , Knudtson, K. , Leviten, D., and M.A. Robertson (2000). Update on the continuation of the DNA Sequencing Research Group 2000 Study: an evaluation of methods used to sequence and isolate bacterial artificial chromosomes. ABRF 2001: The New Biology: Technologies for Resolving Macromolecular Communications. Journal of Biomolecular Techniques 11(4),189 (abstract).
17) Robertson, M.A., Hall, L., Hawes, J., Hunter, T., Jackson-Machelski, E., Knudtson, K., and D. Leviten (2000). Preliminary results from the DNA Sequencing Research Group 2001 Study: factors that affect the sequencing and detection of mixed base sequences in PCR products. ABRF 2001: The New Biology: Technologies for Resolving Macromolecular Communications. Journal of Biomolecular Techniques 11(4), 225 (abstract).
18) M. A. Robertson (2000). Advances in DNA sequencing. ABRF 2001: The New Biology: Technologies for Resolving Macromolecular Communications. Journal of Biomolecular Techniques 11(4), 230 (abstract).
19) Thannhauser, T., Grills, G., Hardin, S., Leviten, D., Robertson, M., and J.I. Van Ee (2000). Preliminary results from the DNA Sequencing Research Group 2000 Study, Part 1: Factors that Affect the Sequencing Performance of a Standard BAC Template. ABRF 2000: From Singular to Global Analyses of Biological Systems. Journal of Biomolecular Techniques 11(1), 30 (abstract).
20) Thannhauser, T., Grills, G., Hardin, S., Leviten, D., Robertson, M., and J.I. Van Ee (2000). Preliminary Results from the DNA Sequencing Research Group 2000 Study Part 2: A Comparison of Methods used to Isolate BAC Templates in Preparation for Sequencing. ABRF 2000: From Singular to Global Analyses of Biological Systems. Journal of Biomolecular Techniques 11(1), 34 (abstract).
21) Thannhauser, T., Adams, P.S., Dolejsi, M.K., Grills, G., Hardin, S., and M. Robertson (2000). Effects of Different DNA Sequencing Methods on Accuracy, Quality and Expansion of a Web-Based Sequencing Resource: Results of the ABRF DNA Sequencing Group 1999 Study. ABRF 2000: From Singular to Global Analyses of Biological Systems. Journal of Biomolecular Techniques 11(1), 56 (abstract).
22) Van Ee, J.I., Grills, G., Hardin, S., Leviten, D., Robertson, M., and T. Thannhauser (2000). Preliminary results from the DNA Sequencing Research Group 2000 Study: An Evaluation of Methods used to Sequence and Isolate Bacterial Artificial Chomosomes (BACs). ABRF 2000: From Singular to Global Analyses of Biological Systems. Journal of Biomolecular Techniques 11(1), 56 (abstract).
23) Leviten, D., Grills, G., Hardin, S., Robertson, M., and T. Thannhauser (2000). Results from the DNA Sequencing Research Group’s General Survey of Core Facilities: A Detailed Summary of the Composition and Configuration of the Average DNA Sequencing Core Laboratory. ABRF 2000: From Singular to Global Analyses of Biological Systems. Journal of Biomolecular Techniques 11(1), 56 (abstract).
24) C.W. Naeve and P.S. Adams (1999) "Nucleic Acids" in M.C. Flickinger and S.W. Drew, eds., Encyclopedia of Bioprocess Technology, John Wiley & Sons, New York. pp. 2089-2120.
25) Adams, P.S., Dolejsi, M.K., Grills, G., McMinimy, D., Morrison, P., Rush, J., Goff, S., Milnamow, M., Morgan, A., Karlovitz, M.A., Dial, C.E., and S. Hardin (1998). An Analysis of Techniques Used to Improve the Accuracy of Automated DNA Sequencing of a GC-Rich Template. Journal of Biomolecular Techniques 9(4), 9-18.
    - View HTML
26) Adams, P.S., M.K. Dolejsi, S. Hardin, S. Mische, B. Nanthakamur, H. Riethman, J. Rush, and P. Morrison. (1996). DNA Sequencing of a Moderately Difficult Template: Evaluation of the Results from a Thermus thermophilus Unknown Test Sample. BioTechniques 21, 678.
27) DSRG Published Abstracts (prior to 2000)
    - View List (html)

Membership History
Member Name Organization Details
Debbie Adam University of British Columbia  Chair: 03/06 - 03/07
Member: 03/04 - 02/06
Ad hoc: 04/07 - 02/08
Pamela Scott Adams Trudeau Institute  Chair: 10/96 - 03/98
Member: 01/95 - 10/99
Ad hocEB Liaison: 02/09 - 03/10
EB Liaison: 01/06 - 04/07
Duane Bartley John Hopkins Univ  Ad hoc: 01/98 - 03/02
Mr. Doug Bintzler Univ of Cincinnati  Member: 04/06 - 10/08
Mr Doug Bintzler DNA Analysis  Member: 10/08 - 11/12
Mr Doug Bintzler DNA Analysis, LLC  Chair: 11/12 - 01/13
Mr. Kip L. Bodi Tufts University School of Medicine  Member: 06/10 - 09/12
Greg Buck Virginia Commonwealth Univ  Ad hoc: 01/97 - 01/98
Michelle M Detwiler Roswell Park Cancer Institute  EB Liaison: 04/07 - 02/08
MaryKay Dolejsi   Member: 06/96 - 06/99
Helaman Escobar Eurofins-MWG|Operon Biotechnologies  Chair: 06/03 - 03/04
Member: 05/02 - 02/06
Ad hoc: 03/06 - 04/07
Assistant Chair: 02/03 - 06/03
Matthew Gray University of Southern California  Member: 03/04 - 10/04
George S. Grills Cornell University  Chair: 04/98 - 04/99
Member: 03/11 - 03/11
Member: 01/97 - 01/00
Ad hoc: 01/00 - 03/04
Dr. Deborah S. Grove Penn State University/Huck Institutes of the Life Sciences  Chair: 02/13 - 03/13
Member: 05/09 - 01/13
Karl Hager Yale Univ  Ad hoc: 01/98 - 01/99
Lawrence Hall   Member: 03/99 - 03/01
Dr Susan H Hardin University of Houston  Member: 01/95 - 01/00
EB Liaison: 01/05 - 12/05
Dr. John W. Hawes Miami University  Chair: 03/02 - 02/03
Member: 02/01 - 02/03
Ad hoc: 02/03 - 03/04
Tim C Hunter Vermont Cancer Ctr  Member: 03/00 - 02/03
Ad hoc: 02/03 - 03/04
Emily Jackson-Machelski   Member: 03/00 - 02/03
Ad hoc: 02/03 - 03/04
Dr Jan Kieleczawa Pfizer Research  Chair: 02/09 - 03/10
Member: 04/10 - 03/12
Member: 04/06 - 02/08
Dr. Kevin L. Knudtson Univ of Iowa  Member: 03/00 - 03/03
Ad hoc: 03/03 - 02/05
Dina Leviten ICOS Corp  Chair: 11/00 - 03/02
Member: 01/99 - 03/02
Ad hoc: 03/02 - 08/02
Dr Kathryn S Lilley University of Cambridge  Ad hoc: 01/99 - 01/00
Heather Lin University of Utah  Member: 03/03 - 02/05
Dr. Mark O. Lively Wake Forest Univ. Sch. of Med.  EB Liason: 01/99 - 01/00
Dr Robert H Lyons Univ of Michigan  Member: 05/09 - 03/13
Douglas McMinimy The Jackson Laboratory  Member: 01/96 - 01/98
Dr Sheenah Mische New York University Langone Medical Center  Member: 03/95 - 03/96
Paul T Morrison MBCF @ Dana-Farber Cancer Institute  Chair: 01/95 - 10/96
Member: 01/95 - 01/98
Ad hoc: 01/98 - 01/00
Betsy Nanthakumar   Member: 03/95 - 03/97
Dr. David S. Needleman USDA/ARS Eastern Regional Research Center  Member: 03/03 - 02/06
Ad hoc: 02/06 - 02/08
Dr Thomas Neubert New York Univ Sch of Med  EB Liaison: 04/10 - 03/11
Dr. Ronald L. Niece Research Resources & Technologies  Ad hoc: 01/99 - 01/00
Anoja G Perera Stowers Institute for Medical Research  Member: 08/08 - 02/11
Rashmi Pershad UT MD Anderson Cancer Ctr  Chair: 02/03 - 05/03
Member: 03/01 - 03/04
Ad hoc: 03/04 - 02/06
Assistant Chair: 06/03 - 03/04
Harold Riethman Wistar Institute  Member: 03/95 - 03/98
Margaret Robertson   Chair: 04/00 - 11/00
Member: 01/99 - 11/00
Ad hoc: 02/01 - 03/02
EB liason: 02/03 - 03/04
Dr. John Rush Cell Signaling Technology  Ad hoc: 01/95 - 01/98
Peter A. Schweitzer Cornell University  Chair: 04/07 - 02/08
Member: 03/04 - 02/06
Dr. Sushmita Singh BioMedical Genomics Center  Member: 07/07 - 02/12
Douglas Spicer Prolinx Inc.  Member: 08/01 - 10/02
Robert Steen Harvard Medical School  Member: 03/07 - 03/12
Theodore W Thannhauser United States Department of Agriculture/Agricultural Research Service  Chair: 04/99 - 04/00
Member: 01/98 - 01/01
EB Liason: 03/04 - 02/05
James Van Ee Cornell University  Ad hoc: 01/99 - 05/01
Glenis J. Wiebe University of Alberta  Chair: 03/04 - 02/06
Member: 11/02 - 02/06
Ad hoc: 02/06 - 04/07
Michael Zianni Plant-Microbe Genomics Facility/Ohio State University  Chair: 04/10 - 02/11
Member: 04/06 - 03/10
Member: 02/12 - 03/12