Nucleic Acids Research Group (NARG)
| Current Members | Studies | Electronic Posters | Protocols | Publications | Links | Membership History |


Introduction to the NARG

The Nucleic Acids Research Group is focused on studying current topics related to any and all aspects of nucleic acids including protocols, sample preparation, and storage. Most recently the focus has been on evaluating the impact of problematic samples, either low quantity or degradation, on various labeling methods for NGS, qPCR and Microarrays. Membership is open to all interested ABRF members.



Current Year Study

1) NARG 2013-14 Research Study

ChIP-Seq from small amounts of DNA

The Nucleic Acids Research Group (NARG) study will characterize alternative library preparation chemistries that require significantly less DNA than the current standard, 10ng DNA. The aim is to evaluate how comparable the sequencing results are when a low input library preparation kit is employed as compared to the standard method. Illumina’s ChIP-Seq Sample Prep Kit will be used as the standard method. Drosophila melanogaster DNA ChIPed with an antibody against H3K4me3 will be prepared at one site and distributed to various laboratories for library preparation. Chemistries will be assessed at multiple laboratories and technical replicates carried out at each site.

Recent studies conducted by the Nucleic Acid Research Group (NARG) have focused on how fixation and degradation affects the detection of DNA methylation using several analysis methods. Mouse tissues were used to generate gDNA from matched source tissues that are both flash-frozen and formalin-fixed paraffin embedded. The resulting gDNA was assayed using conventional methylation detection methods including bisulfite sequencing, methylation sensitive PCR (MSP), methylation (in)sensitive restriction enzymes, methylation DNA immunoprecipitation (MeDIP) and methylated DNA binding protein analysis (MIRA).


Current Membership
Dr Russ Carmical (Chair) - UTMB - Galveston
herbert auer (IRB Barcelona Spain)
Zach Herbert - Dana-Farber Cancer Institute
Jennifer Holbrook - AI Dupont Hospital for Children
Christian H Lytle - Dartmouth College
Vijay Nadella - Ohio University
Dr Sridar V Chittur (Ad-Hoc) - SUNY Albany
Tim C Hunter (EB Liaison) - Vermont Cancer Ctr
Scott Tighe (Ad-Hoc) - Vermont Cancer Center

Studies
1) ChIP-Seq from small amounts of DNA - NARG 2013-14 Research Study
    - Study Presentation (5,295K)
2) Importance of DNA Extraction in Metagenomics - NARG 2013 Study
    - Presentation from Palm Springs
3) 2011Study:Effect of RNA degradation on miRNA expression
    - 2011 NARG presentation-Part A (miRNA RT-QPR) (1,162K)
    - 2011 NARG presentation-PartB (miRNA microarray) (1,423K)
    - 2011 NARG poster presentation (1,667K)
4) NARG2010 Study: Priming Strategies for cDNA synthesis in Real-Time qPCR
    - 2010ABRF: NARG presentation (1,806K)
    - 2010ABRF:RNA degradation and handling methods (707K)
    - 2011ABRF:Results from the most degraded samples
5) NARG 2009 study: Priming strategies for cDNA Synthesis
    - View ABRF2009 presentation
    - View ABRF2009 presentation on routine RNA handling
6) NARG 2008 study: Priming Strategies for cDNA Synthesis
    - View ABRF2008 NARG presentation
    - View ABRF2008 Poster (434K)
7) NARG 2007 Real-Time PCR Survey

The Nucleic Acid Research Group (NARG) of the Association of Biomolecular Resource Facilities (ABRF) invites anyone who uses “Real-Time” quantitative PCR (qPCR) to participate in our on-line survey. The aim of the survey is to determine the current status of real-time PCR technology in laboratories around the world, particularly core laboratories. Your answers will help us "take the pulse" of the real-time qPCR community. Submissions are anonymous and results will be freely available via a "web poster". This survey will be “open” until February 2, 2007. Results will be presented at the ABRF 2007 annual meeting in Tampa Bay, FL, Mar 31-Apr 3, 2007 and will be available "on line" by May 1, 2007. We think it will be worth your time to participate in this study.
    - View_2007_Survey_Presentation
    - View_2007_Survey_Poster
    - View_2007_Survey_Questions
    - View_2007_Survey_RawData
8) NARG 2006 Study: Priming Strategies for Real-time RT-PCR

The purpose of this study is to provide an opportunity for participating laboratories to gain crucial information about the variability of the RT-step of the qPCR assay and about the comparability of qPCR results obtained using different cDNA priming strategies. In addition, the study will act as an audit for participating laboratories, who will be able to compare the results from their protocols, techniques and equipment with those from other laboratories around the world. The study is open for those who use Taqman® probe-based or SYBR Green I-based assay systems. Deadline for sample submission is Dec. 15, 2005. Data will be presented at the ABRF 2006 annual meeting in Long Beach, CA, February 11 - 14, 2006. We think it will be worth your time to participate in this study.
    - View Study announcement (pdf) (46K)
    - ViewStudy information(pdf)
    - View Study Questions(pdf) (124K)
    - View Study Examples (xls) (68K)
    - View Slides of RG Presentation on ABRF 2006 Study (9,505K)
    - View Slides of Multiplex Development/Optimization
9) NARG 2005 Study: Validation of Your Reverse Transcription Real-Time PCR Technique

The purpose of this study is to give investigators an opportunity to test their reverse transcription real-time PCR technique and to gather information about the performance of various platforms, variations due to reagents and how people analyze their data. The study is open for those who use both Taqman® type systems and SYBRgreen systems. Deadline for sample submission is Dec. 15, 2004. A poster containing a table showing (anonymously) how the individual participants fared in their assay efforts will be posted on this page. Data will be presented at the ABRF 2005 annual meeting in Savannah, GA, March 5 - March 8, 2005.
    - View Study Invitation (pdf) (88K)
    - View Study Information (pdf) (96K)
    - View Submission Instructions (pdf) (54K)
    - View Poster of preliminary results
    - View Slides of Research Group Presentation
    - View Study Questions (218K)
10) NARG 2003/2004 Real-Time PCR Survey

This survey was designed to determine the current status of real-time PCR technology in laboratories around the world, especially Core laboratories. The answers allowed us to "take the pulse" of the real-time PCR community. The survey was open from November 15, 2003 until January 15, 2004. Submissions were anonymous . Results were presented at the ABRF 2004 annual meeting in Portland, OR, Feb 28-Mar 2, 2004 and at the Ist International qPCR symposium 3rd - 6th March, 2004 in Freising-Weihenstephan, Germany. Results are available below in several forms. All material is copyrighted and for scientific use only.

  • Raw data: This is a PDF file of the raw data. Please be aware that there are two duplicate entries and 3 null entries in this data.
  • Web poster: A JPG file summarizing the survey data.
  • Research Group presentation from ABRF 2004 by Brian Holloway and Tony Yeung

  •     - View survey questions (53K)
        - View raw data (4,082K)
        - View Poster (804K)
        - View Research Group presentation (312K)
    11) NARG 2004 Taqman Primer/Probe Design Study

    The purpose of this study was to give investigators an opportunity to design an optimal set of primers/probe for a common gene and have them tested empirically for effectiveness. We were able to demonstrate some of the basic principles of Taqman Assay design. A table showing how the individual participants fared in their design efforts is posted below. Final analysis of results will be published in a peer reviewed journal. A copy of the poster presented at the ABRF 2004 annual meeting in Portland, OR, Feb 28-Mar 2, 2004 and at the Ist International qPCR symposium 3rd - 6th March, 2004 in Freising-Weihenstephan, Germany may be obtained by contacting sadams@trudeauinstitute.org.
        - View study invitation (53K)
        - IFNg CDS (11K)
        - Suggestions for assay design/Primer 3 use (352K)
        - Participant Results (47K)
        - View Study Survey Questions (159K)
        - View Poster of preliminary results (258K)
    12) NARG 2003 Study Announcement

    Real-time PCR technology is of increasing importance in research. The commercial cost of dual-labeled probes for real-time PCR reactions is high because of traditional HPLC or gel purification steps. NARG believed that these probes may be used without purification, if carefully prepared, thereby reducing the cost and making the synthesis of real-time PCR probes feasible and practical for any DNA synthesis laboratory.

    NARG proposed to test whether all ABRF DNA synthesis labs are able to make quality dual-labeled probes suitable for real-time PCR reactions without requiring purification. It also wanted to determine the conditions under which highly purified probes may excel over unpurified probes.
        - View Study announcement (pdf) (13K)
        - View Recommended Protocols for Synthesis (pdf)
        - View Sample survey (pdf) (188K)
        - View Examples of Quality Analysis (pdf)
        - View Tutorial on Probe Synthesis (pdf)

    13) NARG 2003 Comparing analysis methods of dual-labeled probe
        - View Summary of Results (12K)
        - View PAGE data (108K)
        - View CE data (943K)
        - View DHPLC data (3,785K)
        - View Taqman® data (3,458K)
        - View 2003 ABRF Poster
        - Go to Biotechniques Publication Information
    14) NARG 2001 Research Group Presentation
        - View slides (1,391K)
    15) Previous NARG studies
        - NARG data repository

    Electronic Posters
    1) Low Concentration Input ChIP-Seq Study 2013-2014
        - View Document (5,295K)
    2) NARG 09-10 study poster
        - View Document (1,753K)
    3) Nucleic Acid Research Group 2008-2009 Study: A comparison of Different Priming Strategies for cDNA synthesis by Reverse Transcriptase, as evaluated by Real-Time RT-qPCR
        - View Document (1,167K)
    4) Nucleic Acids Research Group (NARG) 2005-2006 Study: Priming Strategies for Real-Time RT-PCR
        - View pdf (Poster From ABRF2006) (1,398K)
    5) Nucleic Acids Research Group (NARG) 2004-2005 Real-time PCR Study: Validate Your Real-time PCR Technique/A Comparison of Real-Time RT-PCR Technique, Chemistries and Instrumentation in Laboratories Utilizing the Same Assay
        - View pdf (Poster from ABRF 2005- Bookmarked) (1,621K)
    6) Nucleic Acids Research Group (NARG) 2003-2004 Real-time PCR Study
        - View pdf (Poster from ABRF 2004) (804K)
    7) Nucleic Acids Research Group (NARG) 2002-2003 Study: Evaluation of Taqman® DNA Probes: Can High Quality Syntheses be used in Quantitative Real-Time PCR Assays without Gel or HPLC Purification?
        - View pdf (Poster from ABRF 2003)
    8) Nucleic Acids Research Group (NARG) 2002 Mini-survey Poster
        - View pdf (Poster from ABRF 2002)
    9) Nucleic Acids Research Group (NARG) 2000-2001 Study
        - View pdf (Poster from ABRF 2001)

    Protocols
    1) Protocol
    2) Flow sorted samples and microarrays
        - FACS and microarrays (822K)

    Publications
    1) Yeung, AT, BP Holloway, PS Adams and GL Shipley. "Evaluation of dual-labeled fluorescent DNA probe purity versus performance in real-time PCR". BioTechniques 36 (2): 266-275 (2004)
        - View Abstract
    2) ME Gunthorpe, JW Fox, KM Hager, KS Lilley, S Scaringe, and AT Yeung. "Use of mass spectrometry, capillary electrophoresis, and gel electrophoresis for quality analysis of synthetic oligonucleotides: Perspectives from the ABRF Nucleic Acid Research Group ". Journal of Biomolecular Techniques,12, 16-24 (2001).
        - View Abstract
    3) Hager, K.M., J.W. Fox, M. Gunthorpe, K.S. Lilley, and A. Yeung. "Survey of Current Trends in DNA Synthesis Core Facilities". Journal of Biomolecular Techniques 10: 187-193 (1999).
        - View Abstract
    4) Buck, G.A., Fox, J.W., Gunthorpe, M., Hager, K.M., Naeve, C.W, Pon, R.T., Adams, P.S. , and Rush, J. "Design Strategies and Performance of Custom DNA Sequencing Primers." BioTechniques 27 (3): 528-536 (1999).
        - View Abstract
    5) Pon, R.T., Buck, G.A., Hager, K.M., Naeve, C.W., Niece, R.L., Robertson, M., and Smith, A.J. Multifacility survery of oligonucleotide synthesis and an examination of the performance of unpurified primers in automated DNA sequencing. BioTechniques 21: 680-685 (1996).
        - View Abstract
    6) Naeve, C.W., Buck, G.A., Niece, R.L., Pon, R.T., Robertson, M., and Smith, A. J. "Accuracy of Automated DNA Sequencing: A Multi -Laboratory Comparison of Sequencing Results." BioTechniques 19, 448-453 (1995).
        - View Abstract
    7) Pon, R.T., Buck, G.A., Niece, R.L., Robertson, M., Smith, A.J. and Spicer, E. "A Survey of Nucleic Acid Services in Core Laboratories." BioTechniques 17, 526-534 (1994).
        - View Abstract

    Membership History
    Member Name Organization Details
    Pamela Scott Adams Trudeau Institute  Chair: 04/03 - 03/04
    Member: 03/02 - 04/03
    Member: 03/04 - 01/06
    Ad hocEB Liaison: 01/06 - 04/07
    Ad hoc: 12/96 - 03/02
    Dr. Yongde Bao Univ of Virginia Sch of Med  Member: 05/03 - 03/06
    Greg Buck Virginia Commonwealth Univ  Chair: 03/96 - 09/98
    Member: 11/01 - 12/02
    Member: 06/91 - 03/98
    Prof Stephen A Bustin Queen Mary University of London  Member: 08/04 - 01/07
    Dr Russ Carmical UTMB - Galveston  MemberCo-Chair: 05/10 - 03/13
    Dr. Jay W. Fox Univ of Virginia  Member: 12/96 - 02/01
    Dr. Deborah S. Grove Penn State University/Huck Institutes of the Life Sciences  Chair: 04/05 - 04/07
    Member: 04/07 - 02/09
    Member: 05/03 - 04/05
    Martha Gunthorpe UCSF Medical Center/Diagnositics Laboratories  Chair: 01/00 - 01/01
    Member: 12/96 - 03/02
    Karl Hager Yale Univ  Chair: 09/98 - 09/99
    Member: 01/95 - 02/00
    Dr Susan H Hardin University of Houston  Ad hocEB liaison: 01/02 - 01/06
    Jennifer Holbrook AI Dupont Hospital for Children  MemberCo-Chair: 05/10 - 03/13
    Ms Deborah J Hollingshead University of Pittsburgh  Member: 03/06 - 02/09
    Brian Holloway CDC  Member: 09/00 - 04/05
    Ad hoc: 04/05 - 04/07
    Tim C Hunter Vermont Cancer Ctr  Chair: 04/07 - 02/08
    Member: 02/08 - 02/09
    Member: 05/05 - 04/07
    Ad hoc: 02/09 - 05/10
    Dr. Kevin L. Knudtson Univ of Iowa  Chair: 04/07 - 02/09
    Member: 03/06 - 04/07
    Member: 02/09 - 05/10
    Dr Kathryn S Lilley University of Cambridge  Member: 02/99 - 04/00
    Ad hoc: 04/00 - 03/02
    EB Liaison: 04/07 - 02/08
    Dr. Mark O. Lively Wake Forest Univ. Sch. of Med.  Ad hocEB Liaison: 02/00 - 12/00
    Kathleen Mills Millenium Pharmaceutical, Inc.  Member: 03/01 - 10/02
    Paul T Morrison MBCF @ Dana-Farber Cancer Institute  Ad hocEB Liaison: 03/96 - 12/99
    Clayton Naeve St Jude Childrens Res Hosp  Member: 09/94 - 12/97
    Dr. Ronald L. Niece Research Resources & Technologies  Member: 06/91 - 05/95
    Anoja G Perera Stowers Institute for Medical Research  EB liason: 04/12 - 04/14
    Dr. Richard T. Pon University of Calgary  Chair: 01/94 - 03/96
    Member: 06/91 - 12/98
    Margaret Robertson   Chair: 03/93 - 12/93
    Member: 06/91 - 12/96
    Dr Mark Robinson University of Zurich  Member: 11/11 - 03/13
    Caprice Rosato Oregon State Univ  Member: 05/11 - 03/13
    Dr. John Rush Cell Signaling Technology  : 03/96 - 12/99
    Stephen Scaringe   Member: 03/00 - 03/02
    Ad hoc: 03/02 - 02/05
    Dr Gregory L. Shipley UT Health Science Center - Houston  Chair: 03/04 - 04/05
    Member: 04/02 - 03/04
    Member: 04/05 - 02/09
    Alan J Smith somerset consulting  Chair: 06/91 - 02/93
    Member: 06/91 - 06/94
    Dr Katia Sol-Church AI duPont Hospital for Children  Member: 05/07 - 05/10
    Eleanor Spicer Med Univ of South Carolina  Chair: 03/93 - 12/93
    Member: 06/91 - 09/94
    Dr. William L Taylor UTHSC  Member: 04/08 - 03/10
    Theodore W Thannhauser United States Department of Agriculture/Agricultural Research Service  Ad hocEB liaison: 01/01 - 01/02
    Dr. Anthony T Yeung Fox Chase Cancer Ctr  Chair: 04/01 - 04/03
    Member: 08/99 - 03/01
    Member: 04/03 - 03/06
    EB-liason: 04/08 - 03/12

    Links
    Useful Links
        - GENE QUANTIFICATION web page
        - Real Time PCR Primer and Probe Database
        - Primer/Probe design-Primer 3
        - How to set up a Real-time core facility
        - miRNA database