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DNA Sequencing Research Group (DSRG)

Mission

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.

Current Membership

Marie Adams - Van Andel Institute (Chair)
Zach Herbert - Dana-Farber Cancer Institute (co -Chair)
Jyothi Thimmapuram - Purdue University
Yuriy Alekseyev - Boston University
Jun Fan - Marshall University
Jessica Podnar - University of Texas GSAF, Austin
Yanping Zhang - University of Florida
Fred W. Kolling IV - Dartmouth College
Megan Bowman - Van Andel Institute
Xiaoling Xuei -Indiana University
Jamie Prior Kershner-Muse Biotechnologies
Stuart Levine - Massachusetts Institute of Technology (ad hoc)
Chris Lytle - Dartmouth (EB Liaison)



Studies

 

 

1)

DSRG Study 2017: small RNA Illumina Libraries ---- This study is finished. Dr. Stuart Levine gave a presentation at ABRF 2018 annual meeting ( April 22-25 Myrtle Beach, SC). For more information, please check dsrg18_presentatin.pdf.pdf

2)

DSRG Study 2016: RNAseq Illumina Libraries using Ribosomal Depletion - PHASE I
Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. Most kits perform well on both intact and degraded samples and all identify ~14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. A manuscript is currently under preparation. This project has been completed. The collected data were published https://doi.org/10.1186/s12864-018-4585-1 .  

 - View Presentation about progress, 2017 [pdf]

3)

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.

4)

DSRG Study 2015: Cross-Site Comparison of Enzymatic Illumina Library Construction Kits 
The ability to produce genomic DNA libraries for Illumina sequencing depends on fragmentation of the DNA.   Fragmentation of high molecular weight DNA has typically been accomplished through physical means such as nebulization or sonication.  These techniques are not readily scalable for high throughput production.  In response, various manufacturers have developed strategies for enzymatic fragmentation of the DNA.  An open question is how well these techniques provide unbiased representation of the samples under study, and whether nucleotide composition of the target material plays a role. To address this question the DNA sequencing Research Group (DSRG) of the Association of Biomedical Research Facilities (ABRF) compared four different methods for enzymatic fragmentation of DNA prior to next-gen library generation.  Both human genomic DNA and bacterial pooled DNAs representing a spectrum of GC compositions were assessed. Kits were analyzed for their resulting library complexity as well as bias in sequence as well as genomic context as well as their site-to-site consistency. These results will have implications for the selection of kits for specific experimental contexts.

5)

DSRG Study 2014:  A Snap Shot into the Life Cycle of Sequencing in Genomics Core Facilities

The past couple years have seen a dramatic shift in the genomics core facility environment. The rapid evolution of next-generation sequencers, the increasing number of commercial and institutional service providers, and significant shifts in funding, have created a challenging environment for core facilities to keep current with the services and instrumentation they offer.  The ABRF DNA Sequencing Research Group (DSRG) conducted a web-based survey to gain insight into the current status of sequencing core facilities that offer Sanger or Next Generation Sequencing (NGS) services.  Since the introduction of high throughput DNA sequencing by Roche 454 in 2005, there have been a number of platforms available including the current market leader, Illumina, as well as contenders like the ABI 5500xl SOLiD and Ion Torrent platforms; and the third generation PacBio RS system.  This survey focused on current instrumentation, utilization and shifts between instruments as technologies have evolved.  We have also quantified core involvement in surrounding methodologies, such as Sanger sequencing, NGS library preparation and bioinformatics support allowing us to compare investigator needs, scientific applications and technologies across facilities.  

6)

DSRG Study 2013: Inter-Laboratory Comparisons of DNA and RNA Quality Assessment

Quantifying RNA and DNA samples is one of the most basic methods used in all sequencing and microarray labs.  A broad spectrum of instruments and techniques are used to ascertain nucleic acid quantity and quality, in preparation for more sophisticated analyses.  Each laboratory tends to favor specific methods.  However, beyond the manufacturer’s specifications, there are few standards to indicate how the instruments are performing relative to their optimal behavior, nor are there easy methods to directly compare platforms to examine relative benefits versus costs.  We have surveyed over 40 core facilities to identify what equipment is currently being used.  We have also directly measured the inter-lab reproducibility and inter-platform reproducibility of different DNA/RNA analyzers as well as their dynamic range using both RNA and DNA standards.  We find that there is significant interlab performance variability of the systems.  Test samples sent to fourteen laboratories showed large variation in quantification of samples and in the dynamic range of the instruments.  We have collected the protocols of the best performing labs on each instrument and present them here as a resource to users to help them achieve optimum performance of their quality control processes.

7)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] 
8)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
    - "Storage of plasmids" by J. Kieleczawa [pdf] 
    - "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 thermophilusUnknown 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) 
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