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.
Questions or interest in joining an ABRF research group? Contact us!
Current Membership
Marie Adams - Van Andel Institute
Yuriy Alekseyev - Boston University
Sridar Chittur - SUNY Albany (EB Liaison)
Jun Fan - Marshall University
Michael Heinz, Washington University School of Medicine
Zach Herbert - Dana-Farber Cancer Institute
Fred Kolling IV - Dartmouth College (Co-Chair)
Stuart Levine - Massachusetts Institute of Technology (ad hoc)
Tania Mesa - Moffitt Cancer Center
Jyothi Thimmapuram - Purdue University
Sean Vargas - University of Texas at San Antonio
Xinkun ‘Sequen’ Wang- NUSeq Genomics Core Facility
Xiaoling Xuei - Indiana University
Molly Zeller - University of Wisconsin Madison
Yanping Zhang - University of Florida
Studies
Multi-year study (2019-2021):
Investigating FFPE conditions on downstream nucleic acid assays
There are three specific aims in this study. Aim 1).Creating a set of FFPE samples representative of common variations in clinical processing and storage conditions. Aim 2). Evaluating the quality of nuclei acids of these FFPE samples by DIN/RIN value, A260/280, etc at three storage time points, such as one month, six months and twelve months. Aim 3). Further assessing nuclei acid quality of these FFPE samples through gDNA/RNA amplifiability by qPCR and artifactual mutation occurring during FFPE tissue preparation by NGS library sequencing.
The specific aim 1 in the study B has been finished.
2019 study:
Hybrid Capture Methods for Targeted RNA sequencing
This study aims to evaluate how five commercial exome capture kits perform in a targeted RNA-seq application. Specific Aims : evaluating intra- and inter- site reproducibility of commercially available hybrid capture kits for RNAseq; characterizing absolute quantitative accuracy or limitations of targeted RNAseq; evaluating this method for relative differential gene expression analysis in intact and degraded RNA materials; providing a practical comparison of current capture-based targeted RNAseq protocols.
2018 study:
Cross Site Evaluation of Sanger Sequencing Dye Chemistries
Specific Aims: 1) Evaluate equivalence of routine and difficult Sanger Sequencing templates using a variety of legacy and new-to-market reagents.
2) Provide guidance to ABRF Sanger Sequencing facilities with regard to feasibility of modifying existing dye terminator chemistry
protocols to further cost-savings potential.
This study is finished. Jessica W. Podnar gave a presentation at ABRF 2019 annual meeting ( March 23-26, San Antonio, TX).
For more information, please check https://abrf.org/sites/default/files/abrf_sanger_final_2019.pdf
The manuscript is in preparation.
2017 Study: A poster related to this study was presented at AGBT 2019 by Zachary T. Herbert. https://abrf.org/sites/default/files/agbt_smrna_poster_final.pdf The manuscript is submitted. |
2016 Study: |
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. |
2015 Study |
2014 Study 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. |
2013 Study 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. |
2010 Study 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] |
2009 Study 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] |
Resources
abrf17_presentation.pdf
cross-site_comparison_of_enzymatic_final.pdf
dsrgposter15.pdf
dsrg18_presentatin.pdf.pdf
abrf_sanger_final_2019.pdf
agbt_smrna_poster_final.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 Phase II: 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 Artificial 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) | Herbert ZT, Kershner JP, Butty VL, Thimmapuram J, Choudhari S, Alekseyev YO, Fan J, Podnar JW, Wilcox E, Gipson J, Gillaspy A, Jepsen K, BonDurant SS, Morris K, Berkeley M, LeClerc A, Simpson SD, Sommerville G, Grimmett L, Adams M, Levine SS.(2018) Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction. BMC Genomics. 19(1):199. |
2) | 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) |
3) | Kieleczawa, J. (2010) LIMS Primer J Biomol Tech. 2010 September; 21(3 Suppl): S8. (abstract) |
4) | 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. |
5) | 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). |
6) | 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). |
7) | 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). |
8) | 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). |
9) | 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). |
10) | 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) |
11) | 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). |
12) | 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). |
13) | 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). |
14) | 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). |
15) | 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). |
16) | 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). |
17) | 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). |
18) | 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). |
19) | 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). |
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 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). |
21) | 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). |
22) | 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). |
23) | 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). |
24) | 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). |
25) | 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. |
26) | 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 |
27) | 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. |
28) | DSRG Published Abstracts (prior to 2000) - View List (html) |
Satellite Workshops
organizer_information_sheet.pdf
dr._laframboise_slides.pdf
beckman_coulter_slides.pdf
dr._singh_slides.pdf