1998 ABRF DNA Sequence Research Committee Study

1998 ABRF'98 Poster 

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  ABRF ’98: From Genomes to Function:

Technical Challenges of the Post-Genome Era: An International Symposium Sponsored by the Association of Biomolecular Resource Facilities

1998 ABRF DNA Sequence Research Committee Study:

Assessing the Current State of the Art in DNA Sequencing

and Creating a Quality Control Resource

George Grills¹, Mary Kay Dolejsi², Susan Hardin³, Doug McMinimy⁴, Paul Morrison⁵, John Rush⁶, and Pamela Scott Adams⁷. Association of Biomolecular Resource Facilities (ABRF) DNA Sequence Research Committee.

¹Albert Einstein College of Medicine, Bronx, NY. ²Fred Hutchinson Cancer Research Center, Seattle, WA. ³University of Houston, Houston, TX. ⁴The Jackson Laboratory, Bar Harbor, ME. ⁵Dana-Farber Cancer Institute, Boston, MA. ⁶Howard Hughes Medical Institute, Harvard Medical School Boston, MA. ⁷Adirondack Biomedical Research Institute, Lake Placid, NY.

ABSTRACT

The field of automated DNA sequencing is currently undergoing many changes in instrumentation, dyes for detection, and enzymes. This year's DSRC study requested sequencing groups to submit sequence data for a common standard template using the instruments and chemistry common in their lab. One goal of this study is to evaluate new instrumentation or chemistries. A second goal is to create a database of sequence results that will allow researchers to compare, anonymously, the quality of their sequence data with that of colleagues under similar conditions. Data were collected electronically via FTP and web forms. Sequences were analyzed based on the number of errors in the first 840 bases. The data were further analyzed by instrument manufacturer and model, run conditions, dyes and enzymes. This study is an ongoing effort.

TABLE OF CONTENTS

Introduction

Methods

pGEM sequence

Results

Figure 1: Summary of Submissions

Figure 1a: Number of Laboratories per Machine Type

Figure 1b: Number of Samples per Machine Type

Figure 2: Accuracy of Different Machine Types

Figure 2a: Accuracy at Different Length of Reads

Figure 2b: Accuracy at Longest Length of Read

Figure 3: Accuracy with Different Number of Lanes per Gel

Figure 4: Enzyme and Dye Comparison

Figure 4a: Enzyme and Dye Comparison by Machine Type

Figure 4b: Examples of Accuracy of Different Dye Chemistries

Figure 5: Effects of Dilution and Reaction Volume

Figure 6: Effects of Editing on Sequencing Accuracy

Figure 6a: Effects of Editing with Different Enzymes and Dyes

Figure 6b: Overall Effects of Editing on Sequencing Accuracy

Figure 7: Effects of Sample Cleanup on Sequencing Accuracy

Figure 8: Ranking of Sequences

Figure 8a: Ranking of All Sequences

Figure 8b: Sequences from the Top Ten Laboratories

Figure 8c: Top Three Sequences per Machine Type

Figure 9: The Average Lab Portrait: A General Survey

Conclusions

Future Directions

References

DNA Sequencing Committe Picture

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General information, comments, and suggestions about this poster

ABRF DNA Sequence Research Committee

Association of Biomolecular Resource Facilities (ABRF)

Last modified: July 01, 1998