1999 ABRF DNA Sequence Research Committee Study

ABRF'99 Poster

• Title
• Abstract
• Table of Contents

ABRF’99: Bioinformatics and Biomolecular Technologies: Linking Genomes, Proteomes and Biochemistry

Evaluation of the Effects of Different DNA Sequencing Methods
on Sequencing Standard and Difficult Templates,
Expansion of a Web Based Quality Control Resource,
and Establishing a Test Array of Sequencing Templates:

Results from the ABRF DNA Sequence Research Committee 1999
Standard and Difficult Template Studies
 
George Grills¹, Pamela Scott Adams², Mary Kay Dolejsi³, Susan Hardin⁴, and Theodore Thannhauser⁵.

Association of Biomolecular Resource Facilities (ABRF) DNA Sequence Research Committee.

¹Albert Einstein College of Medicine, Bronx, NY; ²Trudeau Institute, Saranac Lake, NY; ³Fred Hutchinson Cancer Research Center, Seattle, WA; ⁴University of Houston, Houston, TX; ⁵Cornell University, Ithaca, NY.

ABSTRACT

The first goal of this study was to analyze the effect of different DNA sequencing methods on the quality of results.  For the standard template, a wide variety of sequencing groups submitted data for pGEM.  For the difficult template, GC rich templates were sent to sequencing laboratories.  For both parts of this study, sequence data were collected by FTP or HTTP and details of sequencing conditions were collected by web forms.  The effect of factors such as different types of instrumentation and chemistries were examined, the data were compared to our prior studies, and results of using common and new technologies were analyzed.   The second goal of this study was to update and expand a web based resource of sequencing data that we created in 1998 to ensure its continued relevance.  The third goal of the study was to initiate the creation of a standard test array of sequencing templates.  The templates used in this study were evaluated for inclusion in a larger test array.  The results of this study may be used for quality control, trouble shooting, and evaluation of new technologies.

TABLE OF CONTENTS

Introduction

Methods

pGEM sequence

Lunatic sequence

Sasha sequence

Results

Figure 1: Summary of Submissions

Fig. 1a: Number of Samples per Machine Type - Standard Template (pGEM)

Fig. 1b: Number of Samples per Machine Type - Difficult Template (Lunatic)

Fig. 1c: Number of Samples per Machine Type - Difficult Template (Sasha)

Fig. 1d: 377 Upgrades Used for Standard Template (pGEM)

Figure 2: Accuracy of Different Machine Types

Figure 2a: Accuracy of Different Machine Types with a Standard Template (pGEM)

Fig. 2a(i): Accuracy at Different Length of Reads

Fig. 2a(ii): Accuracy at Longest Length of Read

Fig. 2a(iii): Quality at Longest Length of Read

Figure 2b: Accuracy of Different Machine Types with a Difficult Template (Lunatic)

Fig. 2b(i): Accuracy at Different Length of Reads

Fig. 2b(ii): Accuracy at Longest Length of Read

Figure 2c: Accuracy of Different Machine Types with a Difficult Template (Sasha)

Fig. 2c(i): Accuracy at Different Length of Reads

Fig. 2c(ii): Accuracy at Longest Length of Read

Fig. 2d: Sasha: Secondary Structure Analysis

Figure 3: Comparison of Lunatic Results in 1997 versus 1999

Fig. 3a: Types of Machine Used

Fig. 3b: Accuracy of Different Machine Types

Figure 4: Accuracy and Quality of Different Dye Chemistries

Figure 4a: Comparison of Dyes on Different Machine Types Using a Standard Template (pGEM)

Fig. 4a(i): Accuracy with Different Dyes and Machine Types

Fig. 4a(ii): Quality with Different Dyes and Machine Types

Figure 4b: Accuracy of Different Dye Chemistries

Fig. 4b(i): Accuracy of Different Dye Chemistries with pGEM

Fig. 4b(ii): Accuracy of Different Dye Chemistries with Lunatic

Fig. 4b(iii): Accuracy of Different Dye Chemistries with Sasha

Fig. 4b(iv): Examples of Accuracy with Different Dye Chemistries

Figure 5: Effects of Dilution and Reaction Volume

Fig. 5a: Accuracy with Different Dilution and Reaction Volumes with pGEM

Fig. 5b: Accuracy with Different Dilution and Reaction Volumes with Lunatic

Fig. 5c: Accuracy with Different Dilution and Reaction Volumes with Sasha

Figure 6: Effects of Sample Cleanup on Sequencing Accuracy

Figure 7: Ranking of All Sequences

Fig. 7a: Ranking of All Sequences - pGEM

Fig. 7b: Ranking of All Sequences - Lunatic

Fig. 7c: Ranking of All Sequences - Sasha

Fig. 8: Sequences from the Top Ten Laboratories

Fig. 8a: Top Ten Laboratories - pGEM

Fig. 8b: Top Ten Laboratories - Lunatic

Fig. 8c: Top Ten Laboratories - Sasha

Fig. 9: Top Three Lab Sequences per Machine Type

Fig. 9a: Top Three Labs per Machine - pGEM

Fig. 9b: Top Three Labs per Machine - Lunatic

Fig. 9c: Top Three Labs per Machine - Sasha

Conclusions

Acknowledgements

References

Contact Information:

To request general information or to send comments about this poster

ABRF DNA Sequence Research Committee

Association of Biomolecular Resource Facilities (ABRF)

Last modified: June 15, 1999

© copyright ABRF