Created: 3rd January 1999, last updated: 4th January 1999, © 1999 ABRF
The DNA Sequencing Research Group (DSRG) conducted
a study in 1998 on the results of sequencing a standard template. The 1998
study focused on three main goals. The first goal of this study was to analyze
the effect of a wide range of commonly used sequencing methods and instrumentation
on the quality of sequencing results. The second goal was to create a readily
accessible and easily updated resource that could be used as a benchmark
for sequencing and as a reference both for self-evaluation and for making
decisions concerning new technologies. The third goal was to build a current
profile of DNA sequencing laboratories.
An e-mail request was posted to DNA sequencing discussion groups requesting
submission of sequence data for pGEM, a common standard template. Sequencing
data were collected by FTP and the details of the sequencing conditions
were collected using Web forms. The number of errors for each submitted
sequence was determined by comparison with the known sequence. The effects
of factors such as different types of instrumentation, enzymes, dye chemistries,
reagent dilutions, editing, and basecalling programs were examined. In addition,
a Web-based general survey form was used to collect data such as instrumentation,
protocols, services, staffing, and sequencing throughput.
A preliminary analysis of data was presented in March, 1998 at the ABRF
`98 meeting in San Diego. The preliminary study was presented both as a
poster and as part of the DSRG committee report session. In addition, the
preliminary analysis was posted on the web (http://sequence.aecom.yu.edu/oligo/ABRFDNASEQ/dsrc98.htm)
to facilitate the rapid communication of the study results.
A comprehensive analysis of all data was presented in September 1998 at
the 10th International Genome and Sequence Analysis Conference in Miami.
This cumulative analysis examined a total of 242 sequencing data submissions
from 72 different machines in 59 laboratories, all submitted from November
1997 to August 1998. The accuracy of the submitted data was analyzed by
comparison with the known sequence. Furthermore, the quality of each submitted
sequence was examined by reanalyzing all of the submitted sequences with
phred software. The phred analysis was done in collaboration with Dr. Stephen
Goff, Maureen Milnamow and Allan Morgan of Novartis. The results of the
comprehensive study were presented at the genome conference both as a poster
and as part of an ABRF/DSRG workshop presentation titled "Getting it
Right: Current Technology and Methodology in DNA Sequencing Core Laboratories."
The latest analysis results of the 1998 study are posted on the ABRF web page. The
data in this web poster is presented in a format that allows it to be used
as an on-line repository of sequence results. The analyses enable researchers
to anonymously compare the quality of their sequence data with those of
colleagues. Moreover, the results of this study can help core laboratory
personnel make informed decisions regarding equipment upgrades and chemistry
changes.
This is an ongoing study; the DSRG will continue the 1998 study of different
conditions on a standard template in 1999. In addition, the DSRG is preparing
a challenging `problem' template that will be the focus of a new 1999 study.
The long term goal of the new 1999 study will be to identify an array of
well-characterized normal and problem templates that can be used as standards,
for troubleshooting, and as training tools.
In March of 1999, George Grills replaced Scottie Adams as chair of the Committee,
Ted Thannhauser joined the committee, and Paul Morrison "retired"
to an ad hoc position.