created: 10/09/97, last updated: 11th January 1999,© 1999 ABRF
The DNA Sequence Research Committee (DSRC) has initiated a collaboration with a mathematical consulting company that may lead to new methods for evaluating sequence quality and interpreting future DSRC studies.
An agreement has been reached between the DSRC and Daniel H. Wagner Associates, Inc. that will allow Wagner Associates to use data collected from the most recent studies conducted by the DSRC to develop more precise algorithms for analysis of DNA sequence data. Wagner Associates is a mathematical consulting company involved in biotechnology and financial consulting. One of their goals is to develop improved algorithms for interpreting raw data from protein and DNA sequencers. They have obtained Phase I funding from the National Institutes of Health for analyses involving Edman sequence analysis, mass spectrometry, and capillary array DNA sequence analysis. They have also received Phase II funding from the National Institute of Standards and Technology to develop algorithms that assign confidence levels to raw DNA sequence data and Phase II funding from the National Science Foundation (NSF) to work on DNA sequencing quality control.
One of Wagner Associates long-term goals for the NSF project is to develop software tools and protocols that laboratories can use to monitor the quality of their sequence analysis. Their success in understanding the correlations between raw sequence error rates, local base context and gel position, and variability of error rates under different conditions depends upon obtaining sufficient high-quality data. In their Phase I work for the NSF, they analyzed a large data set provided by the Stanford Human Genome Center. In that analysis, they focused on the relationships between gel position (e.g., 50 base vs. 500 base) and local base context (e.g., GGGC vs. AAAA) on raw sequence miscalls. Results from that work led to Phase II funding; however, one shortcoming of that study was that the conclusions were based on data from a single lab. The data collected by the DSRC in its past two annual studies could prove uniquely beneficial to this project due to the wide spectrum of contributors and the variety of sequencing conditions used. The anonymity of all participants will be strictly protected, and the results of Wagner Associates analyses will be made available to the DSRC and the ABRF community on a timely basis.
A major goal of this collaboration with Wagner Associates is to engender new methods of interpreting future DSRC studies. The DSRC may be able to use these methods in future studies to extract additional information from the sequencing data collected from ABRF members.
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