The Broad Institute annually produces 80 million sequenced DNA reads. At this scale, any small change in the sequencing process can result in saving or losing large amounts of time and money. Working with her bioinformatics colleagues, Maya Solomon analyzed how the normalized intensities of base calls and the number of Q20 bases vary with the dilution chemistry of the BigDye® Terminator Sequencing Mix (which contains the dideoxy terminating nucleotides). In their analysis, the researchers sequenced DNA at several different dilutions and ten high-quality reads were picked from each dilution for analysis. In order to perform an appropriate analysis, Maya and her colleagues created three Perl scripts to assist in interpreting the quality of each base read under the different dilutions relative to the intensity of the signal. These diagnostic tools will be used in conjunction with existing software to monitor performance of the sequencing detection process.
The ultimate goal of this work is to identify a threshold average intensity at which the quality of the base call is no longer acceptable. Once found, it may be possible to further optimize the reaction mix, thus reducing costs substantially.
PROJECT: Optimizing DNA Sequencing Costs
Everyone who works at the Broad is so smart, basically everyone has a PhD, MD, or both. It was intimidating to present to such an audience because I felt like everyone knew more about my work than I did. But as it turns out, this was only partly true. While everyone did know more about the DNA sequencing process as a whole, they didn't know anything about the research that I did on average channel intensities. It was pretty cool to be the 'expert' in the room.