Optimization of parameters for the assessment of Unclassified Disease Gene Sequence Variants

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This study examined in depth a range of variables that can affect the outcome of a PON query. From this study we can summarize in a generic setting that:

• Currently T-Coffee is the best MSA tool to use
• Currently PMut is the best PON tool to use

Summary

• rerun the systematic approach with another MSA tool instead of TCoffee such as Dialign to confirm the assumption that the best MSA tool will optimize the PON tool
• include a 'plug-in' module as part of a larger automated tool. This module will consist of the optimal MSA for each of the selected PON tools, the optimal generic MSA and the threshold required for AlignGVGD and PMut for each genetic disease.
• create a fully automated system such that you input the sequences and control data and the process will output the optimal MSAs for each PON tool. It will also allow the storage of these results in some kind of database such that the MSAs found could easily be recalled when required.

Suggested Future Work

• useful for any genetic disease with a large data set to find the optimal MSA, PON tool and corresponding thresholds
• can be used with limited field expertise to explore a large sequence space and tool space to provide an unbiased assessment of current methods within diagnostic laboratories
• provide a benchmark against other newer MSA or PON tools to assess overall ranking

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Conclusion

Copyright (C) 2011 Jennifer D. Warrender, Newcastle Univeristy

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