FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium
2010
FastTagger: A Fast Algorithm for Selecting Tag SNPs
publication
Evidence: high
Author Information
Author(s): Guimei Liu, Yue Wang, Limsoon Wong
Primary Institution: National University of Singapore
Hypothesis
Can a new algorithm improve the efficiency of tag SNP selection using multi-marker linkage disequilibrium?
Conclusion
FastTagger is significantly faster and uses less memory than existing algorithms for tag SNP selection.
Supporting Evidence
- FastTagger is several times faster than existing multi-marker based tag SNP selection algorithms.
- It can work on chromosomes containing more than 100 k SNPs with as little as 50 MB of memory.
- The average accuracy of tagging rules generated by FastTagger is above 96% when r2 ≥ 0.9.
Takeaway
FastTagger is a computer program that helps scientists pick important genetic markers quickly and without using too much memory.
Methodology
FastTagger uses a two-step process to generate tagging rules and select tag SNPs based on multi-marker linkage disequilibrium.
Limitations
The algorithm may still be prone to overfitting with longer tagging rules.
Digital Object Identifier (DOI)
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