FastTagger: an efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium.

BMC Bioinformatics
Guimei LiuLimsoon Wong

Abstract

Human genome contains millions of common single nucleotide polymorphisms (SNPs) and these SNPs play an important role in understanding the association between genetic variations and human diseases. Many SNPs show correlated genotypes, or linkage disequilibrium (LD), thus it is not necessary to genotype all SNPs for association study. Many algorithms have been developed to find a small subset of SNPs called tag SNPs that are sufficient to infer all the other SNPs. Algorithms based on the r2 LD statistic have gained popularity because r2 is directly related to statistical power to detect disease associations. Most of existing r2 based algorithms use pairwise LD. Recent studies show that multi-marker LD can help further reduce the number of tag SNPs. However, existing tag SNP selection algorithms based on multi-marker LD are both time-consuming and memory-consuming. They cannot work on chromosomes containing more than 100 k SNPs using length-3 tagging rules. We propose an efficient algorithm called FastTagger to calculate multi-marker tagging rules and select tag SNPs based on multi-marker LD. FastTagger uses several techniques to reduce running time and memory consumption. Our experiment results show that FastTagger is several ti...Continue Reading

References

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May 21, 2008·Journal of Biomedical Informatics·Yao-Ting Huang, Kun-Mao Chao

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Citations

Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Bo LiaoHaowen Chen
Dec 24, 2014·Clinical Implant Dentistry and Related Research·Andrea Duarte DoetzerPaula Cristina Trevilatto
Dec 25, 2012·Journal of Biomedical Informatics·Ilhan Ilhan, Gülay Tezel
Oct 29, 2013·Briefings in Bioinformatics·Stefan NaulaertsKris Laukens
Nov 5, 2016·Archives of Oral Biology·Rafaela ScariotPaula Cristina Trevilatto
Dec 20, 2016·PloS One·Abdulkadir ElmasDimitris Anastassiou
Feb 28, 2017·Journal of Bioinformatics and Computational Biology·Bo LiaoHaowen Chen
Aug 12, 2014·Interdisciplinary Sciences, Computational Life Sciences·Amer E Mouawad, Nashat Mansour
Oct 20, 2018·Clinical Implant Dentistry and Related Research·Rita de Cássia BrokerPaula Cristina Trevilatto
Jan 25, 2019·PloS One·Shuzhen SunCharles Chen
Jul 29, 2017·BMC Genomics·Robert J SchaeferMolly E McCue

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Methods Mentioned

BETA
genotyping

Software Mentioned

FastTagger
Fast
COOC
Linux
REAPER
FreeBSD
1vsR
Excel
PHASE
Windows

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