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Bioinformatics Advance Access published online on December 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm603
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Association studies for untyped markers with TUNA

Xiaoquan Wen 1 and Dan L. Nicolae 1,2

Departments of 1Statistics and 2Medicine, 5734 S. University Avenue, Chicago, IL 60637, USA

*To whom correspondence should be addressed. Dr. Dan L.Nicolae, E-mail: nicolae{at}galton.uchicago.edu


  Abstract

Summary: The software package TUNA (Testing UNtyped Alleles) implements a fast and efficient algorithm for testing association of genotyped and ungenotyped variants in genome-wide case-control studies. TUNA uses Linkage Disequilibrium (LD) information from existing comprehensive variation datasets such as HapMap to construct databases of frequency predictors using linear combination of haplotype frequencies of genotyped SNPs. The predictors are used to estimate untyped allele frequencies, and to perform association tests. The methods incorporated in TUNA achieve great accuracy in estimation, and the software is computationally efficient and does not demand a lot of system memory and CPU resources.

Availability: The software package is available for download from the website: http://www.stat.uchicago.edu/~wen/tuna/

Contact: nicolae{at}galton.uchicago.edu

Associate Editor: Prof. Keith Crandall

Received on September 23, 2007; revised on November 27, 2007; accepted on November 30, 2007

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