Software

PDA: Pooled DNA analyzer

Hsin-Chou Yang , Chia-Ching Pan , Chin-Yu Lin and Cathy SJ Fann

Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei, 115, Taiwan

author email corresponding author email

BMC Bioinformatics 2006, 7:233doi:10.1186/1471-2105-7-233

Published:	28 April 2006

Abstract

Background

Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data.

Results

We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB^® language, but it can also be executed on a Windows system without installing the MATLAB^®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples.

Conclusion

PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm webcite.