%0 Journal Article
%T PDA: Pooled DNA analyzer
%A Hsin-Chou Yang
%A Chia-Ching Pan
%A Chin-Yu Lin
%A Cathy SJ Fann
%J BMC Bioinformatics
%D 2006
%I BioMed Central
%R 10.1186/1471-2105-7-233
%X 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.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.The millions of single nucleotide polymorphisms (SNPs) now available are ideal for association analyses that identify important genetic variants in populations as well as genes predisposed to diseases involving complex traits [1,2]. Although the cost of individual genotyping has been reduced drastically over the years, the use of DNA pooling has reduced the cost even further, especially for large-scale studies. The first DNA pooling study was performed to identify the association between HLA class II loci and disease genes predisposing type 1 diabetes [3]. DNA pooling was later used to estimate the allele frequency of short tandem repeats and SNPs, map disease susceptibility genes [4,5], and identify polymorphisms [6-8]. A comprehensive review of the history of DNA pooling, the methods and algorithms involved, and the application thereof can refer to [9] and [10].DNA
%U http://www.biomedcentral.com/1471-2105/7/233