A comprehensive review of the history of DNA pooling, the methods and algorithms involved, and the application thereof can refer to and.
DNA pooling was later used to estimate the allele frequency of short tandem repeats and SNPs, map disease susceptibility genes, and identify polymorphisms. The first DNA pooling study was performed to identify the association between HLA class II loci and disease genes predisposing type 1 diabetes. 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 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. PDA is simple to operate and does not require that users have a strong statistical background. All of the PDA functions are illustrated in the four bona fide examples. 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. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. PDA provides estimates of the coefficient of preferential amplification and allele frequency.
PDA is originally implemented with the MATLAB ® language, but it can also be executed on a Windows system without installing the MATLAB ®. We develop the software, PDA, for the analysis of pooled-DNA data.
This motivated the development of the software, 'PDA' (Pooled DNA Analyzer), to analyze pooled DNA data. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. DNA pooling is a reliable and cost-saving alternative genotyping method. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity.
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