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.
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.
Authors: B Hoogendoorn; N Norton; G Kirov; N Williams; M L Hamshere; G Spurlock; J Austin; M K Stephens; P R Buckland; M J Owen; M C O'Donovan Journal: Hum Genet Date: 2000-11 Impact factor: 4.132
Authors: Karen L Mohlke; Michael R Erdos; Laura J Scott; Tasha E Fingerlin; Anne U Jackson; Kaisa Silander; Pablo Hollstein; Michael Boehnke; Francis S Collins Journal: Proc Natl Acad Sci U S A Date: 2002-12-13 Impact factor: 11.205
Authors: John V Pearson; Matthew J Huentelman; Rebecca F Halperin; Waibhav D Tembe; Stacey Melquist; Nils Homer; Marcel Brun; Szabolcs Szelinger; Keith D Coon; Victoria L Zismann; Jennifer A Webster; Thomas Beach; Sigrid B Sando; Jan O Aasly; Reinhard Heun; Frank Jessen; Heike Kolsch; Magdalini Tsolaki; Makrina Daniilidou; Eric M Reiman; Andreas Papassotiropoulos; Michael L Hutton; Dietrich A Stephan; David W Craig Journal: Am J Hum Genet Date: 2006-12-06 Impact factor: 11.025
Authors: Nils Homer; Waibhav D Tembe; Szabolcs Szelinger; Margot Redman; Dietrich A Stephan; John V Pearson; Stanley F Nelson; David Craig Journal: Bioinformatics Date: 2008-07-10 Impact factor: 6.937