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INTRODUCTIONAccurate and reliable estimation of allele frequency in a DNA pooling study relies on an important adjustment factor, coefficient of preferential amplification/hybridization (CPA). The CPA should be estimated based on peak intensity data of heterozygous individuals in individual genotyping experiments. However, collection of additional heterozygous individuals to perform CPA adjustment will increase cost and efforts dramatically and therefore blemish DNA pooling studies. The purpose of this database is to provide a public resource for free adjustment of preferential amplification in a DNA pooling study.

We have constructed a CPA database by using the Affymetrix GeneChip Human Mapping 100K Set, which contains 116,204 SNPs. The contents of this database consist of the three parts: (1) SNP descriptions (Chromosome number, probe set and physical position, genotype, SNP location); (2) Results from all samples (SNP call rate, allele frequency, locus heterozygosity, unadjusted and adjusted p-values for test of HWE); (3) Results from heterozygous individuals (Number of heterozygous individuals used in the CPA calculation, three CPA estimates, the corresponding standard errors and 95% confidence intervals of CPA).



Copyright claim:
We welcome any noncommercial use of this database for your own research, but please don't redistribute the data in any form without the permission of authors. For free resource, we assume no warranty and no responsibility for the results of analyses. If you use this database in analysis to publish your research work, please cite the following reference:

H.-C. Yang, Y.-J. Liang, M.-C. Huang, L.-H. Li, C.-H. Lin, J.-Y. Wu, Y.-T. Chen and C.S.J. Fann. (2006). A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments. Nucleic Acids Research. In press.

Please send an e-mail to the author ( hsinchou@ibms.sinica.edu.tw or csjfann@ibms.sinica. edu.tw) if you have downloaded data from our CPA website. We will inform you if this website is modified or data are updated . Any comments and suggestions are highly appreciated.



Other reference papers:

  1. Hsin-Chou Yang, Chia-Ching Pan, Richard CY Lu, Cathy SJ Fann. (2005). New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification. Genetics 169: 399-410.
  2. Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann. (2006). PDA: pooled DNA analyzer. BMC Bioinformatics, 7: 233. (Pdf file is available at http://www.biomedcentral.com/1471-2105/7/233 , PDA software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm ).


The earlier version CPA database is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/earlier_database.htm