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Introduction:
Accurate 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 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).
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, Y.-T.
Chen and C.S.J. Fann. (2006). A genome-wide study
of preferential amplification/hybridization in microarray-based
pooled DNA experiments. http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/database.htm
Study population:
African-American Asian Caucasian Taiwan
Combination
Chromosome: All Not
all
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