Nucleic Acids Research Advance Access originally published online on August 23, 2006
Nucleic Acids Research 2006 34(15):e106; doi:10.1093/nar/gkl446
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Nucleic Acids Research, 2006, Vol. 34, No. 15 e106
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments
Institute of Biomedical Sciences, Academia Sinica Taipei 115, Taiwan
*To whom correspondence should be addressed at Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2 Nankang, Taipei 115, Taiwan. Tel: 886 2 27899144; Fax: 886 2 27823047; Email: csjfann{at}ibms.sinica.edu.tw
Received March 29, 2006. Revised May 5, 2006. Accepted June 9, 2006.
Microarray-based pooled DNA methods overcome the cost bottleneck of simultaneously genotyping more than 100 000 markers for numerous study individuals. The success of such methods relies on the proper adjustment of preferential amplification/hybridization to ensure accurate and reliable allele frequency estimation. We performed a hybridization-based genome-wide single nucleotide polymorphisms (SNPs) genotyping analysis to dissect preferential amplification/hybridization. The majority of SNPs had less than 2-fold signal amplification or suppression, and the lognormal distributions adequately modeled preferential amplification/hybridization across the human genome. Comparative analyses suggested that the distributions of preferential amplification/hybridization differed among genotypes and the GC content. Patterns among different ethnic populations were similar; nevertheless, there were striking differences for a small proportion of SNPs, and a slight ethnic heterogeneity was observed. To fulfill appropriate and gratuitous adjustments, databases of preferential amplification/hybridization for African Americans, Caucasians and Asians were constructed based on the Affymetrix GeneChip Human Mapping 100 K Set. The robustness of allele frequency estimation using this database was validated by a pooled DNA experiment. This study provides a genome-wide investigation of preferential amplification/hybridization and suggests guidance for the reliable use of the database. Our results constitute an objective foundation for theoretical development of preferential amplification/hybridization and provide important information for future pooled DNA analyses.
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