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The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA

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Abstract

Genome-wide genotyping of a cohort using pools rather than individual samples has long been proposed as a cost-saving alternative for performing genome-wide association (GWA) studies. However, successful disease gene mapping using pooled genotyping has thus far been limited to detecting common variants with large effect sizes, which tend not to exist for many complex common diseases or traits. Therefore, for DNA pooling to be a viable strategy for conducting GWA studies, it is important to determine whether commonly used genome-wide SNP array platforms such as the Affymetrix 6.0 array can reliably detect common variants of small effect sizes using pooled DNA. Taking obesity and age at menarche as examples of human complex traits, we assessed the feasibility of genome-wide genotyping of pooled DNA as a single-stage design for phenotype association. By individually genotyping the top associations identified by pooling, we obtained a 14- to 16-fold enrichment of SNPs nominally associated with the phenotype, but we likely missed the top true associations. In addition, we assessed whether genotyping pooled DNA can serve as an inexpensive screen as the second stage of a multi-stage design with a large number of samples by comparing the most cost-effective 3-stage designs with 80% power to detect common variants with genotypic relative risk of 1.1, with and without pooling. Given the current state of the specific technology we employed and the associated genotyping costs, we showed through simulation that a design involving pooling would be 1.07 times more expensive than a design without pooling. Thus, while a significant amount of information exists within the data from pooled DNA, our analysis does not support genotyping pooled DNA as a means to efficiently identify common variants contributing small effects to phenotypes of interest. While our conclusions were based on the specific technology and study design we employed, the approach presented here will be useful for evaluating the utility of other or future genome-wide genotyping platforms in pooled DNA studies.

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Abbreviations

AF:

Allele frequency

GRR:

Genotypic relative risk

GWA:

Genome-wide association

LD:

Linkage disequilibrium

MEC:

Multi-Ethnic Cohort

QC:

Quality control

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Acknowledgments

The principal acknowledgement is to the participants who contributed their time, biological samples, and phenotype data to the different projects. The authors also thank P.I. de Bakker, P. Sklar, and past and present members of the Hirschhorn laboratory for comments, ideas, and discussions; the past and present team members and investigators at the Tropical Medicine Research Institute and the Hawai’i and Los Angeles Multi-Ethnic Cohort for collecting samples and data. This work was supported by a graduate research fellowship from the National Science Foundation to C.W.K.C. and grants from the National Institutes of Health to J.N.H. (R01DK075787), to R.S.C. (R37HL45508 and R01HL53353), to X.Z. (R01HL074166), and to M.R.P. (R01HD048960). The funders had no role in study design, data collection, analysis, interpretation, decision to publish, or preparation of the manuscript.

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Correspondence to Joel N. Hirschhorn.

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Chiang, C.W.K., Gajdos, Z.K.Z., Korn, J.M. et al. The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA. Hum Genet 130, 607–621 (2011). https://doi.org/10.1007/s00439-011-0974-0

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  • DOI: https://doi.org/10.1007/s00439-011-0974-0

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