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Nucleic Acids Research Advance Access originally published online on February 14, 2008
Nucleic Acids Research 2008 36(6):e35; doi:10.1093/nar/gkm1060
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Nucleic Acids Research, 2008, Vol. 36, No. 6 e35
© 2008 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.

Methods Online

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays

Stuart Macgregor1,*, Zhen Zhen Zhao2, Anjali Henders2, Martin G. Nicholas1, Grant W. Montgomery2 and Peter M. Visscher1

1Genetic Epidemiology, Queensland Institute of Medical Research and 2Molecular Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia

*To whom correspondence should be addressed. Tel: +61 7 3845 3863; Fax: +61 7 3362 0101; Email: stuart.macgregor{at}qims.edu.au

Received August 16, 2007. Revised November 5, 2007. Accepted November 8, 2007.

Genome-wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA-pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and showed that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300-based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII-based pooling only extracts ~30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100-fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing ~20-fold reduction in total cost compared with IG-based alternatives. The large cost savings with Illumina HumanHap300-based pooling imply that future studies need only be limited by the availability of samples and not cost.


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