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Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

Alexandra Schosser14*, Katrina Pirlo1, Darya Gaysina1, Sarah Cohen-Woods1, Leonard C Schalkwyk1, Amanda Elkin1, Ania Korszun2, Cerisse Gunasinghe1, Joanna Gray1, Lisa Jones3, Emma Meaburn1, Anne E Farmer1, Ian W Craig1 and Peter McGuffin1

Author Affiliations

1 MRC SGDP Centre, Institute of Psychiatry, King's College London, London, UK

2 Centre for Psychiatry, Wolfson Institute of Preventive Medicine, Barts and The London Medical School, Queen Mary University of London, London, UK

3 Department of Psychiatry, University of Birmingham, Birmingham, UK

4 Division of Biological Psychiatry, Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria

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BMC Research Notes 2010, 3:274  doi:10.1186/1756-0500-3-274

Published: 1 November 2010



We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations). The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes.


In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods.


Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.