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Type: Journal article
Title: Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays
Author: Schosser, A.
Pirlo, K.
Gaysina, D.
Cohen-Woods, S.
Schalkwyk, L.
Elkin, A.
Korszun, A.
Gunasinghe, C.
Gray, J.
Jones, L.
Meaburn, E.
Farmer, A.
Craig, I.
McGuffin, P.
Citation: BMC Research Notes, 2010; 3(274):Online
Publisher: BioMed Central Ltd.
Issue Date: 2010
ISSN: 1756-0500
Statement of
Alexandra Schosser, Katrina Pirlo, Darya Gaysina, Sarah Cohen-Woods, Leonard C Schalkwyk, Amanda Elkin, Ania Korszun, Cerisse Gunasinghe, Joanna Gray, Lisa Jones, Emma Meaburn, Anne E Farmer, Ian W Craig, Peter McGuffin
Abstract: Background: 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. Findings: 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. Conclusions: 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.
Description: Extent: 6p.
Rights: © 2010 Schosser et al; licensee BioMed Central Ltd.This is an open access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
RMID: 0020124197
DOI: 10.1186/1756-0500-3-274
Appears in Collections:Psychiatry publications

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