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

Schosser, Alexandra, Pirlo, Katrina, Gaysina, Darya, Cohen-Woods, Sarah, Schalkwyk, Leonard C, Elkin, Amanda, Korszun, Ania, Gunasinghe, Cerisse, Gray, Joanna, Jones, Lisa, Meaburn, Emma, Farmer, Anne E, Craig, Ian W and McGuffin, Peter (2010) Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. BMC Research Notes, 3 (1). p. 274. ISSN 1756-0500

[img]
Preview
PDF - Published Version
Available under License Creative Commons Attribution.

Download (289kB) | Preview

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.

Item Type: Article
Schools and Departments: School of Psychology > Psychology
Subjects: Q Science > QH Natural history > QH0301 Biology > QH0426 Genetics
Depositing User: Darya Gaysina
Date Deposited: 17 Jun 2014 06:39
Last Modified: 25 Mar 2017 03:16
URI: http://sro.sussex.ac.uk/id/eprint/46773

View download statistics for this item

📧 Request an update