University of Sussex
Browse
Schosser,_2010.pdf (283.13 kB)

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

Download (283.13 kB)
journal contribution
posted on 2023-06-08, 16:09 authored by Alexandra Schosser, Katrina Pirlo, Darya GaysinaDarya 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
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.

History

Publication status

  • Published

File Version

  • Published version

Journal

BMC Research Notes

ISSN

1756-0500

Publisher

BioMed Central

Issue

1

Volume

3

Page range

274

Department affiliated with

  • Psychology Publications

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2014-06-17

First Open Access (FOA) Date

2014-06-17

First Compliant Deposit (FCD) Date

2014-06-17

Usage metrics

    University of Sussex (Publications)

    Categories

    No categories selected

    Licence

    Exports

    RefWorks
    BibTeX
    Ref. manager
    Endnote
    DataCite
    NLM
    DC