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

Abstract：

: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 approximately 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 approximately 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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Macgregor S,Zhao ZZ,Henders A,Nicholas MG,Montgomery GW,Visscher PM

doi

10.1093/nar/gkm1060

subject

Has Abstract

pub_date

2008-04-01 00:00:00

pages

e35

issue

6

eissn

0305-1048

issn

1362-4962

pii

gkm1060

journal_volume

36

pub_type

杂志文章

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