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A comparison of association statistics between pooled and individual genotypes
Jo Knight1, Scott F Saccone, Zhehao Zhang
1Social Genetic & Developmental Psychiatry MRC Centre, Institute of Psychiatry, Kings College London, London, UK. j.knight@iop.kcl.ac.uk
Human Heredity
|January 28, 2009
Summary
Quantitative genotyping of pooled DNA offers a cost-effective method for selecting genetic markers. This approach demonstrates good power for association studies when pooled genotyping accurately predicts allele frequencies.
Area of Science:
- Genetics
- Bioinformatics
- Population Genetics
Background:
- Quantitative genotyping of pooled DNA is a strategy to identify genetic markers.
- This method aims to reduce time and cost in genetic studies.
Purpose of the Study:
- To evaluate the effectiveness of using pooled DNA for genetic marker selection.
- To investigate the statistical distribution of association test statistics from pooled versus individual genotyping.
Main Methods:
- Analysis of the bivariate distribution of association test statistics.
- Utilized a dataset of approximately 1,000 samples with both individual and pooled genotyping for 40,000 single nucleotide polymorphisms (SNPs).
Main Results:
- The joint test statistics followed a mixture of two bivariate normal distributions.
- One distribution showed zero correlation (likely failed pooled genotyping), while the other showed a correlation of ~0.65 (successful pooled genotyping).
- Approximately 87% of SNPs belonged to the high-correlation distribution, indicating reliable pooled genotyping.
Conclusions:
- Pooled DNA genotyping is effective for identifying SNPs associated with disease-causing variants, particularly when there is high correlation between pooled and individual genotyping data.
- The study provides a method to assess the impact of correlation and selection cut-offs on the power of pooling studies.
- Quantitative genotyping of pooled DNA is a cost-effective tool for genetic association studies.
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