A comparison of association statistics between pooled and individual genotypes

Knight, Jo and Saccone, Scott F. and Zhang, Zhehao and Ballinger, Dennis G. and Rice, John P. (2009) A comparison of association statistics between pooled and individual genotypes. Human Heredity, 67 (4). pp. 219-225. ISSN 0001-5652

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BACKGROUND: Markers for individual genotyping can be selected using quantitative genotyping of pooled DNA. This strategy saves time and money. METHODS: To determine the efficacy of this approach, we investigated the bivariate distribution of association test statistics from pooled and individual genotypes. We used a sample of approximately 1,000 samples with individual and pooled genotyping on 40,000 SNPs. RESULTS AND CONCLUSIONS: We found that the distribution of the joint test statistics can be modelled as a mixture of two bivariate normal distributions. One distribution has a correlation of zero, and is probably due to SNPs whose pooled genotyping was unsuccessful. The other distribution has a correlation of approximately 0.65 in our data. This latter distribution is probably accounted for by SNPs whose pooled genotyping accurately predicts the underlying allele frequency. Approximately 87% of the data belongs to this distribution. We also derived a method to investigate the effect of both the correlation and selection cut-off on the relative power of pooling studies. We demonstrate that pooled genotyping has good power to detect SNPs that are truly associated with disease-causing variants for SNPs showing good correlation between pooled and individual genotyping. Therefore, this approach is a cost effective tool for association studies.

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Journal Article
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Human Heredity
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07 Jun 2016 10:22
Last Modified:
22 Nov 2022 03:22