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Genetics. 2010 Sep;186(1):207-18. doi: 10.1534/genetics.110.114397. Epub 2010 May 10.

The next generation of molecular markers from massively parallel sequencing of pooled DNA samples.

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1
Department of Statistics, University of Vienna, A-1010 Vienna, Austria. andreas.futschik@univie.ac.at

Abstract

Next generation sequencing (NGS) is about to revolutionize genetic analysis. Currently NGS techniques are mainly used to sequence individual genomes. Due to the high sequence coverage required, the costs for population-scale analyses are still too high to allow an extension to nonmodel organisms. Here, we show that NGS of pools of individuals is often more effective in SNP discovery and provides more accurate allele frequency estimates, even when taking sequencing errors into account. We modify the population genetic estimators Tajima's π and Watterson's to obtain unbiased estimates from NGS pooling data. Given the same sequencing effort, the resulting estimators often show a better performance than those obtained from individual sequencing. Although our analysis also shows that NGS of pools of individuals will not be preferable under all circumstances, it provides a cost-effective approach to estimate allele frequencies on a genome-wide scale.

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PMID:
20457880
PMCID:
PMC2940288
DOI:
10.1534/genetics.110.114397
[Indexed for MEDLINE]
Free PMC Article
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