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Optimal DNA pooling for the detection of single nucleotide polymorphisms
Date
2011
Abstract
We consider the optimal pooling of DNA to detect single nucleotide polymorphisms (SNPs), sites along the genome at which a population shows variation. The focus is on the detection of low frequency variants. Pooling individuals increases the probability that a rare variant appears in the sample. However, as the pool size increases, the mean number of reads from an individual decreases, making it harder to distinguish reads of a rare variant from errors. A hypothesis test for the detection of SNPs is defined. On the basis of this test, we determine the asymptotically optimal pool size given the parameters of the genome sequencer used, the number of lanes available and a specified significance level.
Supervisor
Description
peer-reviewed
Publisher
IWSM
Citation
Proceedings of the 26th International Workshop on Statistical Modelling;
Files
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Ramsey_2011_optimal.pdf
Adobe PDF, 108.65 KB
ULRR Identifiers
Funding code
Funding Information
Science Foundation Ireland (SFI)