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Optimal DNA pooling for the detection of single nucleotide polymorphisms

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dc.contributor.author Ramsey, David
dc.contributor.author Futschik, Andreas
dc.date.accessioned 2014-07-01T13:41:50Z
dc.date.available 2014-07-01T13:41:50Z
dc.date.issued 2011
dc.identifier.uri http://hdl.handle.net/10344/3873
dc.description peer-reviewed en_US
dc.description.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. en_US
dc.language.iso eng en_US
dc.publisher IWSM en_US
dc.relation.ispartofseries Proceedings of the 26th International Workshop on Statistical Modelling;
dc.relation.uri http://www.statmod.org/workshops.htm
dc.subject genome sequencing en_US
dc.subject optimal pooling en_US
dc.subject single nucleotide polymorphisms en_US
dc.title Optimal DNA pooling for the detection of single nucleotide polymorphisms en_US
dc.type info:eu-repo/semantics/conferenceObject en_US
dc.type.supercollection all_ul_research en_US
dc.type.supercollection ul_published_reviewed en_US
dc.contributor.sponsor SFI en_US
dc.relation.projectid 07MI012 en_US
dc.rights.accessrights info:eu-repo/semantics/openAccess en_US


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