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Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

ABSTRACT: Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40x, declining only slightly at read depths 20-40x.The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.

SUBMITTER: Holt KE 

PROVIDER: S-EPMC2722999 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature

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Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

Holt Kathryn E KE   Teo Yik Y YY   Li Heng H   Nair Satheesh S   Dougan Gordon G   Wain John J   Parkhill Julian J  

Bioinformatics (Oxford, England) 20090603 16

<h4>Summary</h4>Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded > or =80% sensitivity of SNP detection and strong correlat  ...[more]

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