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

Kathryn E. Holt; Yik Y. Teo; Heng Li; Satheesh Nair; Gordon Dougan; John Wain; Julian Parkhill

doi:10.1093/bioinformatics/btp344

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

Kathryn E. Holt, Yik Y. Teo, Heng Li, Satheesh Nair, Gordon Dougan, John Wain, Julian Parkhill

Norwich Medical School

Research output: Contribution to journal › Article › peer-review

40 Citations (Scopus)

Abstract

Summary: 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 =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.

Original language	English
Pages (from-to)	2074-2075
Number of pages	2
Journal	Bioinformatics
Volume	25
Issue number	16
DOIs	https://doi.org/10.1093/bioinformatics/btp344
Publication status	Published - 15 Aug 2009

Access to Document

10.1093/bioinformatics/btp344Licence: CC BY

Cite this

@article{580788341f2f4b3e879e458d147772c1,

title = "Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA",

abstract = "Summary: 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 =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.",

author = "Holt, {Kathryn E.} and Teo, {Yik Y.} and Heng Li and Satheesh Nair and Gordon Dougan and John Wain and Julian Parkhill",

year = "2009",

month = aug,

day = "15",

doi = "10.1093/bioinformatics/btp344",

language = "English",

volume = "25",

pages = "2074--2075",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "16",

}

TY - JOUR

T1 - Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA

AU - Holt, Kathryn E.

AU - Teo, Yik Y.

AU - Li, Heng

AU - Nair, Satheesh

AU - Dougan, Gordon

AU - Wain, John

AU - Parkhill, Julian

PY - 2009/8/15

Y1 - 2009/8/15

N2 - Summary: 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 =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.

AB - Summary: 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 =80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.

U2 - 10.1093/bioinformatics/btp344

DO - 10.1093/bioinformatics/btp344

M3 - Article

VL - 25

SP - 2074

EP - 2075

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 16

ER -