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Efficient identification of SNPs in pooled DNA samples using a dual mononucleotide addition-based sequencing method.

Authors :
Cao, Changchang
Pan, Rongfang
Tan, Jun
Sun, Xiao
Xiao, Pengfeng
Source :
Molecular Genetics & Genomics. Oct2017, Vol. 292 Issue 5, p1069-1081. 13p.
Publication Year :
2017

Abstract

Identifying single nucleotide polymorphism (SNPs) from pooled samples is critical for many studies and applications. SNPs determined by next-generation sequencing results may suffer from errors in both base calling and read mapping. Taking advantage of dual mononucleotide addition-based pyrosequencing, we present Epds, a method to efficiently identify SNPs from pooled DNA samples. On the basis of only five patterns of non-synchronistic extensions between the wild and mutant sequences using dual mononucleotide addition-based pyrosequencing, we employed an enumerative algorithm to infer the mutant locus and estimate the proportion of mutant sequence. According to the profiles resulting from three runs with distinct dual mononucleotide additions, Epds could recover the mutant bases. Results showed that our method had a false-positive rate of less than 3%. Series of simulations revealed that Epds outperformed the current method ( PSM) in many situations. Finally, experiments based on profiles produced by real sequencing proved that our method could be successfully applied for the identification of mutants from pooled samples. The software for implementing this method and the experimental data are available at . [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
16174615
Volume :
292
Issue :
5
Database :
Academic Search Index
Journal :
Molecular Genetics & Genomics
Publication Type :
Academic Journal
Accession number :
125085649
Full Text :
https://doi.org/10.1007/s00438-017-1332-2