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

Area of Science:

• Genetics
• Bioinformatics
• Molecular Biology

Background:

• Accurate identification of single nucleotide polymorphisms (SNPs) from pooled samples is essential for genetic studies.
• Next-generation sequencing can introduce errors in base calling and read mapping, complicating SNP detection.

Purpose of the Study:

• To develop an efficient method, Epds, for identifying SNPs in pooled DNA samples.
• To leverage dual mononucleotide addition-based pyrosequencing for improved SNP detection accuracy.

Main Methods:

• Utilized dual mononucleotide addition-based pyrosequencing to analyze pooled DNA samples.
• Employed an enumerative algorithm based on five extension patterns to infer mutant loci and proportions.
• Integrated data from three distinct pyrosequencing runs to recover mutant bases.

Main Results:

• The Epds method achieved a false-positive rate below 3%.
• Simulations demonstrated that Epds outperforms the existing PSM method in various scenarios.
• Experimental validation confirmed the successful application of Epds for mutant identification in pooled samples.

Conclusions:

• Epds provides an efficient and accurate approach for SNP identification in pooled DNA.
• The method demonstrates superior performance compared to current techniques, particularly in complex genetic analyses.
• Epds software and data are publicly available for broader research application.