Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species

Area of Science:

• Population Genetics
• Molecular Biology
• Bioinformatics

Background:

• Polymerase chain reaction (PCR)-based DNA sequencing is a common method for studying genetic variation.
• Mutations at primer binding sites can lead to PCR dropouts, where DNA fails to amplify.
• PCR dropouts can introduce biases in genetic variation studies.

Purpose of the Study:

• To develop a coalescent-based theory for the distribution of PCR dropout mutations within a species.
• To analyze the impact of PCR dropouts on population genetic statistics.
• To provide a framework for detecting PCR dropouts and developing unbiased estimators.

Main Methods:

• Development of a coalescent-based theoretical model.
• Derivation of expected coalescence times and pairwise sequence differences under neutrality and background selection.
• Analysis of mutation distribution within coalescent trees.

Main Results:

• PCR dropout mutations typically occur near the base of coalescent trees.
• These mutations can lead to the unamplification of alleles in a large fraction of a species, distorting tree shape.
• Expected genetic variation statistics differ significantly in the presence of PCR dropouts compared to their absence.

Conclusions:

• PCR dropouts can substantially bias population genetic inferences.
• The derived theoretical expectations can form the basis for detecting dropout mutations.
• Unbiased estimators for population genetic statistics can be developed using this theoretical framework.