s-dePooler: determination of polymorphism carriers from overlapping DNA pools

Area of Science:

• Genomics
• Bioinformatics

Background:

• DNA sample pooling reduces costs and labor in large-scale genetic studies.
• Overlapping pools improve accuracy in detecting DNA variants (polymorphisms) and rare variants.
• A lack of computational tools for interpreting pooling data and identifying carriers hinders research.

Purpose of the Study:

• To develop and present s-dePooler, a software application for analyzing DNA pooling experiment data.
• To create an automated pipeline (dePoP) for efficient pooling analysis and carrier identification.

Main Methods:

• s-dePooler analyzes variant information (VCF files) and pooling schemes.
• The dePoP pipeline integrates s-dePooler for automated analysis.
• Performance was validated using a synthetic dataset derived from the 1000 Genomes Project.

Main Results:

• s-dePooler successfully identifies candidate carriers for each polymorphism.
• The dePoP pipeline achieved 97% accuracy in identifying carriers of rare polymorphisms (present in <10% of individuals).

Conclusions:

• s-dePooler and dePoP enable carrier identification in overlapping DNA pools.
• The tools are compatible with various pooling schemes and are freely available with instructions and test data.