FREQ-Seq2

FREQ-Seq2 quantifies allele frequencies in mixed population samples using paired barcode sequences and Illumina sequencing to provide high-throughput, precise measurements for genetic, evolutionary, and disease-risk analyses.

Key Features:

• High Throughput: Utilizes paired barcode sequences to multiplex sample processing from 48 to 2,304 samples per run.
• Targeted Amplification: Enables targeted amplification of specific genomic regions using universal barcoded adapters to construct Illumina sequencing libraries for loci of interest.
• Error Detection and Correction: Implements mechanisms to detect and remove errors that are undetectable by the original FREQ-Seq method and other conventional allele frequency quantification methods.
• Analysis Software: Provides accompanying software to analyze sequenced libraries from multiplexed experiments.

Scientific Applications:

• Population Genetics: Provides precise allele frequency data to support development and testing of population genetic models.
• Genome-Wide Association Studies (GWAS): Supports accurate allele frequency estimation to inform GWAS and genetic association inference.
• Disease Risk Assessment: Facilitates determination of genetic risk factors for disease and related risk analyses.
• Evolutionary Dynamics: Enables tracking of allele frequency changes over time to study evolutionary processes.

Methodology:

Sequencing-based approach using paired barcode sequences and universal barcoded adapters to build Illumina sequencing libraries, validated with highly multiplexed control samples and competitive evolution experiments in Escherichia coli.