IGG

IGG integrates genotype data from high-throughput genotyping platforms and the HapMap repository to enable whole-genome imputation and individual-level meta-analysis in genome-wide association studies (GWAS).

Key Features:

• Cross-platform integration: Integrates genotypic data across high-throughput genotyping platforms including Affymetrix and Illumina and from the HapMap repository and other collaborative projects.
• Support for HapMap genotypes: Accepts both phased and unphased HapMap genotypes, including HapMap III.
• Novel merging algorithm: Implements a novel algorithm to efficiently merge raw genotypes across large datasets.
• Imputation preparation: Generates complete sets of input files for six genotype imputation tools.
• Large-scale validation: Validated by simulation tests demonstrating rapid merging of tens of thousands of large genotype chips, including Affymetrix Genome-Wide Human SNP Array 6.0 and Illumina Human1m-duo.
• GWAS-focused outputs: Produces outputs tailored for downstream whole-genome imputation and individual-level meta-analysis workflows.

Scientific Applications:

• Genome-wide association studies (GWAS): Integration of genotype datasets across platforms to support association testing at scale.
• Whole-genome imputation: Preparation of merged genotype inputs for whole-genome imputation workflows.
• Individual-level meta-analysis: Creation of harmonized genotype datasets suitable for individual-level meta-analysis across cohorts.
• Cross-study genotype harmonization: Combining genotypes from HapMap and multiple genotyping arrays for combined analyses.

Methodology:

Uses a novel algorithm to merge raw genotypes across large datasets, accepts phased and unphased HapMap genotypes, generates complete input files for six genotype imputation tools, and was validated by simulation tests merging datasets including Affymetrix Genome-Wide Human SNP Array 6.0, Illumina Human1m-duo, and HapMap III.