LDAK-KVIK

LDAK-KVIK performs fast and powerful mixed-model association analysis of quantitative and binary phenotypes in genome-wide association studies.

Key Features:

• Computational Efficiency: LDAK-KVIK requires less than ten CPU hours and 5Gb memory to analyse genome-wide data for 350k individuals, with demands similar to REGENIE and approximately ten times less than BOLT-LMM.
• Well-Calibrated Test Statistics: LDAK-KVIK produces well-calibrated test statistics for both homogeneous and heterogeneous datasets.
• Gene-Based Tests: LDAK-KVIK can perform gene-based tests, finding 18% more significant genes than the leading existing tool across 40 quantitative UK Biobank phenotypes.
• Polygenic Score Generation: LDAK-KVIK produces state-of-the-art polygenic scores.

Scientific Applications:

• Genome-Wide Association Studies: LDAK-KVIK detects trait-associated loci with robust control of type 1 error and increased statistical power compared to classical linear regression, BOLT-LMM, and REGENIE.
• Quantitative Phenotype Analysis: LDAK-KVIK analyzes quantitative phenotypes, finding 16% more independent, genome-wide significant loci than classical linear regression across 40 quantitative UK Biobank phenotypes.
• Binary Phenotype Analysis: LDAK-KVIK analyzes binary phenotypes using mixed-model association analysis.
• Gene-Based Association Testing: LDAK-KVIK performs gene-based tests to identify significant genes associated with traits.

Methodology:

LDAK-KVIK uses mixed-model association analysis with computational optimizations that reduce runtime and memory requirements while maintaining statistical power.