Genome-wide Complex Trait Analysis (GCTA): Methods, Data Analyses, and Interpretations

Estimating genetic variance is traditionally performed using pedigree analysis. Using high-throughput DNA marker data measured across the entire genome it is now possible to estimate and partition genetic variation from population samples. In this chapter, we introduce methods and a software tool called Genome-wide Complex Trait Analysis (GCTA) to estimate genomic relationships between pairs of conventionally unrelated individuals using genome-wide single nucleotide polymorphism (SNP) data, to estimate variance explained by all SNPs simultaneously on genomic or chromosomal segments or over the whole genome, and to perform a joint and conditional multiple SNPs association analysis using summary statistics from a meta-analysis of genome-wide association studies and linkage disequilibrium between SNPs estimated from a reference sample.