Trait selection strategy in multi-trait GWAS: Boosting SNP discoverability.

Since the first genome-wide association studies (GWASs), thousands of variant-trait associations have been discovered. However, comprehensively mapping the genetic determinant of complex traits through univariate testing can require prohibitive sample sizes. Multi-trait GWAS can circumvent this issue and improve statistical power by leveraging the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been solved, the strategy to select traits has been overlooked. In this study, we conducted multi-trait GWAS on approximately 20,000 combinations of 72 traits using an omnibus test as implemented in the Joint Analysis of Summary Statistics. We assessed which genetic features of the sets of traits analyzed were associated with an increased detection of variants compared with univariate screening. Several features of the set of traits, including the heritability, the number of traits, and the genetic correlation, drive the multi-trait test gain. Using these features jointly in predictive models captures a large fraction of the power gain of the multi-trait test (Pearson's r between the observed and predicted gain equals 0.43, p < 1.6 × 10-60). Applying an alternative multi-trait approach (Multi-Trait Analysis of GWAS), we identified similar features of interest, but with an overall 70% lower number of new associations. Finally, selecting sets based on our data-driven models systematically outperformed the common strategy of selecting clinically similar traits. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outlines practical strategies for multi-trait testing.

Multi-trait GWAS for diverse ancestries: mapping the knowledge gap.

BACKGROUND: Approximately 95% of samples analyzed in univariate genome-wide association studies (GWAS) are of European ancestry. This bias toward European ancestry populations in association screening also exists for other analyses and methods that are often developed and tested on European ancestry only. However, existing data in non-European populations, which are often of modest sample size, could benefit from innovative approaches as recently illustrated in the context of polygenic risk scores. METHODS: Here, we extend and assess the potential limitations and gains of our multi-trait GWAS pipeline, JASS (Joint Analysis of Summary Statistics), for the analysis of non-European ancestries. To this end, we conducted the joint GWAS of 19 hematological traits and glycemic traits across five ancestries (European (EUR), admixed American (AMR), African (AFR), East Asian (EAS), and South-East Asian (SAS)). RESULTS: We detected 367 new genome-wide significant associations in non-European populations (15 in Admixed American (AMR), 72 in African (AFR) and 280 in East Asian (EAS)). New associations detected represent 5%, 17% and 13% of associations in the AFR, AMR and EAS populations, respectively. Overall, multi-trait testing increases the replication of European associated loci in non-European ancestry by 15%. Pleiotropic effects were highly similar at significant loci across ancestries (e.g. the mean correlation between multi-trait genetic effects of EUR and EAS ancestries was 0.88). For hematological traits, strong discrepancies in multi-trait genetic effects are tied to known evolutionary divergences: the ARKC1 loci, which is adaptive to overcome p.vivax induced malaria. CONCLUSIONS: Multi-trait GWAS can be a valuable tool to narrow the genetic knowledge gap between European and non-European populations.

Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability.

Since the first Genome-Wide Association Studies (GWAS), thousands of variant-trait associations have been discovered. However, the sample size required to detect additional variants using standard univariate association screening is increasingly prohibitive. Multi-trait GWAS offers a relevant alternative: it can improve statistical power and lead to new insights about gene function and the joint genetic architecture of human phenotypes. Although many methodological hurdles of multi-trait testing have been discussed, the strategy to select trait, among overwhelming possibilities, has been overlooked. In this study, we conducted extensive multi-trait tests using JASS (Joint Analysis of Summary Statistics) and assessed which genetic features of the analysed sets were associated with an increased detection of variants as compared to univariate screening. Our analyses identified multiple factors associated with the gain in the association detection in multi-trait tests. Together, these factors of the analysed sets are predictive of the gain of the multi-trait test (Pearson's ρ equal to 0.43 between the observed and predicted gain, P < 1.6 × 10-60). Applying an alternative multi-trait approach (MTAG, multi-trait analysis of GWAS), we found that in most scenarios but particularly those with larger numbers of traits, JASS outperformed MTAG. Finally, we benchmark several strategies to select set of traits including the prevalent strategy of selecting clinically similar traits, which systematically underperformed selecting clinically heterogenous traits or selecting sets that issued from our data-driven models. This work provides a unique picture of the determinant of multi-trait GWAS statistical power and outline practical strategies for multi-trait testing.