… a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts

D Lee, SA Bacanu - Bioinformatics, 2024 - academic.oup.com
… This panel enhances the range and accuracy of imputable variants, including the ability
to impute summary statistics of rarer variants. As a result, GAUSS elevates the quality and …

Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation

T Wang, Y Liu, Q Yin, J Geng, J Chen… - Briefings in …, 2022 - academic.oup.com
impute summary statistics from a single-cell RNA-sequencing-based eQTL study with six
major cell types. We detect a large amount of novel significant eQTL associations (an increase

Adjusting for genetic confounders in transcriptome-wide association studies improves discovery of risk genes of complex traits

S Zhao, W Crouse, S Qian, K Luo, M Stephens, X He - Nature Genetics, 2024 - nature.com
… We found that the gene effect enrichment was still accurately estimated, … summary data to
include gene information. Specifically, we compute the marginal association of each imputed

Estimating colocalization probability from limited summary statistics

EA King, F Dunbar, JW Davis, JF Degner - BMC bioinformatics, 2021 - Springer
… is enriched for regions where there is evidence of multiple causal variants in the GWAS trait.
When multiple causal variants are present, imputed summary statistics … these could increase

Fine-mapping from summary data with the “Sum of Single Effects” model

Y Zou, P Carbonetto, G Wang, M Stephens - PLoS Genetics, 2022 - journals.plos.org
improves model fits in some data sets, and hence improvesfunction known as the “evidence
lower bound” (ELBO). … SNPs from the exact same samples, using genotype imputation if …

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

Z Zheng, S Liu, J Sidorenko, L Yengo, P Turley, A Ani… - bioRxiv, 2022 - biorxiv.org
… , that integrates GWAS summary statistics with functional genomic … c) Improvement in prediction
accuracy increases with the … annotations based on their per-SNP heritability enrichment

Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries

Z Zheng, S Liu, J Sidorenko, Y Wang, T Lin, L Yengo… - Nature Genetics, 2024 - nature.com
summary statistics by collapsing information from SNPs in high LD, leading to significantly
improved computational efficiency and enhanced … per-SNP heritability enrichment, averaged …

The power of TOPMed imputation for the discovery of Latino-enriched rare variants associated with type 2 diabetes

A Huerta-Chagoya, P Schroeder, R Mandla… - Diabetologia, 2023 - Springer
… To evaluate the ability of TOPMed imputation to increase the … blue box) and for functional
evidence in multiple available resources (… by integrating GWAS summary statistics from multiple …

Genome-wide heritability analysis of severe malaria resistance reveals evidence of polygenic inheritance

D Damena, ER Chimusa - Human molecular genetics, 2020 - academic.oup.com
… In this study, we estimated the h 2 g and functional enrichment of malaria resistance in three
… the summary statistics to LDSC format, filtered SNPs with imputation accuracy greater than …

[PDF][PDF] A powerful subset-based method identifies gene set associations and improves interpretation in UK Biobank

D Dutta, P VandeHaar, LG Fritsche, S Zöllner… - The American Journal of …, 2021 - cell.com
… We applied GAUSS to UK Biobank GWAS summary statistics … There was no significant
enrichment in the proportion of … for the imputation of association summary statistics in the …