RAISS: robust and accurate imputation from summary statistics

H Julienne, H Shi, B Pasaniuc, H Aschard - Bioinformatics, 2019 - academic.oup.com
… high accuracy imputation from summary statistics. We demonstrate this accuracy for variants
of all effect sizes on real data … Filtering imputed SNPs by their R 2 improves only slightly the …

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

… 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 …

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 …

Improved polygenic prediction by Bayesian multiple regression on summary statistics

LR Lloyd-Jones, J Zeng, J Sidorenko, L Yengo… - Nature …, 2019 - nature.com
… We establish that SBayesR improves prediction accuracy … as well as minimal imputation error
and data-processing errors … 2\) enrichment 38,57 or understanding genetic architecture via …

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

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 …

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 …