RESOURCES

UK-Biobank Single Variant Association Analysis Results

1. Binary phenome analysis

Using SAIGE, we have analyzed ~1,400 UKBiobank Phecode binary phenotypes (400,000 White British samples) on 28 million imputed variants. All analysis summary statistics are available from the following link. 

• Phenotype information table (Excel file): link

• Pheweb: link

• Summary statistics

  • ftp://share.sph.umich.edu/UKBB_SAIGE_HRC/

Note: we have moved summary statistics from Dropbox to FTP site. 

Acknowledgement: The analysis was done with collaboration with Dr. Willer and Dr. Abecasis groups. The Pheweb was created by Dr. Abecasis

group.

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2. Categorical phenotype analysis

POLMM (Proportional Odds Logistic Mixed Model) approaches are designed for ordinal categorical data analysis in large cohort studies. For UK Biobank data analysis (on 258 ordinal categorical phenotypes including 150 food and other preferences), we use a sparse GRM to adjust for sample relatedness.

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• Pheweb: link

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UK-Biobank Gene-Based

Rare Variant Association Results 

​​1. UK-Biobank Imputed data analysis

Using SAIGE-GENE, we have carried out gene-based rare variant test (MAF < 0.01) for 53 UKBiobank quantitative phenotypes (400,000 White British samples). Missense and stop-gain variants were used in the analysis. The association test p-value are available from the following link.

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• Summary statistics

  • ftp://share.sph.umich.edu/UKBB_SAIGE_GENE_HRC 

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2. UK-Biobank 50K WES, Binary Phenome Analysis

Using robust SKAT-O approach for binary phenotypes, we analyzed UK-Biobank WES data for 791 binary phenotypes. 

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• PheWEB-like visual server for summary statistics

  • http://ukb-50kexome.leelabsg.org/

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UK-Biobank GxE analysis for 80 Phenotype x Environment combinations

UK-Biobank Gene-Set analysis

Using SPAGE, we have carried out GxE analysis for 80 selected phenotype x environment combinations. The association test p-value are available from the following link.

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• Summary statistics

  • ftp://share.sph.umich.edu/UKBB_SPAGE_HRC 

Using Gauss, we carried out gene-set association analysis using UK-Biobank SAIGE results

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• PheWEB-like visual server for summary statistics

  • http://ukb-pathway.leelabsg.org/

UK-Biobank Survival Analysis for 13 Phenotypes

Using SPACox, we have carried out GWAS survival analysis for 13 selected phenotypes. The association test p-value are available from the following link.

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• Summary statistics

  • ftp://share.sph.umich.edu/UKBB_SPACox_HRC/