Prostate Cancer TWAS in OncoArray GWAS Meta-analysis

The repository contains the main results for the transcriptome-wide association study (TWAS) reported in

Large-scale transcriptome-wide association study identifies new prostate cancer risk regions, Nicholas Mancuso, Simon Gayther, Alexander Gusev, Wei Zheng, Kathryn L. Penney, the PRACTICAL consortium, CRUK, BPC3, CAPS, PEGASUS, Zsofia Kote-Jarai, Rosalind Eeles, Matthew Freedman, Christopher Haiman, Bogdan Pasaniuc. Nature Communications doi: 10.1038/s41467-018-06302-1

Results

ONCOARRAY.TWAS.txt contains the main TWAS association statistics.

Column	Description
S.NAME	Short description of the gene expression reference panel
G.ID	Canonical gene name
ID	Canonical gene name (for total expression) or exon/exon junction (for splice variant)
CHR	Chromosome
P0	Transcription start site
P1	Transcription end site
HSQ	SNP-hertiability explained by cis-SNPs in reference panel
BEST.GWAS.ID	SNP ID of the best GWAS SNP in the prediction model (i.e. smallest p-value)
BEST.GWAS.Z	Z-score of the best GWAS SNP
EQTL.ID	SNP ID of the best cis-eQTL SNP in the reference panel
EQTL.R2	Variance-explained in measured gene expression by best cis-eQTL SNP
EQTL.Z	Z-score of the best cis-eQTL SNP
EQTL.GWAS.Z	GWAS Z-score of the best cis-eQTL SNP
NSNP	Number of SNPs in the model
NWGT	Number of SNPs with non-zero weights in the model
MODEL	Model with the best prediction accuracy
MODELCV.R2	Adjusted estimate of variance-explained in measured gene expression using 5-fold CV
MODELCV.PV	P-value of cross-validation R2 estimate
TWAS.Z	Z-score for TWAS test of association
TWAS.P	P-value for TWAS test
PERM.PV	Permutation test P-value for TWAS
PERM.N	Number of permutations performed
PERM.ANL_PV	Analytic P-value determined by re-adjusting Z-score by stdev estimate from permutations

ONCOARRAY.FINEMAP.txt contains the secondary gene-based fine-mapping analysis over TWAS associations.

Column	Description
S.NAME	Short description of the gene expression reference panel
G.ID	Canonical gene name
ID	Canonical gene name (for total expression) or exon/exon junction (for splice variant)
CHR	Chromosome
P0	Transcription start site
P1	Transcription end site
BLOCK	Identifier for a risk region
TWAS.Z	Z-score for TWAS test of association
BF	Bayes-Factor of association
PIP	Marginal posterior probability for explaining observed association signal at BLOCK

Software and support

For performing TWAS using summary-data, computing expression weights using custom expression panels, and additional post-TWAS analyses please see FUSION. See also TWAS hub for interactively exploring hundreds of large-scale TWAS results.

If you have any questions or comments please contact nmancuso@mednet.ucla.edu