Feb 07, 2024

Public workspaceGWAS prioritization analysis

DOI
dx.doi.org/10.17504/protocols.io.q26g7pe61gwz/v1
  • 1University of Oxford
Peter Kilfeather
Open access
DOI: dx.doi.org/10.17504/protocols.io.q26g7pe61gwz/v1
Protocol Citation: Peter Kilfeather 2024. GWAS prioritization analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.q26g7pe61gwz/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 07, 2024
Last Modified: February 07, 2024
Protocol Integer ID: 94807
Funders Acknowledgement:
Aligning Science Across Parkinson's
Grant ID: ASAP-020370
Monument Trust Discovery Award from Parkinson’s UK
Grant ID: J-1403
Abstract
GWAS prioritization analysis from Kilfeather, Khoo et al., 2024
Protocol
Protocol
A list of 303 genes (sourced from Nalls et al., 2019 supplementary materials),  containing SNPs at an r2 > 0.5 and located within ±1 Mb of 107 common risk variants for sporadic PD was used for prioritization analysis. To convert between human and mouse gene symbols, homologene (v1.4.68.19.3.27, RRID:SCR_002924) and biomaRt (v2.52.0, RRID:SCR_019214) were used. TRAP enrichment (measured as the product of the log­2 fold-change and FDR-adjusted P value) and specificity indices for DAT-TRAP samples were used for gene prioritization, per lead SNP.