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SH3GL2 variants and the risk for Parkinson’s disease in diverse ancestry populations

GP2 ❤️ Open Science 😍

Last Updated: November 2023

Summary

This is the online repository for the manuscript titled "SH3GL2 variants and the risk for Parkinson’s disease in diverse ancestry populations". This study focuses on exploring the role of SH3GL2 in existing PD/control datasets from the AMP-PD and GP2 initiatives.

Data Statement

All data was using release 5 GP2 data (access-controlled via single-sign on amp-pd.org).

Helpful Links

Analysis Notebooks

  • Languages: Python, bash, and R
Notebooks Description
SH3GL2_AMP_PD SH3GL2 variants screening in AMP-PD data v3.0 - European ancestry
SH3GL2_GP2_AAC SH3GL2 variants screening in GP2 data (release 5) - African admixed ancestry
SH3GL2_GP2_AFR SH3GL2 variants screening in GP2 data (release 5) - African ancestry
SH3GL2_GP2_AJ SH3GL2 variants screening in GP2 data (release 5) - Ashkenazi Jewish ancestry
SH3GL2_GP2_AMR SH3GL2 variants screening in GP2 data (release 5) - Amerindian ancestry
SH3GL2_GP2_CAS SH3GL2 variants screening in GP2 data (release 5) - Central Asian ancestry
SH3GL2_GP2_EAS SH3GL2 variants screening in GP2 data (release 5) - East Asian ancestry
SH3GL2_GP2_EUR SH3GL2 variants screening in GP2 data (release 5) - European ancestry
SH3GL2_GP2_FIN SH3GL2 variants screening in GP2 data (release 5) - Finnish ancestry
SH3GL2_GP2_MDE SH3GL2 variants screening in GP2 data (release 5) - Middle Eastern ancestry
SH3GL2_GP2_SAS SH3GL2 variants screening in GP2 data (release 5) - South Asian ancestry

Tables and Supplemental Tables

(pending publication)

Software

Software Version(s) Resource URL RRID Notes
ANNOVAR 2020-06-08 http://www.openbioinformatics.org/annovar/ RRID:SCR_012821 refGene; avsnp150; ljb26_all; gnomad312_genome; used for annotation
PLINK 1.7 and 1.9 and 2.0 http://www.nitrc.org/projects/plink RRID:SCR_001757 used for genetic analyses
Python Programming Language 3.8 and 3.9 http://www.python.org/ RRID:SCR_008394 pandas; numpy; seaborn; matplotlib; statsmodel; used for general data wrangling/plotting/analyses
R Project for Statistical Computing 4.2 http://www.r-project.org/ RRID:SCR_001905 tidyverse; dplyr; tidyr; ggplot; data.table; used for general data wrangling/plotting/analyses

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