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Table of Contents
GSCAN–or the GWAS & Sequencing Consortium of Alcohol and Nicotine use–is an international genetic association meta-analysis consortium. Our goal is to aggregate genetic association findings across scores of studies with millions of individuals. GSCAN is composed of three independent but related projects: 1) an exome chip meta-analysis of low-frequency non-synonymous variants, 2) a GWAS meta-analysis, and 3) a whole genome sequencing association meta-analysis.
This wiki page is to help organize GSCAN efforts for the coordinating investigators. If you represent a study that may be interested in participating in GSCAN you can find more information on our more public website. Look on the right-hand side of the page to find analysis plans for each of the three projects.
Meetings
Regular conference calls are held and minutes are **available here**.
GSCAN Exome Chip
File Locations
Freeze 1. We concluded a pilot freeze of the exome chip project in 2015 and are writing up our results now. All of the summary statistics are on twins at /net/twins/svrieze/everything-else/wp/GSCAN/freeze1-25-Mar-2015.
Freeze 2. New studies that will be included in Freeze 2 are located on RC at /work/KellerLab/GSCAN/EXOME. Each folder in that directory is the name of a study and includes two subfolders, one for Phenotypes and one for Genotypes. Genotypes are split by chromosome to facilitate analyses.
GSCAN GWAS
Phenotype definitions and analysis plan
Coordination and organization
Progress, internal and external, are tracked in **this Google Doc**. More specific progress on internal studies is **tracked here**.
Study contact info is tracked in **this Google Sheet**.
Studies available in dbGaP, along with accession numbers, etc. are tracked in **this Airtable**.
File locations
Study data to which we have direct access are located either on twins or RC. Twins data are organized in the folder /net/twins/svrieze/everything-else/wp/GSCAN/GWAS. Within this folder those studies to which we have raw data access are in the folder CU_Boulder_samples (for lack of a better name!). Summary stats generated on these samples are organized within summary_stats_generated_internally. Summary stats generated by outside groups and submitted for meta-analysis are organized within summary_stats_generated_externally.
On RC the organization is similar. Everything is located within the folder /work/KellerLab/GSCAN/GWAS. Study data to which we have raw data access are in the folder individual_level_study_data. Summary stats generated on these samples are organized within summary_stats_generated_internally. Summary stats generated by outside groups and submitted for meta-analysis are organized within summary_stats_generated_externally.
GSCAN Sequencing
The list of dbGaP studies in TOPMed is in **this Airtable**.
