Enrichment Analyses using the Linkage Disequilibrium Score Regression (LDSC)

We employed the LD score regression method as a fundamental tool in our analysis. This method serves a dual purpose, enabling us to calculate both partitioned heritability and conduct enrichment analysis for Genome-Wide Association Studies (GWAS).

Partitioned Heritability: LD score regression allows us to estimate the heritability of a complex trait that is attributable to specific genomic regions or functional categories.

Enrichment Analysis: : In addition to heritability estimation, LD score regression enables us to perform enrichment analysis for GWAS. This involves assessing whether certain categories of genetic variants or functional elements are overrepresented among the variants associated with the trait of interest.

Here is an example analysis link demonstrating how the pipeline works after the user inputs a gene set and summary statistics: LDscore!

Upload Gene List. Please see examples of input datasets: Format #1! , Format #2! and Format #3!

Upload summary statistic. See Example!

* Both the summary statistics and gene list are currently based on build 37. We are in the process of updating it to allow for build 38.

Here are the guideline steps on how to use this site:

1. When you upload your gene list and summary statistics, a Job ID will be generated. Please save this ID and use it in the following link: Job_Search

2.Enter your Job ID to view your results.

References

Huggett, Spencer B., Emma C. Johnson, Alexander S. Hatoum, Dongbing Lai, Jenani Srijeyanthan, Jason A. Bubier, Elissa J. Chesler et al. "Genes identified in rodent studies of alcohol intake are enriched for heritabili> of human substance use." Alcoholism: Clinical and Experimental Research 45, no. 12 (2021): 2485-2494.

Palmer, Rohan HC, Chelsie E. Benca-Bachman, Spencer B. Huggett, Jason A. Bubier, John E. McGeary, Nikhil Ramgiri, Jenani Srijeyanthan et al. "Multi-omic and multi-species meta-analyses of nicotine consumption." Translational psychiatry 11, no. 1 (2021): 98.

Benca-Bachman, Chelsie E., Jason Bubier, Rameez A. Syed, Pamela N. Romero Villela, and Rohan HC Palmer. "Polygenic influences on the behavioral effects of alcohol withdrawal in a mixed-ancestry population from the collaborative study on the genetics of alcoholism (COGA)." Molecular and Cellular Neuroscience 125 (2023): 103851.

BGA Lab

About | Q: rasyed2@emory.edu

1.Which build are the summary statistics and gene list based on?

Both the summary statistics and gene list are currently based on build 37. We are in the process of updating to build 38.

2. Is the summary statistic based on the human or mouse genome?

The gene list is based on the mouse genome, while the summary statistics are based on the human genome.

3. How many megabytes can I upload?

You can upload files up to 100 megabytes in size.