We calculated LD scores (LD Score (LDSC) version 1.0.0) as previously described using the European 1000 Genomes reference panel (phase 3 version 5a) with a minor allele frequency cutoff for SNP inclusion greater than 5%. GWAS summary statistics data was collected from the following resources: Psychiatric Genomics Consortium (MDD, Bipolar Disorder, SCZ1, SCZ1+SWE, SCZ2), the International Genomics of Alzheimer’s Project (IGAP AD), the International Parkinson Disease Genomics Consortium (IPDGC PD), and the Global Lipids Genetics Consortium (GLGC LDL). GWAS data was harmonized using the munge_sumstats.py function, (using the SNP list derived from LD score calculation) and genomic inflation control intercepts were calculated for the 23andMe MDD data, PGC MDD data, and PGC+23andMe meta-analysis data using the ldsc.py function (using all default settings and options). Additionally, we calculated liability heritability estimates for the meta-analysis using the same function, with a population prevalence estimation of 15%, and 25% as previously described13 (link). Finally, we calculated the cross-trait regression between 23andMe MDD GWAS and the PGC datasets, the IGAP data, the IPDGC data, and the GLGC data.
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Genome-wide LD Score Regression Analysis
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Corresponding Organization : Massachusetts General Hospital
Other organizations : Pfizer (United States), 23andMe (United States)
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Variable analysis
independent variables
- LD Score (LDSC) version 1.0.0 using the European 1000 Genomes reference panel (phase 3 version 5a) with a minor allele frequency cutoff for SNP inclusion greater than 5%
- GWAS summary statistics data collected from the following resources: Psychiatric Genomics Consortium (MDD, Bipolar Disorder, SCZ1, SCZ1+SWE, SCZ2), the International Genomics of Alzheimer's Project (IGAP AD), the International Parkinson Disease Genomics Consortium (IPDGC PD), and the Global Lipids Genetics Consortium (GLGC LDL)
- Genomic inflation control intercepts calculated for the 23andMe MDD data, PGC MDD data, and PGC+23andMe meta-analysis data
- Liability heritability estimates for the meta-analysis
- Cross-trait regression between 23andMe MDD GWAS and the PGC datasets, the IGAP data, the IPDGC data, and the GLGC data
- Minor allele frequency cutoff for SNP inclusion greater than 5%
- Population prevalence estimation of 15% and 25% for liability heritability estimates
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