Abstract
Psychiatric disorders are highly genetically correlated, but little research has been conducted on the genetic differences between disorders. We developed a new method (case–case genome-wide association study; CC-GWAS) to test for differences in allele frequency between cases of two disorders using summary statistics from the respective case–control GWAS, transcending current methods that require individual-level data. Simulations and analytical computations confirm that CC-GWAS is well powered with effective control of type I error. We applied CC-GWAS to publicly available summary statistics for schizophrenia, bipolar disorder, major depressive disorder and five other psychiatric disorders. CC-GWAS identified 196 independent case–case loci, including 72 CC-GWAS-specific loci that were not significant at the genome-wide level in the input case–control summary statistics; two of the CC-GWAS-specific loci implicate the genes KLF6 and KLF16 (from the Krüppel-like family of transcription factors), which have been linked to neurite outgrowth and axon regeneration. CC-GWAS loci replicated convincingly in applications to datasets with independent replication data.
Original language | English |
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Pages (from-to) | 445-454 |
Number of pages | 10 |
Journal | Nature Genetics |
Volume | 53 |
Issue number | 4 |
Early online date | 8 Mar 2021 |
DOIs | |
Publication status | Published - 1 Apr 2021 |
Keywords
- Alleles
- Axons/metabolism
- Bipolar Disorder/genetics
- Case-Control Studies
- Datasets as Topic
- Depressive Disorder, Major/genetics
- Gene Expression
- Gene Frequency
- Genetic Loci
- Genetic Predisposition to Disease
- Genome-Wide Association Study
- Humans
- Kruppel-Like Factor 6/genetics
- Kruppel-Like Transcription Factors/genetics
- Neuronal Outgrowth/genetics
- Polymorphism, Single Nucleotide
- Schizophrenia/genetics