Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate
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Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate. / Andreassen, Ole A; Thompson, Wesley K; Schork, Andrew J; Ripke, Stephan; Mattingsdal, Morten; Kelsoe, John R; Kendler, Kenneth S; O'Donovan, Michael C; Rujescu, Dan; Werge, Thomas; Sklar, Pamela; Roddey, J Cooper; Chen, Chi-Hua; McEvoy, Linda; Desikan, Rahul S; Djurovic, Srdjan; Dale, Anders M; Psychiatric Genomics Consortium (PGC).
In: P L o S Genetics (Online), Vol. 9, No. 4, 04.2013, p. e1003455.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Improved detection of common variants associated with schizophrenia and bipolar disorder using pleiotropy-informed conditional false discovery rate
AU - Andreassen, Ole A
AU - Thompson, Wesley K
AU - Schork, Andrew J
AU - Ripke, Stephan
AU - Mattingsdal, Morten
AU - Kelsoe, John R
AU - Kendler, Kenneth S
AU - O'Donovan, Michael C
AU - Rujescu, Dan
AU - Werge, Thomas
AU - Sklar, Pamela
AU - Roddey, J Cooper
AU - Chen, Chi-Hua
AU - McEvoy, Linda
AU - Desikan, Rahul S
AU - Djurovic, Srdjan
AU - Dale, Anders M
AU - Psychiatric Genomics Consortium (PGC)
PY - 2013/4
Y1 - 2013/4
N2 - Several lines of evidence suggest that genome-wide association studies (GWAS) have the potential to explain more of the "missing heritability" of common complex phenotypes. However, reliable methods to identify a larger proportion of single nucleotide polymorphisms (SNPs) that impact disease risk are currently lacking. Here, we use a genetic pleiotropy-informed conditional false discovery rate (FDR) method on GWAS summary statistics data to identify new loci associated with schizophrenia (SCZ) and bipolar disorders (BD), two highly heritable disorders with significant missing heritability. Epidemiological and clinical evidence suggest similar disease characteristics and overlapping genes between SCZ and BD. Here, we computed conditional Q-Q curves of data from the Psychiatric Genome Consortium (SCZ; n = 9,379 cases and n = 7,736 controls; BD: n = 6,990 cases and n = 4,820 controls) to show enrichment of SNPs associated with SCZ as a function of association with BD and vice versa with a corresponding reduction in FDR. Applying the conditional FDR method, we identified 58 loci associated with SCZ and 35 loci associated with BD below the conditional FDR level of 0.05. Of these, 14 loci were associated with both SCZ and BD (conjunction FDR). Together, these findings show the feasibility of genetic pleiotropy-informed methods to improve gene discovery in SCZ and BD and indicate overlapping genetic mechanisms between these two disorders.
AB - Several lines of evidence suggest that genome-wide association studies (GWAS) have the potential to explain more of the "missing heritability" of common complex phenotypes. However, reliable methods to identify a larger proportion of single nucleotide polymorphisms (SNPs) that impact disease risk are currently lacking. Here, we use a genetic pleiotropy-informed conditional false discovery rate (FDR) method on GWAS summary statistics data to identify new loci associated with schizophrenia (SCZ) and bipolar disorders (BD), two highly heritable disorders with significant missing heritability. Epidemiological and clinical evidence suggest similar disease characteristics and overlapping genes between SCZ and BD. Here, we computed conditional Q-Q curves of data from the Psychiatric Genome Consortium (SCZ; n = 9,379 cases and n = 7,736 controls; BD: n = 6,990 cases and n = 4,820 controls) to show enrichment of SNPs associated with SCZ as a function of association with BD and vice versa with a corresponding reduction in FDR. Applying the conditional FDR method, we identified 58 loci associated with SCZ and 35 loci associated with BD below the conditional FDR level of 0.05. Of these, 14 loci were associated with both SCZ and BD (conjunction FDR). Together, these findings show the feasibility of genetic pleiotropy-informed methods to improve gene discovery in SCZ and BD and indicate overlapping genetic mechanisms between these two disorders.
U2 - 10.1371/journal.pgen.1003455
DO - 10.1371/journal.pgen.1003455
M3 - Journal article
C2 - 23637625
VL - 9
SP - e1003455
JO - P L o S Genetics
JF - P L o S Genetics
SN - 1553-7390
IS - 4
ER -
ID: 48609764