WALTERS GROUP DATA REPOSITORY
Principal Investigator: James T. R. Walters
Part of the Psychosis and Major Affective Disorders Research Theme and the Psychiatric Genomics Consortium.
DISCLAIMER
These data are provided "as is", and without warranty, for scientific and educational use only. If you download these data, you acknowledge that these data will be used only for non-commercial research purposes; that the investigator is in compliance with all applicable state, local, and federal laws or regulations and institutional policies regarding human subjects and genetics research; that secondary distribution of the data without registration by secondary parties is prohibited; and that the investigator will cite the appropriate publication in any communications or publications arising directly or indirectly from these data. You also acknowledge that yourself or any member of your research team will never attempt to identify any participant in these studies.
"Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia" (2017)
Publication.Neutropenia
GWAS summary statistics: Download
[MD5
checksum]
Neutropenia ExomeChip
summary statistics: Download
[MD5
checksum]
Neutropenia
HLA summary statistics: Download
[MD5
checksum]
Severe
Neutropenia GWAS summary statistics: Download
[MD5
checksum]
Severe Neutropenia
ExomeChip summary statistics: Download
[MD5
checksum]
Severe
Neutropenia HLA summary statistics: Download
[MD5
checksum]
Description:
Summary
statistics files in various formats (maximum N=5649), please see
header lines (commented with hashes #) for data and column
descriptions.
Citation:
Legge SE, Hamshere ML, Ripke S, Pardiñas AF, Goldstein JI, Rees E,
et al. Genome-wide common and rare variant analysis provides novel
insights into clozapine-associated neutropenia. Mol Psychiatry.
2017. doi: 10.1038/mp.2016.97.
"Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection" (2018)
Publication.CLOZUK+PGC2
meta-analysis summary statistics: Download
[MD5 checksum]
CLOZUK+PGC2
meta-analysis high-quality imputed SNP list: Download
[MD5
checksum]
Description:
Meta-analysis
of schizophrenia GWAS data from samples of European ancestry
(N=105318; 40675 cases and 64643 controls)
SNP:
SNP name in IMPUTE2
format.
Freq.A1: Frequency of effect allele in 1000
Genomes EUR
super-population.
CHR: Chromosome code.
BP: Base-pair position.
A1: Effect allele.
A2: Non-effect allele.
OR: Odds ratio.
SE: Standard error of the regression beta
(log OR).
P: P-value.
Companion
file supplies SNP names of high-quality imputed (INFO > 0.9)
markers, in LD-Score --merge-alleles
format.
Citation:
Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S,
Carrera N, et al. Common schizophrenia alleles are enriched in
mutation-intolerant genes and in regions under strong background
selection. Nat Genet. 2018. doi: 10.1038/s41588-018-0059-2.
Update
31/05/2018: Corrected OR of X-chromosome SNP rs5937157, which was
shown as a regression beta. Thanks to Lucy Riglin for
reporting this error.
"A genome-wide association study in individuals of African ancestry reveals the importance of the Duffy-null genotype in the assessment of clozapine-related neutropenia" (2019)
Publication.CLOZUK2-AFR
lowest absolute neutrophil count GWAS summary statistics: Download
[MD5
checksum]
Description:
GWAS
of lowest absolute neutrophil count during clozapine treatment in
individuals of African ancestry (N=552)
Chr:
Chromosome code.
SNP:
SNP name in HRC
format.
bp:
Base-pair position.
A1:
Effect allele.
A2: Non-effect allele.
Freq: Frequency of effect allele.
b:
Linear mixed model regression statistic.
se: Standard error of the regression beta.
p: P-value.
Citation:
Legge SE, Pardiñas
AF, Helthuis M, Jansen JA, Jollie K, Knapper S, et al. A
genome-wide association study in individuals of African ancestry
reveals the importance of the Duffy-null genotype in the assessment of
clozapine-related neutropenia. Mol Psych. 2019. doi:
10.1038/s41380-018-0335-7.
"Pharmacogenomic variants and drug interactions identified through the genetic analysis of clozapine metabolism" (2019)
Publication.CLOZUK2-EUR
clozapine plasma concentrations GWAS summary statistics: Download
[MD5
checksum]
CLOZUK2-EUR
norclozapine plasma concentrations GWAS summary statistics: Download
[MD5
checksum]
CLOZUK2-EUR
clozapine/norclozapine metabolic ratio GWAS summary statistics:
Download
[MD5
checksum]
Description:
GWAS
of plasma concentrations of clozapine metabolites in individuals of
European ancestry (N=2989)
Chr:
Chromosome code.
SNP:
SNP name in HRC
format.
bp:
Base-pair position.
A1:
Effect allele.
A2: Non-effect allele.
Freq: Frequency of effect allele.
b:
Linear mixed model regression statistic.
se: Standard error of the regression beta.
p: P-value.
Citation:
Pardiñas AF, Nalmpanti M, Pocklington AJ, Legge SE, Medway C, King A,
et al. Pharmacogenomic Variants and Drug Interactions Identified
Through the Genetic Analysis of Clozapine Metabolism. Am J
Psychiatry. 2019. doi: 10.1176/appi.ajp.2019.18050589.
UK
Biobank "any psychotic experience" GWAS summary statistics: Download
[MD5
checksum]
UK Biobank "multiple
psychotic experiences" GWAS summary statistics:
Download
[MD5
checksum]
UK Biobank "distressing
psychotic experiences" GWAS summary statistics:
Download
[MD5
checksum]
Description:
GWAS
of psychotic experiences reported by adults in a population-based
study of European ancestry (N=127966; 6123 cases and 121843
controls; see manuscript for details)
CHR: Chromosome code.
SNP: SNP name in UK
Biobank format.
BP: Base-pair position.
A1: Effect allele.
A2: Non-effect allele.
FRQ_A: Frequency of A1 in cases.
FRQ_U: Frequency of A1 in comparator group
("controls").
INFO: Imputation quality score.
OR: Odds ratio.
SE: Standard error of the regression beta
(log OR).
P: P-value.
Citation:
Legge SE, Jones HJ, Kendall KK, Pardiñas AF, Menzies G, Bracher-Smith M, et al. Genetic
association study of psychotic experiences in UK Biobank. JAMA
Psychiatry. 2019. doi: 10.1001/jamapsychiatry.2019.2508.
"Web-Based Cognitive Testing in Psychiatric Research: Validation and Usability Study" (2022)
Publication.Cognitive
and clinical dataset: Download
[MD5 checksum]
Data dictionary:
Download
[MD5
checksum]
Description:
Citation: Lynham AJ,
Jones IR, Walters, JT. Web-Based Cognitive Testing in Psychiatric
Research: Validation and Usability Study. Journal of Medical
Internet Research. 2022. doi: 10.2196/28233. Cognitive
and limited clinical data on the participants recruited online
as part of the Cognition in Mood, Psychosis and Schizophrenia
Study (CoMPaSS Web, N=1227).
Please
note, some information has been stripped or grouped to prevent
identification of participants.
Companion
file provides full variable descriptions and codings.
"Interaction testing and polygenic risk scoring to estimate the contribution of common genetic variants to treatment resistance in schizophrenia" (2022)
Publication.TRS
"interaction test" summary statistics: Download
[MD5 checksum]
Description:
Citation: Pardiñas AF,
Smart SE, Willcocks IR, Holmans PA, Dennison CA, Lynham AJ, et al.
Interaction testing and polygenic risk scoring to estimate the
contribution of common genetic variants to treatment resistance in
schizophrenia. JAMA
Psychiatry. 2022. doi: 10.1001/jamapsychiatry.2021.3799.
Interaction
analysis of a TRS GWAS (N=35043; 10501 cases and 24542 controls)
against a non-TRS GWAS (N=50447; 20325 cases and 30122
controls). See manuscript for details.
SNP:
SNP name in dbSNP
142 format.
CHR:
Chromosome code (the notation "23" is used for the
X-chromosome).
BP:
Base-pair position.
A1:
Effect allele.
A2: Non-effect allele.
N:
Total sample size (cases+controls) across both GWAS.
MAF: Weighted average minor allele
frequency across both GWAS.
OR:
Interaction odds-ratio (see Altman
& Bland 2003).
SE: Interaction standard error (see Altman
& Bland 2003).
Z:
Interaction Z-score.
P: Interaction P-value.
"Genetic Liabilities Differentiating Bipolar Disorder, Schizophrenia, and Major Depressive Disorder, and Phenotypic Heterogeneity in Bipolar Disorder" (2022)
Publication.Summary
statistics for SZ/BD/MDD shared component: Download
[MD5
checksum]
Summary
statistics for SZ differentiating component: Download
[MD5
checksum]
Summary
statistics for BD differentiating component: Download
[MD5
checksum]
Summary
statistics for MDD differentiating component: Download
[MD5
checksum]
Description:
Citation: Richards
AL, Cardno A, Harold G, Craddock NJ, DiFlorio A, Jones L, et al.
Genetic Liabilities Differentiating Bipolar Disorder,
Schizophrenia, and Major Depressive Disorder, and Phenotypic
Heterogeneity in Bipolar Disorder. JAMA
Psychiatry. 2022. doi: 10.1001/jamapsychiatry.2022.2594.Genomic
SEM (gSEM) summary statistics from a common factor analysis
model of schizophrenia (SZ; N=130644), bipolar disorder (BD;
N=398495) and major depressive disorder (MDD; N=173005). See
manuscript for details.
SNP:
SNP name.
CHR:
Chromosome code.
BP:
Base-pair position.
MAF:
Minor allele frequency.
A1:
Effect allele.
A2: Non-effect allele.
est:
gSEM effect size.
SE: Standard error.
Z_estimate:
Z-score.
P: P-value.
"Pharmacokinetics and pharmacogenomics of clozapine in an ancestrally diverse sample: a longitudinal analysis and genome-wide association study using UK clinical monitoring data" (2023)
Publication.CLOZUK2+3
clozapine plasma concentrations GWAS summary statistics: Download
[MD5
checksum]
CLOZUK2+3 norclozapine
plasma concentrations GWAS summary statistics:
Download
[MD5
checksum]
CLOZUK2+3 clozapine/norclozapine
metabolic ratio GWAS summary statistics:
Download [MD5 checksum]
Description:
GWAS
of plasma concentrations of clozapine metabolites (N=4495;
longitudinal cross-ancestry analysis; see manuscript for
details)
chr: Chromosome code.
pos: Base-pair position.
A1: Effect allele.
A2: Non-effect allele.
Freq:
Frequency of effect allele.
b:
TrajGWAS
regression statistic.
se: Standard error of the regression
beta.
p: P-value.
. Citation:
Pardiñas
AF, Kappel DB, Roberts M, Tipple F, Shitomi-Jones LM, King A, et al. Pharmacokinetics and
pharmacogenomics of clozapine in an ancestrally diverse sample:
a longitudinal analysis and genome-wide association study using
UK clinical monitoring data. Lancet Psychiatry. 2023.
doi: 10.1016/S2215-0366(23)00002-0.
