UKBiobank depression GWAS summary stats

2020-03-26T08:52:09Z (GMT) by Na Cai
This folder contains the summary statistics of GWAS performed on different definitions of depression in UKBiobank described in Cai N., et al. Minimal phenotyping yields genome-wide association signals of low specificity for major depression. Nature Genetics (2020) doi:10.1038/s41588-020-0594-5.

The phenotypes are described briefly below. For more details please see description in the paper and its supplemental methods. All phenotypes are case-control phenotypes (coded cases = 1, controls = 0), defined using criteria as described. Cases are those who have answered the relevant questions in UKBiobank and fulfil case criteria, controls are those who have answered the same questions but did not fulfil the case criteria.

Please note there are overlaps between cases and controls between phenotypes, these are described in the paper and its supplemental methods.

1. LifetimeMDD - Lifetime MDD derived with DSM-V symptom and impairment criteria using the PHQ-9 questionnaire in the Online Mental Health follow-up in UKBiobank

2. MDDRecur - Lifetime MDD with recurrence derived with DSM-V symptom and impairment criteria using the PHQ-9 questionnaire in the Online Mental Health follow-up in UKBiobank, with additional criteria on recurrence

3. GPpsy - Having gone to a General Practitioner (GP) for nerves, anxiety, tension or depression, answered in the touchscreen interview in UKBiobank. Please note this is the most similar phenotype to "Broad Depression" introduced in Howard et al 2018 Nature Communications (doi:10.1038/s41467-018-03819-3)

4. Psypsy - Having gone to a psychiatrist for nerves, anxiety, tension or depression, answered in the touchscreen interview in UKBiobank

5. DepAll - Having either of the two cardinal symptoms for MDD (low mood or anhedonia) for more than two weeks in addition to having gone to either the GP or psychiatrist for nerves, anxiety, tension or depression, answered in the touchscreen interview in UKBiobank. Please note phenotype is first introduced as "Probable Depression" in Smith et al 2013 PloS One (doi:10.1371/journal.pone.0075362.s001), and the most similar phenotype to "Probable Depression" introduced in Howard et al 2018 Nature Communications (doi:10.1038/s41467-018-03819-3)

6. GPNoDep - Having gone to the GP for nerves, anxiety, tension or depression, but did not report having cardinal symptoms of MDD in the touchscreen interview in UKBiobank.

7. SelfRepDep - Self-reported depression or depression symptoms described to a trained nurse during verbal interview of medical conditions, classified under "Non-cancer illness" in the UKBiobank dataset.

8. ICD10Dep - Electronic health record indicating ICD-10 primary and secondary codes for depression in ICD-10 information linked to participants in UKBiobank

GWAS on each of the phenotypes was performed with logistic regression in PLINK, with PCs 1-20 and genotyping array as covariates. Columns of the summary statistics files *.covararraypcs.assoc.logistic are:

CHR: Chromosome
SNP: SNP rsid
BP: SNP position in basepairs along the chromosome indicated
A1: Effect allele (also minor allele)
TEST: Test performed (output from PLINK)
NMISS: Number of samples with non-missing values for both SNP genotype and phenotype tested
OR: Odd ratio
SE: Standard error of OR
L95: Lower bound of 95% confidence interval for OR
U95: Upper bound of 95% confidence interval for OR
STAT: T-statistic
P: P value for T-statistic
A0: Other allele (also major allele)
A1FREQ: Effect/minor allele frequency

The *.hits files contain the statistics at all SNPs with P values below 5 x 10^-8

The *.manhattan.jpeg files contain the manhattan plots, and *.qqplot.jpeg files contain the QQ-plots for the GWAS.

Please refer carefully to the methods and supplementary methods of the paper for more detailed information when using these summary statistics.