UKBiobank depression GWAS summary stats

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. <br>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. <br>Please note there are overlaps between cases and controls between phenotypes, these are described in the paper and its supplemental methods. <br>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<br>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 <br><br>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)<br>4. Psypsy - Having gone to a psychiatrist for nerves, anxiety, tension or depression, answered in the touchscreen interview in UKBiobank <br>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)<br>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. <br>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. <br>8. ICD10Dep - Electronic health record indicating ICD-10 primary and secondary codes for depression in ICD-10 information linked to participants in UKBiobank <br>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: <br>CHR: ChromosomeSNP: SNP rsid BP: SNP position in basepairs along the chromosome indicatedA1: 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 ratioSE: Standard error of ORL95: Lower bound of 95% confidence interval for ORU95: Upper bound of 95% confidence interval for ORSTAT: T-statisticP: P value for T-statisticA0: Other allele (also major allele) A1FREQ: Effect/minor allele frequency <br>The *.hits files contain the statistics at all SNPs with P values below 5 x 10^-8 <br>The *.manhattan.jpeg files contain the manhattan plots, and *.qqplot.jpeg files contain the QQ-plots for the GWAS. <br>Please refer carefully to the methods and supplementary methods of the paper for more detailed information when using these summary statistics.

本文件夹包含针对英国生物库（UK Biobank）中不同抑郁症表型定义开展的全基因组关联研究（GWAS, Genome-Wide Association Study）的汇总统计数据，相关研究由Cai N.等人完成，题为《Minimal phenotyping yields genome-wide association signals of low specificity for major depression》，发表于《自然-遗传学（Nature Genetics）》(2020)，DOI: 10.1038/s41588-020-0594-5。

下文将对各表型进行简要介绍，详细信息请参见论文及其补充方法。所有表型均为病例-对照表型（病例编码为1，对照编码为0），按照所述标准定义：病例为在英国生物库中回答了相关问题且符合病例判定标准的参与者，对照为回答了相同问题但未符合病例判定标准的参与者。

请注意不同表型的病例与对照之间存在重叠，相关细节已在论文及其补充方法中说明。

1. LifetimeMDD：基于英国生物库在线心理健康随访中通过PHQ-9问卷，结合DSM-V症状及功能损害标准定义的终身重性抑郁症（MDD, Major Depressive Disorder）
2. MDDRecur：在LifetimeMDD基础上增加复发判定标准，结合PHQ-9问卷与DSM-V症状、功能损害标准定义的复发性终身重性抑郁症
3. GPpsy：指在英国生物库触摸屏访谈中报告曾因神经症、焦虑、紧张或抑郁就诊于全科医生（GP, General Practitioner）的参与者。请注意该表型与Howard等人2018年发表于《自然-通讯（Nature Communications）》的“广泛性抑郁症（Broad Depression）”表型最为相似，DOI: 10.1038/s41467-018-03819-3
4. Psypsy：指在英国生物库触摸屏访谈中报告曾因神经症、焦虑、紧张或抑郁就诊于精神科医生的参与者
5. DepAll：指在英国生物库触摸屏访谈中报告同时满足以下两项条件的参与者：一是出现抑郁核心症状（情绪低落或快感缺失）时长超过两周，二是曾因神经症、焦虑、紧张或抑郁就诊于全科医生或精神科医生。请注意该表型最初由Smith等人2013年发表于《PLOS ONE（PloS One）》的研究中以“疑似抑郁症（Probable Depression）”为名提出，且与Howard等人2018年《自然-通讯（Nature Communications）》中提出的“疑似抑郁症”表型最为相似，DOI: 10.1371/journal.pone.0075362.s001
6. GPNoDep：指在英国生物库触摸屏访谈中报告曾因神经症、焦虑、紧张或抑郁就诊于全科医生，但未报告存在重性抑郁症核心症状的参与者
7. SelfRepDep：指在英国生物库参与者医疗状况口头访谈中向经过培训的护士自述患有抑郁症或存在抑郁症状，且在英国生物库数据集被归类为“非肿瘤性疾病”的参与者
8. ICD10Dep：指英国生物库参与者关联的电子健康记录中标注有ICD-10编码的原发性和继发性抑郁诊断的表型

针对上述每个表型，研究团队均使用PLINK软件通过logistic回归开展全基因组关联分析，以主成分1-20及基因分型芯片作为协变量。汇总统计文件*.covararraypcs.assoc.logistic的各列含义如下：
CHR：染色体编号
SNP：SNP的rsID
BP：SNP在对应染色体上的碱基位置
A1：效应等位基因（同时为次要等位基因）
TEST：执行的检验类型（PLINK软件输出结果）
NMISS：同时具有SNP基因型和表型非缺失数据的样本量
OR：比值比
SE：比值比的标准误
L95：比值比95%置信区间的下限
U95：比值比95%置信区间的上限
STAT：T统计量
P：T统计量对应的P值
A0：其他等位基因（同时为主要等位基因）
A1FREQ：效应等位基因/次要等位基因频率

*.hits文件包含所有P值低于5×10^-8的SNP的统计信息。*.manhattan.jpeg文件为全基因组关联研究的曼哈顿图，*.qqplot.jpeg文件为对应的Q-Q图。

使用本汇总统计数据时，请务必仔细参考论文及其补充方法中的详细说明。