UKBiobank depression PRS weights

This folder contains the clumped summary statistics (in daner format) 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.These files are used for assessing polygenic risk score (PRS) prediction of depression status in individual cohorts of Major Depressive Disorder Psychiatric Genomics Consortium from the PGC29 release, as described in the paper. GWAS summary statistics from this study, accessible through https://doi.org/10.6084/m9.figshare.11733753.v1, are first pruned for SNPs present in the PGC29 cohorts, with their effect alleles also aligned with those specified in PGC29 cohorts. They then undergo LD-clumping using the clump_nav3 function in the Ricopilli pipeline, with the following parameters: clump_nav3 --noindel \ --pfile $pheno_clumpOut.gz \ --hq_f 0.01 \ --hq_i 0.6 \ --outname $pheno_clumpOut \ --clu_p1 1.0 \ --clu_p2 1.0 \ --clu_window 500 \ --clu_r2 0.1 \ --refdir $refdir --popname eur \ --force1They are then used in PRS prediction of MDD status in PGC29 cohorts using the my_postimp_navi function in Ricopilli. Please note that these files do not contain SNPs filtered based on P value thresholds; they contain SNPs across the whole range of association P values in their respective GWAS, and P value thresholds were only imposed when calculating PRS prediction statistics. ====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 UKBiobank2. 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 recurrence3. 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 UKBiobank5. 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本文件夹包含针对英国生物库（UKBiobank）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）的成簇汇总统计数据（格式为daner格式），相关研究为Cai N.等人发表于《自然·遗传学》（Nature Genetics, 2020）的《Minimal phenotyping yields genome-wide association signals of low specificity for major depression》，DOI: 10.1038/s41588-020-0594-5。 如论文所述，这些文件用于评估来自PGC29版本的重度抑郁症精神疾病基因组学联盟（PGC, Psychiatric Genomics Consortium）队列中抑郁症状态的多基因风险评分（PRS, Polygenic Risk Score）预测性能。本研究的GWAS汇总统计数据可通过https://doi.org/10.6084/m9.figshare.11733753.v1获取，首先会针对PGC29队列中存在的单核苷酸多态性（SNP, Single Nucleotide Polymorphism）进行筛选，并将效应等位基因与PGC29队列中指定的等位基因对齐。随后使用Ricopilli流程中的clump_nav3函数进行连锁不平衡（LD, Linkage Disequilibrium）成簇分析，参数如下： clump_nav3 --noindel --pfile $pheno_clumpOut.gz --hq_f 0.01 --hq_i 0.6 --outname $pheno_clumpOut --clu_p1 1.0 --clu_p2 1.0 --clu_window 500 --clu_r2 0.1 --refdir $refdir --popname eur --force1 之后使用Ricopilli中的my_postimp_navi函数，在PGC29队列中开展重度抑郁症（MDD, Major Depressive Disorder）状态的PRS预测。请注意，这些文件未包含基于P值阈值筛选的SNP，而是包含了对应GWAS中所有关联P值范围的SNP，仅在计算PRS预测统计量时才会施加P值阈值。 ====以下简要介绍各表型，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），采用既定标准定义。病例为在英国生物库中回答相关问题且符合病例标准的参与者，对照为回答了相同问题但未符合病例标准的参与者。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的PHQ-9问卷，采用精神障碍诊断与统计手册第五版（DSM-V）症状及功能损害标准定义的终身重度抑郁症。 2. MDDRecur：在LifetimeMDD基础上额外增加复发判定标准，同样基于英国生物库在线心理健康随访中的PHQ-9问卷与DSM-V标准定义的复发性终身重度抑郁症。 3. GPpsy：指在英国生物库触摸屏访谈中报告过因神经、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, DOI: 10.1038/s41467-018-03819-3）中提出的"Broad Depression"表型最为相似。 4. Psypsy：指在英国生物库触摸屏访谈中报告过因神经、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：一是出现重度抑郁症核心症状（情绪低落或快感缺失）超过两周，二是因神经、焦虑、紧张或抑郁就诊于全科医生或精神科医生。该表型最初由Smith等人2013年发表于《公共科学图书馆·综合》（PLoS One, DOI: 10.1371/journal.pone.0075362.s001）中以"Probable Depression"之名提出，与Howard等人2018年《自然·通讯》中提出的"Probable Depression"表型最为相似。 6. GPNoDep：指在英国生物库触摸屏访谈中报告过因神经、焦虑、紧张或抑郁就诊于全科医生，但未报告存在重度抑郁症核心症状的参与者。 7. SelfRepDep：指在英国生物库的医疗状况口头访谈中向受训护士自述患有抑郁症或抑郁症状，在数据集中归类为"非肿瘤疾病"的参与者。 8. ICD10Dep：指在与英国生物库参与者关联的国际疾病分类第十次修订版（ICD-10, International Classification of Diseases 10th Revision）信息中，标注有抑郁症ICD-10主要及次要诊断编码的电子健康记录参与者。