Chapter 4 - Rare pathogenic FADS variants, Major Depressive Disorder and Omega-3 Fatty Acids

Supplementary data to accompany Chapter 4 of my PhD thesis. 

Supplementary Data 1: VEP output for the prioritised variants identified in FADS1 in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 2: VEP output for the prioritised variants identified in FADS2 in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 3: VEP output for the prioritised variants identified in FADS3 in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 4: VEP output for the prioritised variants identified in FEN1 in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 5: VEP output for the prioritised variants identified in MYRF in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 6: VEP output for the prioritised variants identified in TMEM258 in the MDD cohort. The priority criteria that each variant met to become prioritised is shown in the 'priority_criteria' column. The AC, AN and AF columns all relate to the MDD cohort. The "in_metabolite_cohort" denotes whether the variant was carried in any participant in the metabolite cohort. 

Supplementary Data 7: Results from Welchs t-test which tested the association of carrier status of variants within a mask and metabolite levels, for each mask in each gene. The results are ordered by Benjamini-Hochberg corrected p-value (P_BH). 

Supplementary Data 8: Aggregate variant testing results for each individual gene/mask with each trait. The AVT test used is shown in the TEST column, which included the traditional burden test (BURDEN), the sequence kernel association test (SKAT), the aggregated Cauchy combination test (ACAT-V) alongside the omnibus tests (SKAT-O and ACAT-O). Results are ordered by Gene, Trait and Test.

Supplementary Data 9: Results from leave-one-out variant analysis for prioritised variants in FADS1 (Mask 5, AF < 0.01) with MDD and metabolite traits. The AVT used for each test was the one with the highest significance using the whole mask. Each row denotes the AVT results utilising the same mask with one variant removed. Results are ordered by trait and -LOG10P value.

本数据集为本人博士论文第4章的配套补充数据。

补充数据1：重度抑郁症（Major Depressive Disorder, MDD）队列中FADS1基因内筛选得到的优先级变异的变异效应预测器（Variant Effect Predictor，VEP）输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列（metabolite cohort）的任意受试者中存在携带情况。

补充数据2：MDD队列中FADS2基因内筛选得到的优先级变异的VEP输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列的任意受试者中存在携带情况。

补充数据3：MDD队列中FADS3基因内筛选得到的优先级变异的VEP输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列的任意受试者中存在携带情况。

补充数据4：MDD队列中FEN1基因内筛选得到的优先级变异的VEP输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列的任意受试者中存在携带情况。

补充数据5：MDD队列中MYRF基因内筛选得到的优先级变异的VEP输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列的任意受试者中存在携带情况。

补充数据6：MDD队列中TMEM258基因内筛选得到的优先级变异的VEP输出结果。各变异通过筛选的优先级判定标准已在`priority_criteria`列中列明。AC、AN及AF列均对应MDD队列。`in_metabolite_cohort`字段用于标注该变异是否在代谢物队列的任意受试者中存在携带情况。

补充数据7：韦尔奇t检验（Welch's t-test）结果。该检验用于检测每个基因的各变异组中，变异携带状态与代谢物水平之间的关联。结果已按本杰明尼-霍赫贝格（Benjamini-Hochberg）校正p值（P_BH）排序。

补充数据8：各基因/变异组与各表型的变异聚集检测（Aggregate Variant Testing，AVT）汇总结果。所用的AVT检验方法已在`TEST`列中列明，包括传统负担检验（BURDEN）、序列核关联检验（Sequence Kernel Association Test，SKAT）、聚集柯西组合检验（Aggregated Cauchy Combination Test，ACAT-V）以及综合检验（SKAT-O与ACAT-O）。结果已按基因、表型及检验方法排序。

补充数据9：针对MDD队列及代谢物表型中FADS1基因（变异组5，AF < 0.01）内优先级变异的留一变异分析结果。每项检验所用的AVT方法均为基于完整变异组得到的显著性最高的检验方法。每一行代表移除某一个变异后的同一变异组的AVT检测结果。结果已按表型及-LOG10P值排序。