DOI: 10.5281/zenodo.15101441
title: Chapter 4 - Rare pathogenic FADS variants, Major Depressive Disorder and Omega-3 Fatty Acids

description: 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.