EU-GEI WP2 study
Clinical, environmental and genetic data have been collected through the EU-GEI WP2 (named “Functional Enviromics”), a multicentre case-sibling-control study of genetic and environmental determinants of the occurrence and severity of psychotic disorders. Population-based unaffected controls were recruited across 6 countries: Brazil, France, Italy, the Netherlands, Spain, and the United Kingdom. These controls were recruited using a mixture of random and quota sampling to ensure that they were broadly representative of the at-risk populations on predefined variables (age, sex, and migration) [47].
Ethical approval was obtained from local research ethics committees in each country. The EU-GEI Project was funded by the European Community’s Seventh Framework Program under grant agreement no. HEALTH-F2-2010-241909.
Subclinical psychosis and psychosocial stressors assessment
The Community Assessment of Psychic Experiences (CAPE) is a 42-item self-report questionnaire that has been developed to assess lifetime subclinical psychotic dimensions in the general population [48]. For each item, 4 answers were possible according to the frequency of their occurrences (from never to nearly always). To construct the dimension scores (positive, negative and depressive [49]), we dichotomized answers of each CAPE item (never vs. sometimes or more) and summed the positive answers. The cross-national invariance of the CAPE score in the EU-GEI WP2 samples was previously demonstrated [50].
Childhood trauma was assessed with a short version of the Childhood Trauma Questionnaire (CTQ), with 25 items assessing five different domains (emotional and physical neglect, emotional, physical and sexual abuse) [51]. Only the total score was used. Lifetime self-reported discrimination experiences were assessed with a modified version of the 12-item Williams’ major experiences of discrimination scale (unfairly fired or not hired because of your ethnicity/sex/weight/etc., unfairly stopped/questioned/physically threatened or abused by the police, etc.) [52, 53]. Perceived social capital in each participant’s immediate neighborhood was assessed using the Social Environment Assessment Tool (SEAT), a 23-item questionnaire, that was designed to capture four dimensions of social capital: civic disorder (CD), impact of civic disorder (ICD), informal social control (ISC), and social cohesion and trust (SCT) [54–57]. Subjects answer according to a five-point Likert-scale (1: unusual, to 5: very common), and a sum of the weighted scores of the 4 subscales were calculated to obtain the total social capital score (SEAT score = zCD + 0.51*zICD + 1.6*zISC + zSCT). Finally, stressful life events were assessed using the List of Threatening Experiences (LTE) which comprises 20 binary items of events usually associated with major stress over the course of the previous 6 months (e.g., serious injury, death of a parent, separation from a partner, financial difficulties) [58, 59].
Calculation of a Polygenic Risk Score for Schizophrenia (PRS-SZ)
Blood samples of the control sample were genotyped by the Medical Research Council Centre for Neuropsychiatric Genetics and Genomics (Cardiff, United-Kingdom) using a custom “Illumina HumanCoreExome-24 BeadChip” genotyping array, covering 570,038 genetic variants. As described elsewhere [24], the PRS-SZ were generated using PRSice from the summary results of the Psychiatric Genomics Consortium (PGC), wave 2 [60]. Clumping was performed to obtain SNPs in approximate linkage disequilibrium with an r2 < 0.25 within a 250kb window. PRS-SZ were calculated, at p-value thresholds of 0.05. The sample was restricted to 706 European descendant unaffected subjects (due to over-representation of European descendant subjects in the PGC2 training sample used to calculate the PRS-SZ).
Statistical analyses
The G-E association has been assessed by Spearman correlation tests between the 4 psychosocial stressors and the PRS-SZ. Then, linear regression models were used to assess the relationships between the CAPE dimensions scores (positive, negative, depressive), environmental and genetic variables, and to look for GxE interactions. Of note, we consider multiplicative interactions [61, 62].
The different models were adjusted for age, sex, and the 10 first principal components (PCs) of the genetic analyses of the ethnic variance. For each CAPE dimension, thirteen models were tested:
- A “Genetic model”, with the sole PRS-SZ;
- Four “Environmental models” for each of the 4 psychosocial stressors variables: childhood trauma, stressful life-events, self-reported discrimination experiences and low social capital;
- Four “Independent models”: one for each of the 4 psychosocial stressors variables and the PRS-SZ, without interaction term;
- Four “Interaction models”: each of the 4 psychosocial stressors variables and the PRS-SZ, with a GxE interaction term.
To compare the fit of the different models (and particularly the Independent and the Interaction models), we compared the explained variances (R2), and use likelihood ration test (LRT) to assess whether the addition of a factor (E + G vs. G, E + G vs. 3, E + G + E*G vs. E + G) improved the fit of the model.
Psychosocial variables and PRS-SZ were standardized to Z-scores (i.e., to a mean equal to 0, and a standard-deviation equal to 1). The SEAT (social capital) score was inverted, so that higher scores were associated with lower social capital. Missing data of the CAPE (between 3 and 5 % according to the different dimensions) and the psychosocial stressors variables (between 0.5 and 20 %) were imputed with multivariate imputation by chained equations (MICE) in 20 resamples. R software version 3.6.0 was used for the statistical analyses.