2021-03-11

042_ An integrative genomic and proteomic data approach to identify relevant circulating pQTLs to psychiatry

Research Question and Aims

The use of state-of-the-art proteomics and genomics techniques and the integration of both data modalities holds promise for the identification of relevant pQTLs in the context of biomarker discovery in psychiatry (Comes, A. L. et al. 2018). In this research proposal, our main objective is to study the relationship between both genomics markers and expression levels of proteins in circulating blood of BD and SCZ patients.

Analytic Plan

Biological data:
Proteomics: A first-pass screening (Mass Spectrometry) of ~450 proteins in the serum of ~120 BD patients and also ~100 proteins quantified by high-throughput antibody-based assay in serum of 113 SCZ and 125 BD patients (Papiol et al., 2019) are already available for analysis from the PsyCourse cohort. Genomics: Raw genotypes (GSA chip) and imputed data from PsyCourse patients.

Association analyses & statistical approach
Using the aforementioned data, we will investigate the influence of genetic variations on proteins abundance (Cis-pQTLs analyses). These analyses will be adjusted for age, sex, treatment, population stratification (PCA or MDS components) and other relevant covariates in the context of linear models.

Resources needed

For those subjects with "Y" in v1_prot_id, v2_prot_id, v3_prot_id, v4_prot_id, v1_ab_prof_id, v2_ab_prof_id, v3_ab_prof_id:

Demographics, treatment and diagnostic
v1_sex

v1_age
v2_age
v3_age
v4_age

v1_cur_psy_trm
v2_cur_psy_trm
v3_cur_psy_trm
v4_cur_psy_trm

v1_scid_dsm_dx_cat

Raw data on medication and drug use
200715_v4.1_psycourse_clin_raw_med_(visit1 to visit4).RData
200715_v4.1_psycourse_clin_raw_ill_drg_(visit1 to visit4).RData

Genomics: Raw genotypes (GSA chip) and imputed data from PsyCourse patients.

Proteomics: The first-pass screening (Mass Spectrometry) of ~450 proteins in the serum of ~120 BD patients and also the ~100 proteins quantified by high-throughput antibody-based assay in serum of 113 SCZ and 125 BD patients that are already available for analysis from the PsyCourse cohort.