BIONIC Standard Operating Procedure for Sample QC and Data Upload - molgenis/systemsgenetics GitHub Wiki

This document contains the SOP for performing sample quality control and data upload for the BIONIC project.

SOP Content

  1. Project background
  2. Obtaining an account for the upload server
  3. Phenotype data
  4. Genotype data software download
  5. Genotype data sample quality control
  6. Step-by-step data upload

Project Background Cohorts that take part in the BBMRI-NL consortium have already agreed to the collaboration in data collection and data upload regarding the BIONIC project.

What is the BIONIC project? In the BIObanks Netherlands Internet Collective (BIONIC) project, Dutch academic institutions and biobanks collaborate in the standardised and harmonised assessment of Major Depressive Disorder, with the aim of uncovering its genetic etiology. In the first phase of the project, our team developed and validated a rapid online DSM 5-based MDD assessment tool which would serve as BIONIC’s main tool for data collection (Bot et al., 2017). In the second phase, Fedko et al. (2020) used a subset of the newly acquired MDD data to introduce the cohorts, and demonstrate the large alignment between estimates of prevalence and heritability found in BIONIC and those of previous MDD efforts. Now, in the third phase, we plan to identify the specific genetic variants associated with MDD in the Dutch population. To this end, we will perform a genome-wide association meta-analysis on the MDD and genotype data from all participating cohorts. Additional projects involve symptom-specific genetic association analyses and networking analyses using the phenotype data.