*Netherlands Twin Registry (NTR)*. The NTR has collected longitudinal data on twins and their families via 8 surveys every 2-3 years, beginning in 1991 (~22,000 participants from ~5,000 families). Most twins were recruited as young adults through City Council registration, and additional twins via a variety of approaches. Longitudinal phenotyping includes assessment of DSM-IV MDD by CIDI, depressive symptoms (multiple instruments), anxiety, neuroticism, and other personality measures. Additionally, subjects are asked about major medical illnesses/health, medications, life events, and lifestyle, and a genetic factor score for MDD liability is available. There are banked RNA and DNA samples from ~1600 pairs, with an almost equal distribution of monozygotic and dizygotic twin pairs. Most of these individuals are controls but some meet case definitions.

*Netherlands Study of Depression and Anxiety (NESDA)*. NESDA is an ongoing cohort study designed to investigate the long-term course and consequences of depressive and anxiety disorders. Participants were 18-65 years at baseline in 2004-2007 and were recruited from the community (19%), general practice (54%), and mental health settings (27%). At baseline, there were ~1000 individuals with current MDD and ~1100 with past but not current history of MDD. The baseline assessment included the CIDI, demography, and medical assessment. DSM-IV MDD diagnoses were established with the CIDI which has high inter-rater reliability, test-retest reliability, and validity for MDD. Of the baseline subjects, 87% participated in a two year follow-up. The CIDI was repeated to query MDD in the time since baseline (augmented by the use of a Life Chart Interview). These measures allow classification into distinct clinical trajectories over two years of follow-up: chronic or recurrent course with symptoms >1y (poor course) and remission within one year (good course, initial MDD episode lasts <1y with complete remission >1y). Of subjects with current MDD at baseline, a minority (44.9%) were taking antidepressants (usually SSRIs). Antidepressant use data are now being coded. Most NESDA subjects are cases but an independent, longitudinally-assessed sample of controls was also collected.

*Harmonized Biological Sampling*. Processing and storage protocols were harmonized between the NESDA and NTR studies. Blood sampling in NESDA took place between 0830-0930h and between 0700-1000h for NTR. All venous blood samples were taken after an overnight fast.

*RNA Sampling*. Within 20 minutes of sampling, heparinized blood was transferred into PAXgene tubes and stored at −20°C. DNA isolation. EDTA tubes were used. For NESDA, FlexiGene DNA AGF3000 kits were used on an AutoGenFlex 3000 workstation. For NTR, Puregene DNA isolation kits were used on frozen whole blood samples. DNA concentrations were determined using PicoGreen dsDNA kits. All procedures were performed via manufacturer's protocols.

*Covariates*. Available covariates include: sampling time/date; age at sampling; sex; complete blood count with differential; consumption/quantity of tobacco and alcohol near the time of sampling; detailed list of medications (including antidepressants); and detailed health status (chronic/recent acute medical illness, allergies, etc.).

*Data upload*: The GODOT project has typed DNA and RNA from peripheral blood for large samples from both the NESDA and NTR studies. The available data are Affy6 genotype assays, as well as Affymetrix U219 expression assays on the same set of individuals (except for minor lack of overlap due to quality control flagging). Additional subject information includes twin pedigree descriptions (for the NTR subjects), major depressive disorder phenotyping for the NESDA subjects, and a set of patient/covariates that may influence expression levels.