paperKB
coga / coga-kb
Help
Sign in

Chunk #73 — Methods — Deep phenotyping of the AFA top hit rs115539978

Source
International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.
Embedded
yes

Text

Neuroimaging: Scanning of 87 GTPC subjects took place on a 3.0 T Siemens Trio with echo-planar imaging (Siemens, Malvern, PA). High-resolution T1-weighted anatomical scans were collected using a 3D MP-RAGE sequence, with 176 contiguous 1 mm sagittal slices (TR/TE/TI = 2000/3.02/900 ms, 1 mm3 voxel size). T1 images were processed in Freesurfer version 5.3 (https://surfer.nmr.mgh.harvard.edu). Gray matter volume from subcortical structures was extracted through automated segmentation, and data quality checks were performed following the ENIGMA 2 protocol (http://enigma.ini.usc.edu/protocols/imaging-protocols/), a method designed to standardize quality control procedures across laboratories to facilitate replication. Briefly, segmented T1 images were visually examined for errors, and summary statistics and a summary of outliers ± 3 SD from the mean were generated from the segmentation of the left and right amygdala and hippocampus. Regional volumes that were visually confirmed to contain a segmentation error were discarded.