The following GWAS were carried out with the BIG40 22k discovery sample subjects; the sumstats files contain the following columns:
chr rsid pos a1 a2 beta se pval(-log10)
Download: QSMandT2s_IDPs.tar.gz (Discovery sample) and QSMandT2s_IDPs_repro.tar.gz (Replication sample) (11GB each file).
The 18 QSM IDPs are:
QSM_Left_thalamus (0001.txt): median susceptibility in left thalamus
QSM_Right_thalamus (0002.txt): median susceptibility in right thalamus
QSM_Left_caudate (0003.txt): median susceptibility in left caudate
QSM_Right_caudate (0004.txt): median susceptibility in right caudate
QSM_Left_putamen (0005.txt): median susceptibility in left putamen
QSM_Right_putamen (0006.txt): median susceptibility in right putamen
QSM_Left_pallidum (0007.txt): median susceptibility in left pallidum
QSM_Right_pallidum (0008.txt): median susceptibility in right pallidum
QSM_Left_hippocampus (0009.txt): median susceptibility in left hippocampus
QSM_Right_hippocampus (0010.txt): median susceptibility in right hippocampus
QSM_Left_amygdala (0011.txt): median susceptibility in left amygdala
QSM_Right_amygdala (0012.txt): median susceptibility in right amygdala
QSM_Left_accumbens (0013.txt): median susceptibility in left accumbens
QSM_Right_accumbens (0014.txt): median susceptibility in right accumbens
QSM_Left_SN (0015.txt): median susceptibility in left substantia nigra
QSM_Right_SN (0016.txt): median susceptibility in right substantia nigra
QSM_WMH_ori (0017.txt): original QSM white matter hyperintensity IDP
QSM_WMH_WMHVout (0018.txt): QSM white matter hyperintensity IDP with WMH volume regressed out
The 10 new T2* IDPs are:
T2*_Left_hippocampus (0027.txt): median T2* in left hippocampus with additional deconfounding of background field gradient
T2*_Right_hippocampus (0028.txt): median T2* in right hippocampus with additional deconfounding of background field gradient
T2*_Left_amygdala (0029.txt): median T2* in left amygdala with additional deconfounding of background field gradient
T2*_Right_amygdala (0030.txt): median T2* in right amygdala with additional deconfounding of background field gradient
T2*_Left_accumbens (0031.txt): median T2* in left accumbens with additional deconfounding of background field gradient
T2*_Right_accumbens (0032.txt): median T2* in right accumbens with additional deconfounding of background field gradient
T2*_Left_SN (0033.txt): median T2* in left substantia nigra
T2*_Right_SN (0034.txt): median T2* in right substantia nigra
T2*_WMH_ori (0035.txt): original T2* white matter hyperintensity IDP
T2*_WMH_WMHVout (0036.txt): T2* white matter hyperintensity IDP with WMH volume regressed out
The following GWAS were carried out with the 8428 subjects as
described in
the Elliott
et al bioRxiv paper.
SNPs were preselected requiring that MAF>=0.001.
First-pass GWAS summary-statistic outputs for various IDP groups include:
b.txt betas (one row per SNP, one column per IDP, no header row)
s.txt error standard deviation (ditto)
z.txt z statistics (ditto)
p.txt -log10p (ditto)
stats.txt other information, with headers on the first row: chr rsid pos a1 a2 af info.
See BGENIE documentation for more information.
The 11 IDPs are:
IDP_T2_FLAIR_BIANCA_WMH_volume original WMH IDP: total WMH volume
pvent_adj_vol volume of periventricular WMH, defined with the continuity to ventricles criterion
deep_adj_vol volume of deep WMH, defined with the continuity to ventricles criterion
pvent_vol_10mm volume of periventricular WMH, defined with the 10 mm distance criterion
deep_vol_10mm volume of deep WMH, defined with the 10 mm distance criterion
juxtavent_vol_3mm volume of juxtaventricular WMH, defined with the 3-13 mm distance criterion
pvent_vol_3_13mm volume of periventricular WMH, defined with the 3-13 mm distance criterion
deep_vol_over13mm volume of deep WMH, defined with the 3-13 mm distance criterion
LesionCount total number of WMH clusters
LesionCountPeriVent total number of periventricular WMH clusters, derived with the 10mm criterion
LesionCountDeepWM total number of deep WMH clusters, derived with the 10mm criterion
For pvent_adj_vol, deep_adj_vol and lesion count IDPs, WMH clusters are first thresholded at
volume>=10mm3.
The different criteria are described and
compared in Griffanti et al., 2017, Neuroimage (doi:
10.1016/j.neuroimage.2017.03.024). Briefly:
- Continuity to ventricles
(Fazekas et al., 1987; Fazekas et al., 1993; van den Heuvel et al.,
2006): a WMH adjacent to the ventricle surface is periventricular,
otherwise it is deep.
- 10 mm distance (DeCarli et al., 2005): a WMH
less than 10 mm distance from the ventricles is periventricular,
otherwise it is deep.
- 3-13 mm distance (Kim et al., 2008): a lesion
less than 3 mm from the ventricles is classified as juxtaventricular;
a lesion between 3 and 13mm distance from the ventricles is
periventricular, otherwise it is deep.
The 16 tfMRI IDPs are as listed (and in same order) as found in the complete IDP list.
Contributors
UKB brain image processing (including WMH IDP generation): Steve
Smith, Fidel Alfaro-Almagro, Karla Miller, Mark Jenkinson, Ludovica
Griffanti, Chaoyue Wang.
UKB genetic imputation and GWAS software: Jonathan Marchini and Lloyd Elliott.