TWAS association statistics from Mancuso et al AJHG 2017
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README.md
am.txt
bmi.txt
cd.txt
col.txt
ey.txt
fa.txt
fg.txt
fi.txt
fn.txt
hb.txt
hba1c.txt
hdl.txt
height.txt
homa-b.txt
homa-ir.txt
ibd.txt
ldl.txt
ls.txt
mch.txt
mchc.txt
mcv.txt
pcv.txt
plt.txt
ra.txt
rbc.txt
scz.txt
t2d.txt
tc.txt
tg.txt
uc.txt

README.md

TWAS30

This repository contains transcriptome-wide association study (TWAS) summary statistics for the 30 traits reported in

Integrating gene expression with summary association statistics to identify susceptibility genes for 30 complex traits., Nicholas Mancuso, Huwenbo Shi, Pagé Goddard, Gleb Kichaev, Alexander Gusev, Bogdan Pasaniuc. American Journal of Human Genetics. 2017 Feb. doi: 10.1016/j.ajhg.2017.01.031

Each *.txt file contains the TWAS results for a particular trait. Each file is prefixed with a header naming the 12 columns. A description of each of these columns is provided below,

Column Description
TRAIT GWAS trait
GENE Gene or transcript used to test for association with GWAS trait
CHR Chromosome the gene is located on
TxS Transcription start site
TxE Transcription end site
STUDY The original panel expression levels were measured in
TWAS.Z TWAS association statistic
TWAS.P TWAS association p-value
BEST.GWAS.RSID RSID of the best GWAS SNP within 1 Mb of the gene TxS (i.e. smallest p-value)
BEST.GWAS.P P-value of the best GWAS SNP
GWAS.HSQ.LOCAL Local heritability estimate of GWAS trait
ALPHA Standardized effect of gene/transcript expression on trait

Traits

Our study made use of 30 publically available GWAS summary statistics to identify genes whose cis-regulated expression is associated with trait/disease status. The original GWAS publications, along with our shorthand notation, are listed below.

Shortname Trait
BMI Body Mass Index
HEIGHT Height
HB Haemoglobin
MCH Mean Cell Haemoglobin
MCHC MCH Concentration
MCV Mean Cell Volume
PCV Packed Cell Volume
RBC Red Blood Cell Count
PLT Number of Platelets
FG Fasting Glucose
FI Fasting Insulin
HOMA-B HOMA-B
HOMA-IR HOMA-IR
HBA1C HBA1C
HDL High Density Lipoprotein
LDL Low Density Lipoprotein
TG Triglycerides
TC Total Cholesterol
EY Education Years
COL College
FA Forearm BMD
FN Femoral Neck BMD
LS Lumbar Spine
AM Age at Menarche
RA Rheumatoid Arthritis
SCZ Schizophrenia
CD Crohn's Disease
IBD Inflammatory Bowel Disease
UC Ulcerative Colitis
T2D Type 2 Diabetes

Gene Expression

Similarly, we incorporated gene expression measured in more than 40 tissues from 5 studies. The shorthand notation for the original eQTL study and publication are detailed below.

Shortname Expression Study
CMC Commonmind consortium
GTEX Genotype-Tissue Expression Consortium
MET Metabolic Syndrome in Men Study (METSIM)
NTR National Twins Registry
YFS Cardiovascular Risk in Young Finns Study

Software and support

To compute the genetic correlation of two traits using estimated effects of gene expression, please see RHOGE.

For performing TWAS using summary-data, computing expression weights using custom expression panels, and additional post-TWAS analyses please see FUSION.

If you have any questions or comments please contact nmancuso@mednet.ucla.edu