bogdanlab / twas30

TWAS association statistics from Mancuso et al AJHG 2017

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 [email protected]