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 |
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 |
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 |
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