Table 1 Summary of the basic information of TWAS studies in CD
From: Transcriptome-wide association studies associated with Crohn’s disease: challenges and perspectives
Year | GWAS data | eQTL | Methods | Associated tissue type | Association screening criteria | ||||
|---|---|---|---|---|---|---|---|---|---|
Country | Database | N | Country | Tissue type of RNA-seq | N | ||||
Diez-Obrero et.al. [15] | Europe | IBD GWASs of European ancestries | IBD: 25,042 HC: 34,915 | Spain (BarcUVa-Seq) Europe (CEDAR) | Ascending colon | HC:138 | S-PrediXcan | Ascending colon, Transverse colon, Descending colon | P Bonferroni < 0.05 |
Transverse colon | HC:143 | ||||||||
Descending colon | HC:164 | ||||||||
Uellendahl-Werth et. Al. [13] | 15 countries cross Europe, North America, Australia | Ten case–control GWAS datasets | CD: 21,771 HC: 41,206 | US (GTEx), Sweden (STARNET), UK (BLUEPRINT) | Small intestine | non‐IBD 77 | UTMOST | Small intestine, Sigmoid colon, Transverse colon, Whole blood, CD14 + Monocytes, CD16 + Neutrophils, Naïve T cell | P Bonferroni < 0.05 |
Sigmoid colon | non‐IBD 124 | ||||||||
Transverse colon | non‐IBD 169 | ||||||||
Whole blood | non‐IBD:338 | ||||||||
CD14 + Monocytes, CD16 + Neutrophils, Naïve T cell | non‐IBD 338 | ||||||||
Kakuta et.al. [9] | Japan | CD GWASs of Japanese | CD: 713 HC: 2063 | Japan | Intestines | active CD: 15 active UC: 5 | GWAS-eQTL analysis | Effector memory T cells from inflammation sites | Susceptibility: P FDR < 0.05 Candidate: P FDR < 0.1 |
US (GTEx) | Sigmoid colon | HC: 203 | FUSION | Sigmoid colon, Transverse colon, Small Intestine, Whole blood, EBV transformed lymphocytes | |||||
Transverse colon | HC: 246 | ||||||||
Small Intestine | HC: 122 | ||||||||
Whole blood | HC: 369 | ||||||||
EBV transformed lymphocytes | HC: 117 | ||||||||
Jung et.al. [10] | Korea | CD GWAS of Korean | CD: 899 HC: 3805 | Korea | Peripheral blood | CD:101 | FUSION | Whole blood | P Bonferroni < 0.05 |
Gettler et.al. [11] | Cross countries | 15 GWAS of CD and/or UC | CD: 6299 HC: 15,148 | America (GEO) | Terminal ileum | CD: 213, UC: 50, Unspecified IBD:4, HC: 35 | COLOC | Terminal ileum | P FDR < 0.1 |
Dai et.al. [12] | Europe | IIIBDGC | CD: 5956 HC: 21,770 | British | Whole blood | CD: 24 HC: 23 | TESA MetaXcan | Terminal ileum Whole blood Spleen | FC ≥ 1.5 or ≤ 0.67 P Pascal < 0.05 |
Cheng et. al. [14] | Europe | IBD GWAS of European ancestries | CD: 18,405 UC: 14,308 HC: 34,241 | Cross countries (GEO) | Intestinal | IBD: 134, non‐IBD: 134 | FUSION | Sigmoid colon, Transverse colon, Whole blood/ Peripheral blood, Small Intestine terminal ileum EBV transformed lymphocytes | P-value < 0.05 & FC > 1.5 |
Whole blood | IBD: 75, HC:12 | ||||||||
Peripheral blood | HC:42, UC:26, CD:59 | ||||||||