Table 1.
Study and sample summary
| Study | Schadt et al.18 | Schroeder et al.19 | Innocenti et al.17 | GTEx Start/Mida | Meta-analysis | Mega-analysis |
|---|---|---|---|---|---|---|
| Sample size before/after QC | 178/178 | 149/149 | 208/178 | 97/83 | 588 | 588 |
| Origin of liver tissue | Post-mortem tissue and resections from donor livers | Normal tissue resected during surgery for liver cancer | Post mortem tissue and resections from donor livers | Post mortem tissue | — | — |
| Transcriptome profiling platform | Agilent Custom 44k | Illumina Human WG-6v2.0 | Agilent 4 × 44 k | RNA-seq (Illumina HiSeq2000) | — | — |
| Probes/genes before QC | 40,638 | 48,701 | 45,015 | 56,318 | — | — |
| Genes after QC | 24,123 | 24,123 | 24,123 | 24,123 | 24,123 | 24,123 |
| Genotyping platform | Affymetrix 500k; Illumina 650 Y | Illumina HumanHap300 | Illumina 610 Quad | Illumina Omni 5 M/2.5 Ma | — | — |
| Variants before QC | 449,699 | 318,237 | 620,901 | 2,526,494/2,378,075a | — | — |
| Variants after QC | 383,719 | 296,718 | 545,886 | 2,389,798/2,119,410a | — | — |
| Variants merged before imputationb | 861,575 | 861,575 | 861,575 | 861,575 | 861,575 | 861,575 |
| Variants after imputation and QC | 6,256,941 | 6,256,941 | 6,256,941 | 6,256,941 | 6,256,941 | 6,256,941 |
| eQTL variants (Q-Value < 1 × 10−3) | 29,546 | 71,423 | 52,565 | 19,802 | 101,148 | 202,489 |
| eQTL variants (Q-Value < 1 × 10−3, unique) | 27,689 | 69,292 | 49,594 | 16,953 | 95,257 | 183,872 |
| eQTL genes (Q-Value < 1 × 10−3, unique) | 363 | 913 | 670 | 387 | 1,313 | 1,959 |
| Overlapping eQTL genes with meta-analysis (Q-Value < 1 × 10−3) | 215 (59.23%) | 491 (53.78%) | 408 (60.9%) | 149 (38.5%) | 1,313 (100%) | 1,260 (64.32%) |
| Overlapping eQTL genes with mega-analysis (Q-Value < 1 × 10−3) | 288 (79.34%) | 688 (75.36%) | 537 (80.15%) | 207 (53.49%) | 1,260 (95.96%) | 1,959 (100%) |
| Independent signals (P-Value < 1 × 10−6) | — | — | — | — | — | 2,060 |
QC = quality control; aOmni 2.5 M for the first data release (GTEx start) and Omni 5 M for the mid-point release (GTEx mid). bAfter quality control the genotype files of the four studies were merged into a single file and variants, which did not overlap in-between datasets, were assigned missing. We only kept variants which were genotyped in at least 100 samples.