Table 1.
Summary of candidate protein prioritisation across four different COVID-19 outcomes
| colocalisation PP | Protein | COVID-19 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Protein name | Plt | Gene | outcome | H3 | H4 | LD* | rsid | EA | NEA | EAF | Effect | SE | P value | Effect | SE | P value |
| Tier 1 – genome-wide statistical significance (p < 5 × 10−8) in protein and COVID-19 summary statistics | ||||||||||||||||
| Histo-blood group ABO system transferase | S | ABO | B2 | 0.89% | 99.11% | 1.00 | rs505922 | t | c | 0.67 | −1.23 | 0.01 | <1E-300 | −0.100 | 0.011 | 2.09E-20 |
| 2′–5′-oligoadenylate synthase 1 | S | OAS1 | B2 | 11.75% | 88.25% | 0.99 | rs6489868 | c | g | 0.64 | −0.08 | 0.01 | 5.94E-09 | 0.070 | 0.012 | 1.31E-09 |
| 2′–5′-oligoadenylate synthase 1 | S | OAS1 | A2 | 12.55% | 87.44% | 0.92 | rs6489868 | c | g | 0.64 | −0.08 | 0.01 | 5.94E-09 | 0.115 | 0.019 | 2.06E-09 |
| Tier 2 – genome-wide statistical significance (p < 5 × 10−8) in protein or COVID-19 summary statistics | ||||||||||||||||
| ETS-related transcription factor Elf5 | S | ELF5 | B2 | 0.47% | 99.07% | 1.00 | rs766826 | t | c | 0.36 | −0.07 | 0.01 | 5.38E-06 | −0.082 | 0.012 | 1.16E-11 |
| Pulmonary surfactant-associated protein D | O | SFTPD | B2 | 0.24% | 99.73% | 1.00 | rs721917 | g | a | 0.40 | −0.67 | 0.05 | 5.37E-31 | 0.055 | 0.011 | 2.08E-07 |
| 2′–5′-oligoadenylate synthase 1 | S | OAS1 | C2 | 11.92% | 87.70% | 0.92 | rs6489868 | c | g | 0.64 | −0.08 | 0.01 | 5.94E-09 | 0.021 | 0.004 | 1.67E-06 |
| DnaJ homologue subfamily B member 1 | S | DNAJB1 | A2 | 1.68% | 93.62% | 0.98 | rs35258260 | a | g | 0.85 | −0.11 | 0.02 | 4.61E-10 | −0.105 | 0.027 | 1.29E-04 |
| ADP-sugar pyrophosphatase | S | NUDT5 | B2 | 1.43% | 86.27% | 1.00 | rs7895525 | t | c | 0.76 | −0.11 | 0.02 | 3.29E-12 | 0.047 | 0.012 | 1.34E-04 |
| Ras-related protein Rab2A | S | RAB2A | B2 | 11.98% | 84.01% | 0.98 | rs6995515 | a | c | 0.63 | −0.07 | 0.01 | 2.57E-08 | −0.041 | 0.011 | 1.47E-04 |
| Tier 3 – suggestive statistical significance (5 × 10−8 < p < 1 × 10−4) in protein and COVID-19 summary statistics | ||||||||||||||||
| ETS-related transcription factor Elf5 | S | ELF5 | B1 | 0.67% | 96.68% | 1.00 | rs766826 | t | c | 0.36 | −0.07 | 0.01 | 5.38E-06 | −0.078 | 0.017 | 4.01E-06 |
| ETS-related transcription factor Elf5 | S | ELF5 | A2 | 0.75% | 97.93% | 1.00 | rs766826 | t | c | 0.36 | −0.07 | 0.01 | 5.38E-06 | −0.105 | 0.023 | 5.05E-06 |
| Granulocyte colony-stimulating factor | O | CSF3 | C2 | 6.04% | 88.20% | 0.88 | rs3826331 | c | t | 0.62 | −0.25 | 0.06 | 7.54E-05 | 0.019 | 0.004 | 5.47E-06 |
outcome = type of COVID-19 outcome; A2 = severe COVID-19 vs population; B1 = Hospitalised COVID-19 vs non-hospitalised COVID-19; B2 = Hospitalised COVID-19 vs population; C2 = SARS-CoV-2 positive vs population; Plt = Platform: S – SomaScan v4 or O – Olink PEA; PP = posterior probability; H3 = distinct genetic signals; H4 = shared genetic signal; LD* = linkage disequilibrium between respective regional lead genetic variants for protein levels and COVID-19 outcomes. Effect estimates, standard errors (SE), and p values from linear regression models are shown for candidate genetic variants and were obtained from Pietzner et al.30, 32 for protein levels and the COVID-19 HGI for COVID-19 outcomes15.