Table 1 Summary of candidate protein prioritisation across four different COVID-19 outcomes

From: ELF5 is a potential respiratory epithelial cell-specific risk gene for severe COVID-19

    

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

  1. 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.
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