Table 4 Proteins associated with platform-discordant cis-pQTL containing a protein altering variant (PAV) in discordant credible set

From: Cross-ancestry comparison of aptamer and antibody protein measures

Credible set summary

Overall protein measure correlation (Pearson’s r)

PAV cis-pQTL summary statistics

Allele frequency per ancestry group

SomaScan

Olink

Variant ID

Entrez

gene

name

SeqID

OlinkID

Amino acid change* (Ref/Alt)

UniProt

Without PAV adjustment

With PAV adjustment

B

SE

PVAL

B

SE

PVAL

All

AFR

AMR

EAS

EUR

Ancestry differentiated variant

chr15:78944905:C:G

CTSH**

seq.8465.52

OID20113

C/S

P09668

0.28

0.45

0.42

0.03

2.18E-37

−0.50

0.03

6.47E-49

0.48

0.28

0.49

0.12

0.68

TRUE

chr19:43665370:T:C

PLAUR

seq.2652.15

OID20764

T/A

Q03405

0.43

0.57

−2.10

0.07

2.03E-155

0.61

0.07

2.58E-17

0.03

0.10

0.01

0.00

0.00

TRUE

chr2:138002079:C:T

HNMT

seq.23178.95

OID20975

T/I

P50135

0.32

0.47

0.66

0.05

5.52E-39

−1.05

0.04

4.52E-146

0.07

0.01

0.08

0.03

0.11

FALSE

chr16:12803721:G:T

CPPED1

seq.21108.5

OID21053

A/D

Q9BRF8

−0.02

0.47

−1.20

0.02

1.00E-300

0.66

0.02

1.20E-148

0.33

0.61

0.28

0.37

0.20

TRUE

chr1:150755063:G:A

CTSS

seq.3181.50

OID21056

R/W

P25774

0.41

0.50

0.35

0.03

8.43E-37

−0.37

0.03

1.92E-43

0.35

0.28

0.40

0.35

0.38

FALSE

chr6:41198411:A:G

TREML2

seq.5736.1

OID21120

V/A

Q5T2D2

0.67

0.76

0.57

0.05

3.97E-33

−0.58

0.04

1.50E-54

0.10

0.03

0.10

0.07

0.13

FALSE

chr7:100374211:A:G

PILRA**

seq.10816.150

OID21129

R/G

Q9UKJ1

−0.39

0.26

−1.35

0.02

1.00E-300

0.92

0.02

2.98E-300

0.34

0.14

0.53

0.60

0.32

TRUE

chr1:156743766:G:A

HDGF

seq.16758.96

OID21455

P/L

P51858

0.48

0.68

−0.33

0.02

1.69E-42

1.02

0.02

1.00E-300

0.22

0.11

0.14

0.10

0.32

FALSE

chr4:55113391:C:T

KDR

seq.3651.50

OID21497

V/I

P35968

0.57

0.59

0.26

0.04

5.79E-09

−0.30

0.04

3.25E-12

0.14

0.24

0.09

0.15

0.09

FALSE

chr1:10413143:G:A

PGD

seq.4187.49

OID30344

D/N

P52209

0.49

0.50

−0.21

0.03

4.60E-12

0.74

0.06

2.65E-39

0.04

0.05

0.04

0.06

0.03

FALSE

chr2:277003:A:G

ACP1

seq.3858.5

OID30524

Q/R

P24666

0.15

0.36

1.25

0.01

1.00E-300

−0.17

0.03

2.74E-07

0.29

0.23

0.24

0.26

0.35

FALSE

chr14:20781965:G:A

RNASE6

seq.5646.20

OID30689

R/Q

Q93091

0.35

0.63

1.16

0.02

1.00E-300

−0.24

0.03

1.45E-18

0.23

0.10

0.26

0.41

0.23

FALSE

chr22:36265284:G:A

APOL1

seq.11510.31

OID30708

E/K

O14791

0.54

0.59

0.51

0.03

9.77E-49

−0.22

0.03

1.12E-10

0.29

0.63

0.14

0.18

0.20

TRUE

chr19:44908822:C:T

APOE

seq.2937.10

OID30727

R/C

P02649

0.36

0.40

−0.26

0.05

3.63E-08

0.51

0.06

1.71E-19

0.08

0.10

0.02

0.10

0.08

FALSE

chr8:27599962:C:T

CLU

seq.4542.24

OID30732

D/N

P10909

0.12

0.16

0.66

0.10

5.66E-11

−1.51

0.12

2.61E-32

0.01

0.03

0.00

0.00

0.00

FALSE

chr19:15472052:C:T

PGLYRP2

seq.5601.2

OID30742

R/Q

Q96PD5

0.40

0.61

0.26

0.04

3.78E-12

−1.01

0.03

5.63E-199

0.21

0.17

0.26

0.28

0.19

FALSE

chr11:57614516:G:A

SERPING1**

seq.13710.6

OID30777

V/M

P05155

0.28

0.45

1.12

0.03

1.21E-217

−0.18

0.03

1.98E-08

0.20

0.11

0.14

0.13

0.28

FALSE

chr11:9748015:C:G

SWAP70

seq.13552.7

OID31477

Q/E

Q9UH65

0.40

0.50

−0.52

0.03

8.05E-76

0.22

0.03

3.17E-16

0.41

0.49

0.38

0.57

0.33

FALSE

  1. Protein-altering variants (PAVs) significantly associated (credible-set lead variant p < 5 × 10−8, traditional genome-wide significance threshold) with protein measures in cis- on both SomaScan and Olink, with different directions of effect across platforms, for all probe pairs measuring a protein measured on both platforms. 15 PAVs were found in main analyses (considering one probe per platform for each protein), while 3 platform-discordant PAV associations were found only when considering all probes targeting a protein measured on both platforms (marked with **). pQTL summary statistics were generated with linear regression under an additive model (two-sided test of significance). Ancestry-differentiated allele frequencies were determined according to the Chi-square test (one-sided) using allele frequencies derived in each contributing ancestry group (significant difference in allele frequencies across ancestries defined as a X2 value in or above the 75th percentile).
  2. AFR African, AMR Admixed American, EAS East Asian, EUR European Ancestry.
  3. *Amino acid changes encoded by the PAV, as obtained from Variant Effect Predictor.
  4. **Indicates proteins with a platform-discordant PAV association found only when considering all probes targeting a protein measured on both platforms.
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