Table 1 Characterization of cis-pQTL status for proteins with heterogeneous inter-platform correlation estimates by ancestry

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

Category

N

cis-

pQTL

PAV cis-pQTL

Ancestry-differentiated cis-pQTL

Ancestry-differentiated

PAV

cis-pQTL

Trans-pQTL

Ancestry-differentiated

trans-pQTL

Cis+ trans-pQTL

Ancestry-differentiated cis+trans-pQTL

All proteins

2157

1239 (57%)

425 (20%)

563

(26%)

119

(5.5%)

605

(28%)

190

(8.8%)

348

(16%)

58

(2.7%)

Proteins with ancestry-heterogeneous

inter-platform correlation estimates

Nominal significance (p < 0.05)

611

417

(68%)

150 (25%)

228

(37%)

58

(9.5%)

166

(27%)

54

(8.8%)

115

(19%)

25

(4%)

Bonferroni significance (p < 0.05/2708)

80

69

(86%)

31 (39%)

45

(56%)

13

(16%)

29

(36%)

16

(20%)

24

(30%)

10

(13%)

  1. Counts of proteins with nominal (p < 0.05) and Bonferroni significant (Cochran’s Q p < 0.05/2,708, with correction for 2708 probe pairs tested) differences in inter-platform correlation estimates across ancestries according to the Cochran’s Q test of heterogeneity (rows, one-sided test of significance) and proteins which associate with a cis-pQTL, a cis-pQTL driven by a protein altering variant (PAV), a cis-pQTL with ancestry-differentiated effect allele frequencies, a PAV-driven cis-pQTL with ancestry-differentiated effect allele frequencies, a trans-pQTL, an ancestry-differentiated trans-pQTL, a cis- and trans-pQTL, or an ancestry-differentiated cis- and trans-pQTL on either platform (columns). pQTL were generated with linear regression under an additive model (two-sided test of significance). Variants with ancestry-differentiated allele frequencies were determined according to the Chi-square test (one-sided test) using allele frequencies derived in each contributing ancestry group (significance defined as a X2 value in the 75th percentile). Counts displayed reflect one probe per UniProt ID.
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