Table 3 Summary of pQTL signals identified by platform

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

  

SomaScan

Olink

cis-pQTL

Total N probes/UniProt IDs assesseda

2157

2157

N UniProt IDs with a significant cis-pQTL credible set

840

1036

Number of credible sets

1476

1779

Positive directions of effect

659

748

Negative directions of effect

817

1031

Containing PAVb (for protein-encoding gene)

292

359

Containing ancestry-differentiatedc PAV

74

84

Containing GTEx cis-eQTL for protein-encoding gene

459

587

deCODE cis-pQTL in region

1156

1163

UKB cis-pQTL in region

1375

1753

Containing MS-pQTLd lead variant

7

11

MS-pQTLd in region

49

78

Containing MS potential non-abundance QTLe lead variant

3

5

MS non-abundance QTLe in region

35

53

Containing GWAS catalog reported lead variant

1337

1779

trans-pQTL

N UniProt IDs with a significant trans-pQTL credible set (p < 1 × 10−11)

424

262

Number of credible sets

529

315

Positive directions of effect

341

182

Negative directions of effect

188

133

Containing PAV

200

65

Containing ancestry-differentiated variant

133

97

Maps to pleiotropic regionf

276

158

Maps to platform shared pleiotropic regiong

140

151

Maps to platform “specific” pleiotropic regionh

136

7

deCODE trans-pQTL in region

310

139

UKB trans-pQTL in region

172

279

Containing MS-pQTLd lead variant

1

1

MS-pQTLd for protein target in region

4

6

Containing MS- potential non-abundance QTLe lead variant

0

0

MS-potential non-abundance QTLe for protein target in region

0

0

  1. Significant cis-pQTL and trans-pQTL credible set characteristics and overlap with previously identified GTEx version 8 expression quantitative trait loci (eQTL)75, affinity-based pQTL identified in deCODE (n = 35,559)1 or UK BioBank (n = 54,219)5, mass-spectrometry based pQTL (MS-pQTL) and non-abundance MS-PAVs from the QMDiab Study (n = 345 participants)10 and/or from the Tarkin Study (n = 1260 participants)18 and GWAS catalog variants75. pQTL were generated with linear regression under an additive model (two-sided test of significance). cis-pQTL were considered significant at a traditional genome-wide significance p-value threshold (p < 5 × 10−8). trans-pQTL were considered significant at a traditional genome-wide significance threshold further corrected for the 2708 probe pairs tested (p < 1 × 10−11). Signals (defined by credible sets) identified in the present study were compared to previously reported signals either with a signal level approach, in which we assessed overlap between previously reported lead variants and credible sets identified in the present study, or with a region-based approach, where we assessed whether previously reported lead variants fell within a 1 Megabase (Mb) window of the lead variants for the signals identified in the present study.
  2. aCounts correspond to results from one probe per UniProt ID.
  3. bPAV protein altering variant.
  4. cAncestry-differentiated = EAF X2 value in 75th percentile. Variants with ancestry-differentiated allele frequencies were determined with the Chi-square test using allele frequencies derived in each contributing ancestry group (significance defined as a X2 value in the 75th percentile, one-sided test).
  5. dPlasma mass-spectrometry (MS) pQTL lead variants were obtained from two previous studies10,18.
  6. ePlasma MS-potential non-abundance QTL lead variants were generated in the QMDiab study10 and are considered most likely to impact peptide measurements (and potentially, protein measurements), rather than circulating protein abundances.
  7. fPleiotropic regions are defined as signal regions collectively associated with at least 5 proteins on the platform.
  8. gPlatform-shared pleiotropic regions are defined as platform-overlapping regions associated with at least 5 proteins (but not necessarily the same proteins) on both platforms.
  9. hPlatform “specific” pleiotropic regions are defined as regions associated with at least 5 proteins on one platform, and 0 or 1 proteins on the other platform.
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