Table 1 Genes associated with cSCC in the discovery-validation TWAS

From: Gene expression imputation identifies candidate genes and susceptibility loci associated with cutaneous squamous cell carcinoma

   

PrediXcan

Kaiser GERA analysis

23andMe analysis

Locus

Gene

Tissue

R 2

P-value

Beta

Beta SE

P-value

Beta

Beta SE

A. Novel loci

 1q21

CTSS

LCLs

0.397

9.68E-06

−0.106

0.024

4.85E-08

−0.065

0.012

 

HORMAD1

Skin (sun-exp)

0.541

8.59E-05

−0.086

0.022

4.68E-04

−0.038

0.011

 

GOLPH3L

Skin (sun-exp)

0.446

8.83E-05

−0.094

0.024

5.09E-04

−0.041

0.012

 

ANXA9

Skin (sun-exp)

0.203

5.12E-04

−0.111

0.032

7.51E-04

−0.053

0.016

 2q33

CASP8

Skin (sun-exp)

0.413

1.85E-04

−0.097

0.026

1.12E-08

−0.073

0.013

  

Skin (non-sun-exp)

0.401

2.58E-04

−0.101

0.028

1.60E-07

−0.071

0.014

 6q23

AHI1

Skin (sun-exp)

0.493

4.79E-04

0.077

0.022

1.65E-05

0.046

0.011

  

Skin (non-sun-exp)

0.473

7.25E-04

0.076

0.022

1.74E-05

0.047

0.011

  

LCLs

0.276

1.24E-03

0.085

0.026

2.56E-04

0.046

0.013

 12q23

HAL

Skin (sun-exp)

0.439

9.98E-04

−0.079

0.024

6.83E-08

−0.064

0.012

  

Skin (non-sun-exp)

0.314

1.53E-03

−0.085

0.027

5.63E-07

−0.066

0.013

 17q21

ORMDL3

LCLs

0.577

2.50E-04

0.081

0.022

9.49E-04

0.036

0.011

B. Previously associated loci

 6p21

HLA-DOB

Whole blood

0.439

3.77E-04

−0.079

0.022

3.38E-06

−0.051

0.011

 

SKIV2L

Whole blood

0.259

8.20E-06

−0.143

0.032

3.58E-04

−0.056

0.016

 

HLA-DRB5

Whole blood

0.592

4.03E-05

−0.081

0.020

9.98E-04

−0.037

0.011

 15q13

HERC2

Whole blood

0.357

1.52E-04

−0.106

0.028

2.69E-12

−0.097

0.014

 16q24

CDK10

Skin (non-sun-exp)

0.383

5.57E-34

−0.281

0.023

5.02E-81

−0.209

0.011

  

Skin (sun-exp)

0.396

2.02E-23

−0.264

0.026

4.77E-58

−0.212

0.013

  

LCLs

0.208

1.71E-22

−0.295

0.030

6.58E-63

−0.245

0.015

  

Whole blood

0.423

9.09E-22

−0.213

0.022

1.14E-60

−0.176

0.011

 

FANCA

LCLs

0.207

7.19E-11

−0.238

0.037

4.12E-31

−0.201

0.017

 20q11

FAM83C

Skin (non-sun-exp)

0.215

2.80E-05

0.164

0.039

4.05E-13

0.133

0.018

  1. Results from the TWAS discovery phase (Kaiser GERA analysis) and validation phase (23andMe analysis) are shown for all validated genes associated with cSCC.
  2. R2, squared correlation coefficient for the prediXcan imputation model; P-value, from Wald test; Beta SE, standard error in effect size (beta); exp, exposed
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