Table 1 Novel GWAS loci

From: Multi-ancestry GWAS meta-analyses of lung cancer reveal susceptibility loci and elucidate smoking-independent genetic risk

Lung cancer subtype

rsID

Chromosome:

Position (hg19)

Candidate gene

EA/

NEA

EAF

Discovery P

Replication P

Combined meta-analysis OR (95% CI)

Combined meta-analysis P

Novel loci from the European ancestry GWAS meta-analysis

 Overall

rs77045810a

1:168,505,017

XCL2

A/C

0.89

1.43 × 10−10

5.72 × 10−3

1.09 (1.07, 1.12)

3.94 × 10−12

 Overall

rs144840030

3:117,147,326

LSAMP

T/G

0.01

1.09 × 10−8

0.487

1.26 (1.16, 1.37)

5.01 × 10−8

 Overall

rs62400619

5:152,343,053

NMUR2

T/C

0.68

6.33 × 10−9

0.156

1.05 (1.03, 1.07)

1.10 × 10−8

 Overall

rs9988980a

12:3,038,917

TULP3

T/C

0.39

5.34 × 10−8

2.16 × 10−3

1.05 (1.04, 1.07)

3.72 × 10−10

 LUAD

rs67824503a

8:129,535,264

MYC

T/C

0.75

1.81 × 10−8

5.05 × 10−5

1.10 (1.07, 1.14)

4.09 × 10−12

 LUAD

rs11855650a

15:70,431,773

TLE3

T/G

0.38

1.12 × 10−8

1.22 × 10−7

1.10 (1.07, 1.13)

1.15 × 10−14

 LUSC

rs36229791a

10:101,991,135

BLOC1S2

A/T

0.04

4.04 × 10−8

1.49 × 10−4

1.26 (1.18, 1.35)

2.48 × 10−11

Novel loci from the African ancestry GWAS

 Overall

rs78994068

12:127,225,803

LINC00944

C/A

0.01

1.87 × 10−9

0.901

1.76 (1.42, 2.17)

1.81 × 10−7

Novel loci from the multi-ancestry meta-analysis (not genome-wide significant in the European meta-analysis)

 Overall

rs329122a

5:133,864,599

JADE2

A/G

0.43

1.12 × 10−8

0.0529

0.96 (0.94, 0.97)

3.69 × 10−9

 Overall

rs7300571a

12:47,857,826

RPAP3

T/C

0.11

3.47 × 10−8

4.44 × 10−3

1.08 (1.06, 1.11)

6.48 × 10−10

Novel loci after conditioning the European ancestry GWAS meta-analysis on cigarettes per day

 Overall

rs1124241a

6:97,722,453

MMS22L

A/G

0.22

1.26 × 10−8

6.15 × 10−3

1.07 (1.05, 1.10)

3.39 × 10−10

 LUSC

rs61494113a

19:17,401,859

ABHD8

A/G

0.29

4.90 × 10−8

3.12 × 10−3

1.11 (1.08, 1.15)

6.39 × 10−10

  1. Novel genome-wide significant GWAS index variants for lung cancer risk in European-ancestry meta-analyses from MVP and ILCCO7 cohorts, MVP African ancestry, multi-ancestry meta-analyses, and in European-ancestry meta-analyses after conditioning on cigarettes per day. Replication of these novel variants was conducted in the external OncoArray dataset. Finally, we performed a combined meta-analysis of our discovery results with the OncoArray replication results. Discovery P-values were assessed for genome-wide significance (P < 5 × 10−8), replication using a nominal significance threshold (P < 0.05), and combined meta-analysis using the conservative threshold of P < 4.17 × 10−9 (5 × 10−8/12 total GWAS analyses). Significant alleles meeting this threshold after replication are indicated witha. All meta-analyses in this table refer to fixed-effect inverse variance-weighted meta-analysis.
  2. LUAD lung adenocarcinoma, LUSC squamous cell lung carcinoma, EA effect allele, NEA non-effect allele, EAF effect allele frequency in the given population, OR (95% CI) odds ratio and 95% confidence interval.
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