Association analysis of driver-gene related genetic variants identified novel lung cancer susceptibility loci with 20,871 lung cancer cases and 15,971 controls

Yuzhuo Wang, Olga Y Gorlova, Ivan P Gorlov, Meng Zhu, Juncheng Dai, Demetrius Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Gary E Goodman, Stig E Bojesen, Maria Teresa Landi, Mattias Johansson, Angela Risch, Heunz-Erich Wichmann, Heike Bickeböller, David C Christiani, Gad Rennert, Susanne M Arnold, Paul BrennanJohn K Field, Sanjay Shete, Loic Le Marchand, Olle Melander, Hans Brunnström, Geoffrey Liu, Rayjean J Hung, Angeline S Andrew, Lambertus A Kiemeney, Shanbeh Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil E Caporaso, Penella J Woll, Philip Lazarus, Matthew B Schabath, Melinda C Aldrich, Victoria L Stevens, Hongxia Ma, Guangfu Jin, Zhibin Hu, Christopher I Amos, Hongbing Shen

Research output: Contribution to journalArticle

Abstract

BACKGROUND: A substantial proportion of cancer driver genes (CDGs) are also cancer predisposition genes. However, the associations between genetic variants in lung CDGs and the susceptibility to lung cancer have rarely been investigated.

METHODS: We selected expression-related single nucleotide polymorphisms (eSNPs) and nonsynonymous variants of lung CDGs, and tested their associations with lung cancer risk in two large-scale genome-wide association studies (20,871 cases and 15,971 controls of European descent). Conditional and joint association analysis was performed to identify independent risk variants. The associations of independent risk variants with somatic alterations in lung CDGs or recurrently altered pathways were investigated using data from The Cancer Genome Atlas (TCGA) project.

RESULTS: We identified seven independent SNPs in five lung CDGs that were consistently associated with lung cancer risk in discovery (P < 0.001) and validation (P < 0.05) stages. Among these loci, rs78062588 in TPM3 (1q21.3) was a new lung cancer susceptibility locus (OR = 0.86, P = 1.65×10-6). Subgroup analysis by histological types further identified nine lung CDGs. Analysis of somatic alterations found that, in lung adenocarcinomas, rs78062588[C] allele (TPM3 in 1q21.3) was associated with elevated somatic copy number of TPM3 (OR = 1.16, P = 0.02). In lung adenocarcinomas, rs1611182 (HLA-A in 6p22.1) was associated with truncation mutations of the transcriptional misregulation in cancer pathway (OR = 0.66, P = 1.76×10-3).

CONCLUSIONS: Genetic variants can regulate functions of lung CDGs and influence lung cancer susceptibility.

IMPACT: Our findings might help unravel biological mechanisms underlying lung cancer susceptibility.

Original languageEnglish
JournalCancer Epidemiology Biomarkers and Prevention
DOIs
Publication statusE-pub ahead of print - 10 Apr 2020

Bibliographical note

Copyright ©2020, American Association for Cancer Research.

Fields of Science and Technology Classification 2012

  • 106 Biology

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