Fine mapping of chromosome 5p15.33 identifies novel lung cancer susceptibility loci in Han Chinese

Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer Genome wide association studies (GWASs) with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations. These were rs10054203 in TERT (resequencing: OR=1.69, p=2.70 x 10(-4); validation: OR=1.34, p=2.10 x 10(-23) for Asian, and OR=1.09, p=6.00 x 10(-3) for European), and rs397640 in CLPTM1L (resequencing: OR=0.37, p=1.19 x 10(-4); validation: OR=0.75, p=5.89 x 10(-8) for Asian, and OR=0.90, p=2.40 x 10(-2) for European). Expression quantitative trait loci analysis showed the risk allele (C) of rs10054203 was significantly associated with lower mRNA expression of CTD-2245Ef15.3 (p=0.019) and Tubulin Polymerization-Promoting Protein (TPPP, p=0.031) in 167 lung tissues. In conclusion, in this largest and first resequencing-based fine-mapping analysis of 5p15.33 region in Han Chinese, we identified two novel variants associated with lung cancer susceptibility. Further validation studies and functional work is required to confirm the roles of the newly discovered variants. What's new? While cigarette smoking continues to be the leading cause of lung cancer deaths in China, nearly one-sixth of patients have never smoked. Genetic factors likely influence lung cancer susceptibility in these individuals, and of particular interest are variants in TERT and CLPTM1L, genes located on chromosome 5p15.33, that appear to be linked to lung cancer in diverse populations. In this fine-mapping analysis of 5p15.33 in Han Chinese, two novel variants, one in TERT and the second in CLPTM1L, were identified and associated with lung cancer susceptibility. The variants were validated in genome-wide association studies in Asians and Europeans.