Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk
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Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk. / Dai, Juncheng; Huang, Mingtao; Amos, Christopher I.; Hung, Rayjean J.; Tardon, Adonina; Andrew, Angeline; Chen, Chu; Christiani, David C.; Albanes, Demetrius; Rennert, Gadi; Fan, Jingyi; Goodman, Gary; Liu, Geoffrey; Field, John K.; Grankvist, Kjell; Kiemeney, Lambertus A.; Le Marchand, Loic; Schabath, Matthew B.; Johansson, Mattias; Aldrich, Melinda C.; Johansson, Mikael; Caporaso, Neil; Lazarus, Philip; Lam, Stephan; Bojesen, Stig E.; Arnold, Susanne; Landi, Maria Teresa; Risch, Angela; Wichmann, H. Erich; Bickeboller, Heike; Brennan, Paul; Shete, Sanjay; Melander, Olle; Brunnstrom, Hans; Zienolddiny, Shan; Woll, Penella; Stevens, Victoria; Hu, Zhibin; Shen, Hongbing.
In: International Journal of Cancer, Vol. 146, No. 10, 2020, p. 2855-2864.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genome-wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk
AU - Dai, Juncheng
AU - Huang, Mingtao
AU - Amos, Christopher I.
AU - Hung, Rayjean J.
AU - Tardon, Adonina
AU - Andrew, Angeline
AU - Chen, Chu
AU - Christiani, David C.
AU - Albanes, Demetrius
AU - Rennert, Gadi
AU - Fan, Jingyi
AU - Goodman, Gary
AU - Liu, Geoffrey
AU - Field, John K.
AU - Grankvist, Kjell
AU - Kiemeney, Lambertus A.
AU - Le Marchand, Loic
AU - Schabath, Matthew B.
AU - Johansson, Mattias
AU - Aldrich, Melinda C.
AU - Johansson, Mikael
AU - Caporaso, Neil
AU - Lazarus, Philip
AU - Lam, Stephan
AU - Bojesen, Stig E.
AU - Arnold, Susanne
AU - Landi, Maria Teresa
AU - Risch, Angela
AU - Wichmann, H. Erich
AU - Bickeboller, Heike
AU - Brennan, Paul
AU - Shete, Sanjay
AU - Melander, Olle
AU - Brunnstrom, Hans
AU - Zienolddiny, Shan
AU - Woll, Penella
AU - Stevens, Victoria
AU - Hu, Zhibin
AU - Shen, Hongbing
PY - 2020
Y1 - 2020
N2 - Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple human diseases, including lung cancer. However, limited studies with large-scale samples have been available to systematically evaluate the effects of INDELs on lung cancer risk. Here, we performed a large-scale meta-analysis to evaluate INDELs and their risk for lung cancer in 23,202 cases and 19,048 controls. Functional annotations were performed to further explore the potential function of lung cancer risk INDELs. Conditional analysis was used to clarify the relationship between INDELs and SNPs. Four new risk loci were identified in genome-wide INDEL analysis (1p13.2: rs5777156, Insertion, OR = 0.92, p = 9.10 × 10−8; 4q28.2: rs58404727, Deletion, OR = 1.19, p = 5.25 × 10−7; 12p13.31: rs71450133, Deletion, OR = 1.09, p = 8.83 × 10−7; and 14q22.3: rs34057993, Deletion, OR = 0.90, p = 7.64 × 10−8). The eQTL analysis and functional annotation suggested that INDELs might affect lung cancer susceptibility by regulating the expression of target genes. After conducting conditional analysis on potential causal SNPs, the INDELs in the new loci were still nominally significant. Our findings indicate that INDELs could be potentially functional genetic variants for lung cancer risk. Further functional experiments are needed to better understand INDEL mechanisms in carcinogenesis.
AB - Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple human diseases, including lung cancer. However, limited studies with large-scale samples have been available to systematically evaluate the effects of INDELs on lung cancer risk. Here, we performed a large-scale meta-analysis to evaluate INDELs and their risk for lung cancer in 23,202 cases and 19,048 controls. Functional annotations were performed to further explore the potential function of lung cancer risk INDELs. Conditional analysis was used to clarify the relationship between INDELs and SNPs. Four new risk loci were identified in genome-wide INDEL analysis (1p13.2: rs5777156, Insertion, OR = 0.92, p = 9.10 × 10−8; 4q28.2: rs58404727, Deletion, OR = 1.19, p = 5.25 × 10−7; 12p13.31: rs71450133, Deletion, OR = 1.09, p = 8.83 × 10−7; and 14q22.3: rs34057993, Deletion, OR = 0.90, p = 7.64 × 10−8). The eQTL analysis and functional annotation suggested that INDELs might affect lung cancer susceptibility by regulating the expression of target genes. After conducting conditional analysis on potential causal SNPs, the INDELs in the new loci were still nominally significant. Our findings indicate that INDELs could be potentially functional genetic variants for lung cancer risk. Further functional experiments are needed to better understand INDEL mechanisms in carcinogenesis.
KW - genome-wide association studies
KW - INDELs
KW - lung cancer
UR - http://www.scopus.com/inward/record.url?scp=85074828493&partnerID=8YFLogxK
U2 - 10.1002/ijc.32698
DO - 10.1002/ijc.32698
M3 - Journal article
C2 - 31577861
AN - SCOPUS:85074828493
VL - 146
SP - 2855
EP - 2864
JO - International Journal of Cancer
JF - International Journal of Cancer
SN - 0020-7136
IS - 10
ER -
ID: 260201718