Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan

Yan Shen Shan; Li Tzong Chen; Jin Shang Wu; Yin Fan Chang; Chih Ting Lee; Chih Hsing Wu; Nai Jung Chiang; Hsin En Huang; Chia Jui Yen; Ying Jui Chao; Hui Jen Tsai; Chiung Yu Chen; Jui Wen Kang; Chin Fu Kuo; Chia Rung Tsai; Ya Ling Weng; Han Chien Yang; Hui Chin Liu; Jeffrey S. Chang

doi:10.1186/s12929-020-00664-9

Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan

Yan Shen Shan, Li Tzong Chen, Jin Shang Wu, Yin Fan Chang, Chih Ting Lee, Chih Hsing Wu, Nai Jung Chiang, Hsin En Huang, Chia Jui Yen, Ying Jui Chao, Hui Jen Tsai, Chiung Yu Chen, Jui Wen Kang, Chin Fu Kuo, Chia Rung Tsai, Ya Ling Weng, Han Chien Yang, Hui Chin Liu, Jeffrey S. Chang

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Abstract

Background: Due to differences in genetic background, it is unclear whether the genetic loci identified by the previous genome-wide association studies (GWAS) of pancreatic cancer also play significant roles in the development of pancreatic cancer among the Taiwanese population. Methods: This study aimed to validate the 25 pancreatic cancer GWAS-identified single nucleotide polymorphisms (SNPs) in a case-control study (278 cases and 658 controls) of pancreatic cancer conducted in Taiwan. Statistical analyses were conducted to determine the associations between the GWAS-identified SNPs and pancreatic cancer risk. Gene-environment interaction analysis was conducted to evaluate the interactions between SNPs and environmental factors on pancreatic cancer risk. Results: Among the 25 GWAS-identified SNPs, 7 (rs2816938 (~ 11 kb upstream of NR5A2), rs10094872 (~ 28 kb upstream of MYC), rs9581943 (200 bp upstream of PDX1) and 4 chromosome 13q22.1 SNPs: rs4885093, rs9573163, rs9543325, rs9573166) showed a statistically significant association with pancreatic cancer risk in the current study. Additional analyses showed two significant gene-environment interactions (between poor oral hygiene and NR5A2 rs2816938 and between obesity and PDX1 rs9581943) on the risk of pancreatic cancer. Conclusions: The current study confirmed the associations between 7 of the 25 GWAS-identified SNPs and pancreatic risk among the Taiwanese population. Furthermore, pancreatic cancer was jointly influenced by lifestyle and medical factors, genetic polymorphisms, and gene-environment interaction. Additional GWAS is needed to determine the genetic polymorphisms that are more relevant to the pancreatic cancer cases occurring in Taiwan.

Original language	English
Article number	69
Journal	Journal of biomedical science
Volume	27
Issue number	1
DOIs	https://doi.org/10.1186/s12929-020-00664-9
Publication status	Published - 2020 May 26

All Science Journal Classification (ASJC) codes

Endocrinology, Diabetes and Metabolism
Molecular Biology
Clinical Biochemistry
Cell Biology
Biochemistry, medical
Pharmacology (medical)

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Shan, Y. S., Chen, L. T., Wu, J. S., Chang, Y. F., Lee, C. T., Wu, C. H., Chiang, N. J., Huang, H. E., Yen, C. J., Chao, Y. J., Tsai, H. J., Chen, C. Y., Kang, J. W., Kuo, C. F., Tsai, C. R., Weng, Y. L., Yang, H. C., Liu, H. C., & Chang, J. S. (2020). Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan. Journal of biomedical science, 27(1), Article 69. https://doi.org/10.1186/s12929-020-00664-9

@article{ce91b09c9b8240db8ed875ed2574c003,

title = "Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan",

abstract = "Background: Due to differences in genetic background, it is unclear whether the genetic loci identified by the previous genome-wide association studies (GWAS) of pancreatic cancer also play significant roles in the development of pancreatic cancer among the Taiwanese population. Methods: This study aimed to validate the 25 pancreatic cancer GWAS-identified single nucleotide polymorphisms (SNPs) in a case-control study (278 cases and 658 controls) of pancreatic cancer conducted in Taiwan. Statistical analyses were conducted to determine the associations between the GWAS-identified SNPs and pancreatic cancer risk. Gene-environment interaction analysis was conducted to evaluate the interactions between SNPs and environmental factors on pancreatic cancer risk. Results: Among the 25 GWAS-identified SNPs, 7 (rs2816938 (~ 11 kb upstream of NR5A2), rs10094872 (~ 28 kb upstream of MYC), rs9581943 (200 bp upstream of PDX1) and 4 chromosome 13q22.1 SNPs: rs4885093, rs9573163, rs9543325, rs9573166) showed a statistically significant association with pancreatic cancer risk in the current study. Additional analyses showed two significant gene-environment interactions (between poor oral hygiene and NR5A2 rs2816938 and between obesity and PDX1 rs9581943) on the risk of pancreatic cancer. Conclusions: The current study confirmed the associations between 7 of the 25 GWAS-identified SNPs and pancreatic risk among the Taiwanese population. Furthermore, pancreatic cancer was jointly influenced by lifestyle and medical factors, genetic polymorphisms, and gene-environment interaction. Additional GWAS is needed to determine the genetic polymorphisms that are more relevant to the pancreatic cancer cases occurring in Taiwan.",

author = "Shan, {Yan Shen} and Chen, {Li Tzong} and Wu, {Jin Shang} and Chang, {Yin Fan} and Lee, {Chih Ting} and Wu, {Chih Hsing} and Chiang, {Nai Jung} and Huang, {Hsin En} and Yen, {Chia Jui} and Chao, {Ying Jui} and Tsai, {Hui Jen} and Chen, {Chiung Yu} and Kang, {Jui Wen} and Kuo, {Chin Fu} and Tsai, {Chia Rung} and Weng, {Ya Ling} and Yang, {Han Chien} and Liu, {Hui Chin} and Chang, {Jeffrey S.}",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s).",

year = "2020",

month = may,

day = "26",

doi = "10.1186/s12929-020-00664-9",

language = "English",

volume = "27",

journal = "Journal of biomedical science",

issn = "1021-7770",

publisher = "BioMed Central",

number = "1",

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Shan, YS, Chen, LT, Wu, JS , Chang, YF , Lee, CT , Wu, CH, Chiang, NJ, Huang, HE , Yen, CJ , Chao, YJ, Tsai, HJ, Chen, CY , Kang, JW, Kuo, CF, Tsai, CR, Weng, YL, Yang, HC, Liu, HC & Chang, JS 2020, 'Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan', Journal of biomedical science, vol. 27, no. 1, 69. https://doi.org/10.1186/s12929-020-00664-9

TY - JOUR

T1 - Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan

AU - Shan, Yan Shen

AU - Chen, Li Tzong

AU - Wu, Jin Shang

AU - Chang, Yin Fan

AU - Lee, Chih Ting

AU - Wu, Chih Hsing

AU - Chiang, Nai Jung

AU - Huang, Hsin En

AU - Yen, Chia Jui

AU - Chao, Ying Jui

AU - Tsai, Hui Jen

AU - Chen, Chiung Yu

AU - Kang, Jui Wen

AU - Kuo, Chin Fu

AU - Tsai, Chia Rung

AU - Weng, Ya Ling

AU - Yang, Han Chien

AU - Liu, Hui Chin

AU - Chang, Jeffrey S.

PY - 2020/5/26

Y1 - 2020/5/26

N2 - Background: Due to differences in genetic background, it is unclear whether the genetic loci identified by the previous genome-wide association studies (GWAS) of pancreatic cancer also play significant roles in the development of pancreatic cancer among the Taiwanese population. Methods: This study aimed to validate the 25 pancreatic cancer GWAS-identified single nucleotide polymorphisms (SNPs) in a case-control study (278 cases and 658 controls) of pancreatic cancer conducted in Taiwan. Statistical analyses were conducted to determine the associations between the GWAS-identified SNPs and pancreatic cancer risk. Gene-environment interaction analysis was conducted to evaluate the interactions between SNPs and environmental factors on pancreatic cancer risk. Results: Among the 25 GWAS-identified SNPs, 7 (rs2816938 (~ 11 kb upstream of NR5A2), rs10094872 (~ 28 kb upstream of MYC), rs9581943 (200 bp upstream of PDX1) and 4 chromosome 13q22.1 SNPs: rs4885093, rs9573163, rs9543325, rs9573166) showed a statistically significant association with pancreatic cancer risk in the current study. Additional analyses showed two significant gene-environment interactions (between poor oral hygiene and NR5A2 rs2816938 and between obesity and PDX1 rs9581943) on the risk of pancreatic cancer. Conclusions: The current study confirmed the associations between 7 of the 25 GWAS-identified SNPs and pancreatic risk among the Taiwanese population. Furthermore, pancreatic cancer was jointly influenced by lifestyle and medical factors, genetic polymorphisms, and gene-environment interaction. Additional GWAS is needed to determine the genetic polymorphisms that are more relevant to the pancreatic cancer cases occurring in Taiwan.

AB - Background: Due to differences in genetic background, it is unclear whether the genetic loci identified by the previous genome-wide association studies (GWAS) of pancreatic cancer also play significant roles in the development of pancreatic cancer among the Taiwanese population. Methods: This study aimed to validate the 25 pancreatic cancer GWAS-identified single nucleotide polymorphisms (SNPs) in a case-control study (278 cases and 658 controls) of pancreatic cancer conducted in Taiwan. Statistical analyses were conducted to determine the associations between the GWAS-identified SNPs and pancreatic cancer risk. Gene-environment interaction analysis was conducted to evaluate the interactions between SNPs and environmental factors on pancreatic cancer risk. Results: Among the 25 GWAS-identified SNPs, 7 (rs2816938 (~ 11 kb upstream of NR5A2), rs10094872 (~ 28 kb upstream of MYC), rs9581943 (200 bp upstream of PDX1) and 4 chromosome 13q22.1 SNPs: rs4885093, rs9573163, rs9543325, rs9573166) showed a statistically significant association with pancreatic cancer risk in the current study. Additional analyses showed two significant gene-environment interactions (between poor oral hygiene and NR5A2 rs2816938 and between obesity and PDX1 rs9581943) on the risk of pancreatic cancer. Conclusions: The current study confirmed the associations between 7 of the 25 GWAS-identified SNPs and pancreatic risk among the Taiwanese population. Furthermore, pancreatic cancer was jointly influenced by lifestyle and medical factors, genetic polymorphisms, and gene-environment interaction. Additional GWAS is needed to determine the genetic polymorphisms that are more relevant to the pancreatic cancer cases occurring in Taiwan.

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UR - http://www.scopus.com/inward/citedby.url?scp=85085420120&partnerID=8YFLogxK

U2 - 10.1186/s12929-020-00664-9

DO - 10.1186/s12929-020-00664-9

M3 - Article

C2 - 32456644

AN - SCOPUS:85085420120

SN - 1021-7770

VL - 27

JO - Journal of biomedical science

JF - Journal of biomedical science

IS - 1

M1 - 69

ER -

Validation of genome-wide association study-identified single nucleotide polymorphisms in a case-control study of pancreatic cancer from Taiwan

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