Genetic variants and risk of gastric cancer: a pathway analysis of a genome-wide association study

SpringerPlus

Volumn 4, Issue 1, 2015, Pages

  Lee, Ju Han ^a   Kim, Younghye ^a   Choi, Jung Woo ^a   Kim, Young Sik ^a  

^a Korea University   (South Korea)

Author keywords

Gastric cancer; Genome wide association study; Pathway based analysis

Indexed keywords

EID: 84929340032     PISSN: None     EISSN: 21931801     Source Type: Journal    
DOI: 10.1186/s40064-015-1005-8     Document Type: Article

References (27)

1. Abnet CC, Freedman ND, Hu N, Wang Z, Yu K, Shu XO, Yuan JM, Zheng W, Dawsey SM, Dong LM, Lee MP, Ding T, Qiao YL, Gao YT, Koh WP, Xiang YB, Tang ZZ, Fan JH, Wang C, Wheeler W, Gail MH, Yeager M, Yuenger J, Hutchinson A, Jacobs KB, Giffen CA, Burdett L, Fraumeni JF Jr, Tucker MA, Chow WH et al (2010) A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma. Nat Genet 42(9):764–767, doi:10.1038/ng.649
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29, doi:10.1038/75556
3. Bunney TD, Baxendale RW, Katan M (2009) Regulatory links between PLC enzymes and Ras superfamily GTPases: signalling via PLCepsilon. Adv Enzyme Regul 49(1):54–58, doi:10.1016/j.advenzreg.2009.01.004
4. Elbers CC, van Eijk KR, Franke L, Mulder F, van der Schouw YT, Wijmenga C, Onland-Moret NC (2009) Using genome-wide pathway analysis to unravel the etiology of complex diseases. Genet Epidemiol 33(5):419–431, doi:10.1002/gepi.20395
5. Gusella M, Bertolaso L, Bolzonella C, Pasini F, Padrini R (2011) Frequency of uridine monophosphate synthase Gly(213)Ala polymorphism in Caucasian gastrointestinal cancer patients and healthy subjects, investigated by means of new, rapid genotyping assays. Genet Test Mol Biomarkers 15(10):691–695, doi:10.1089/gtmb.2011.0021
6. Hohenberger P, Gretschel S (2003) Gastric cancer. Lancet 362(9380):305–315, doi:S014067360313975X
7. Jia P, Wang L, Meltzer HY, Zhao Z (2011) Pathway-based analysis of GWAS datasets: effective but caution required. Int J Neuropsychopharmacol 14(4):567–572, doi:10.1017/S1461145710001446
8. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38(Database issue):D355–D360, doi:10.1093/nar/gkp896
9. Kupcinskas J, Wex T, Link A, Bartuseviciute R, Dedelaite M, Kevalaite G, Leja M, Skieceviciene J, Kiudelis G, Jonaitis L, Kupcinskas L, Malfertheiner P (2014) PSCA and MUC1 gene polymorphisms are linked with gastric cancer and pre-malignant gastric conditions. Anticancer Res 34(12):7167–7175
10. Lambert JC, Grenier-Boley B, Chouraki V, Heath S, Zelenika D, Fievet N, Hannequin D, Pasquier F, Hanon O, Brice A, Epelbaum J, Berr C, Dartigues JF, Tzourio C, Campion D, Lathrop M, Amouyel P (2010) Implication of the immune system in Alzheimer’s disease: evidence from genome-wide pathway analysis. J Alzheimers Dis 20(4):1107–1118, doi:10.3233/JAD-2010-100018
11. Li Y, Nie Y, Cao J, Tu S, Lin Y, Du Y (2012) G-A variant in miR-200c binding site of EFNA1 alters susceptibility to gastric cancer. Mol Carcinog. doi:10.1002/mc.21966
12. Li WQ, Hu N, Hyland PL, Gao Y, Wang ZM, Yu K, Su H, Wang CY, Wang LM, Chanock SJ, Burdett L, Ding T, Qiao YL, Fan JH, Wang Y, Xu Y, Shi JX, Gu F, Wheeler W, Xiong XQ, Giffen C, Tucker MA, Dawsey SM, Freedman ND, Abnet CC, Goldstein AM, Taylor PR (2013) Genetic variants in DNA repair pathway genes and risk of esophageal squamous cell carcinoma and gastric adenocarcinoma in a Chinese population. Carcinogenesis 34(7):1536–1542, doi:10.1093/carcin/bgt094
13. Luo D, Gao Y, Wang S, Wang M, Wu D, Wang W, Xu M, Zhou J, Gong W, Tan Y, Zhang Z (2011) Genetic variation in PLCE1 is associated with gastric cancer survival in a Chinese population. J Gastroenterol 46(11):1260–1266, doi:10.1007/s00535-011-0445-3
14. Manolio TA (2010) Genomewide association studies and assessment of the risk of disease. N Engl J Med 363(2):166–176, doi:10.1056/NEJMra0905980
15. Milne AN, Carneiro F, O’Morain C, Offerhaus GJ (2009) Nature meets nurture: molecular genetics of gastric cancer. Hum Genet 126(5):615–628, doi:10.1007/s00439-009-0722-x
16. Nakamura R, Kataoka H, Sato N, Kanamori M, Ihara M, Igarashi H, Ravshanov S, Wang YJ, Li ZY, Shimamura T, Kobayashi T, Konno H, Shinmura K, Tanaka M, Sugimura H (2005) EPHA2/EFNA1 expression in human gastric cancer. Cancer Sci 96(1):42–47, doi:10.1111/j.1349-7006.2005.00007.x
17. Palmer AJ, Lochhead P, Hold GL, Rabkin CS, Chow WH, Lissowska J, Vaughan TL, Berry S, Gammon M, Risch H, El-Omar EM (2012) Genetic variation in C20orf54, PLCE1 and MUC1 and the risk of upper gastrointestinal cancers in Caucasian populations. Eur J Cancer Prev 21(6):541–544, doi:10.1097/CEJ.0b013e3283529b79
18. Polk DB, Peek RM Jr (2010) Helicobacter pylori: gastric cancer and beyond. Nat Rev Cancer 10(6):403–414, doi:10.1038/nrc2857
19. Ramanan VK, Shen L, Moore JH, Saykin AJ (2012) Pathway analysis of genomic data: concepts, methods, and prospects for future development. Trends Genet 28(7):323–332, doi:10.1016/j.tig.2012.03.004
20. Rizzato C, Kato I, Plummer M, Muñoz N, Canzian F (2013) Genetic variation in PSCA and risk of gastric advanced preneoplastic lesions and cancer in relation to Helicobacter pylori infection. PLoS One 8(9):e73100, doi:10.1371/journal.pone.0073100
21. Sakamoto H, Yoshimura K, Saeki N, Katai H, Shimoda T, Matsuno Y, Saito D, Sugimura H, Tanioka F, Kato S, Matsukura N, Matsuda N, Nakamura T, Hyodo I, Nishina T, Yasui W, Hirose H, Hayashi M, Toshiro E, Ohnami S, Sekine A, Sato Y, Totsuka H, Ando M, Takemura R, Takahashi Y, Ohdaira M, Aoki K, Honmyo I, Chiku S et al (2008) Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer. Nat Genet 40(6):730–740, doi:10.1038/ng.152
22. Shi Y, Hu Z, Wu C, Dai J, Li H, Dong J, Wang M, Miao X, Zhou Y, Lu F, Zhang H, Hu L, Jiang Y, Li Z, Chu M, Ma H, Chen J, Jin G, Tan W, Wu T, Zhang Z, Lin D, Shen H (2011) A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1. Nat Genet 43(12):1215–1218, doi:10.1038/ng.978
23. Velayati A, Yu WH, Sidransky E (2010) The role of glucocerebrosidase mutations in Parkinson disease and Lewy body disorders. Curr Neurol Neurosci Rep 10(3):190–198, doi:10.1007/s11910-010-0102-x
24. Wang M, Zhang R, He J, Qiu L, Li J, Wang Y, Sun M, Yang Y, Wang J, Yang J, Qian J, Jin L, Ma H, Wei Q, Zhou X (2012) Potentially functional variants of PLCE1 identified by GWASs contribute to gastric adenocarcinoma susceptibility in an eastern Chinese population. PLoS One 7(3):e31932, doi:10.1371/journal.pone.0031932
25. Wykosky J, Debinski W (2008) The EphA2 receptor and ephrinA1 ligand in solid tumors: function and therapeutic targeting. Mol Cancer Res 6(12):1795–1806, doi:10.1158/1541-7786.MCR-08-0244
26. Zhang K, Chang S, Cui S, Guo L, Zhang L, Wang J (2011a) ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework. Nucleic Acids Res 39(Web Server issue):W437–W443, doi:10.1093/nar/gkr391
27. Zhang H, Jin G, Li H, Ren C, Ding Y, Zhang Q, Deng B, Wang J, Hu Z, Xu Y, Shen H (2011b) Genetic variants at 1q22 and 10q23 reproducibly associated with gastric cancer susceptibility in a Chinese population. Carcinogenesis 32(6):848–852, doi:10.1093/carcin/bgr051