title: Systematic evaluation of genetic variants in three biological pathways on patient survival in low-stage non-small cell lung cancer.
abstract: BACKGROUND
  Studies from selected candidate genes suggest that single-nucleotide polymorphisms (SNPs) involved in glutathione metabolism, DNA repair, or inflammatory responses may affect overall survival (OS) in stages I to II or low-stage non-small cell lung cancer (LS-NSCLC); however, results are inconclusive. In this study, we took a systematic pathway-based approach to simultaneously evaluate the impact of genetic variation from these three pathways on OS after LS-NSCLC diagnosis.
  
  
  METHODS
  DNA from 647 patients with LS-NSCLC was genotyped for 480 SNPs (tag-SNPs) tagging 57 genes from the three candidate pathways. Associations of tag-SNPs with OS were assessed at the individual SNP and whole gene levels, adjusting for age, tumor stage, surgery type, and adjuvant therapy. The genotype combinations of the SNPs associated with OS were also estimated.
  
  
  RESULTS
  Among the 412 tag-SNPs that were successfully genotyped and passed quality assessments, 28 showed association with OS (p < 0.05). Two of the 28 were estimated to have less than a 20% chance of being false positives (rs3768490 in GSTM5: p = 1.32 × 10, q = 0.06; rs1729786 in ABCC4: p = 9.25 × 10, q = 0.20). Gene-based analysis suggested that in addition to GSTM5 and ABCC4, variation in two other genes, PTGS2 and GSTA2, was also associated with OS.
  
  
  CONCLUSIONS
  We describe further evidence that variations in genes involved in the glutathione and inflammatory response pathways are associated with OS in patients with LS-NSCLC. Further studies are warranted to verify our findings and elucidate their functional mechanisms and clinical utility leading to improved survival for patients with lung cancer.
authors.affiliation: Division of Biomedical Statistics and Informatics, Jinling Hospital, Nanjing University, School of Medicine, Nanjing, People's Republic of China.
authors.forename: V Shane
authors.initials: VS
authors.lastname: Pankratz
authors.forename: Zhifu
authors.initials: Z
authors.lastname: Sun
authors.forename: Jeremiah
authors.initials: J
authors.lastname: Aakre
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Cassandra
authors.initials: C
authors.lastname: Johnson
authors.forename: Yolanda I
authors.initials: YI
authors.lastname: Garces
authors.forename: Marie C
authors.initials: MC
authors.lastname: Aubry
authors.forename: Julian R
authors.initials: JR
authors.lastname: Molina
authors.forename: Dennis A
authors.initials: DA
authors.lastname: Wigle
authors.forename: Ping
authors.initials: P
authors.lastname: Yang
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000401:mortality; D000368:Aged; D014408:Biomarkers, Tumor / Q000235:genetics*; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000401:mortality*; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000401:mortality; D051546:Cyclooxygenase 2 / Q000235:genetics; D004260:DNA Repair / Q000235:genetics; D004273:DNA, Neoplasm / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D005838:Genotype; D005978:Glutathione / Q000378:metabolism; D005982:Glutathione Transferase / Q000235:genetics; D006801:Humans; D007527:Isoenzymes / Q000235:genetics; D008297:Male; D015233:Models, Statistical; D027425:ATP-Binding Cassette, Sub-Family C Proteins / Q000235:genetics; D009367:Neoplasm Staging; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011379:Prognosis; D012307:Risk Factors; D015996:Survival Rate
chemical_list: D014408:Biomarkers, Tumor; D051546:Cyclooxygenase 2; D004273:DNA, Neoplasm; D005978:Glutathione; D005982:Glutathione Transferase; D007527:Isoenzymes; D027425:ATP-Binding Cassette, Sub-Family C Proteins; C073492:ABCC4 protein, human; C496540:PTGS2 protein, human; C524366:GSTM5 protein, human; C119995:glutathione S-transferase alpha