Systematic evaluation of genetic variants in three biological pathways on patient survival in low-stage non-small cell lung cancer

V. Shane Pankratz, Zhifu D Sun, Jeremiah Aakre, Yan Li, Cassandra Johnson, Yolanda Isabel Garces, Marie C. Aubry, Julian R Molina, Dennis A Wigle, Ping Yang

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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 -4, q = 0.06; rs1729786 in ABCC4: p = 9.25 × 10 -4, 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.

Original languageEnglish (US)
Pages (from-to)1488-1495
Number of pages8
JournalJournal of Thoracic Oncology
Volume6
Issue number9
DOIs
StatePublished - Sep 2011

Fingerprint

Non-Small Cell Lung Carcinoma
Single Nucleotide Polymorphism
Survival
Genes
Glutathione
Cyclooxygenase 2
DNA Repair
Lung Neoplasms
Genotype
DNA
Neoplasms

Keywords

  • DNA repair
  • Genetic polymorphisms
  • Glutathione metabolism
  • Inflammation response
  • Non-small cell lung cancer
  • Survival analysis

ASJC Scopus subject areas

  • Oncology
  • Pulmonary and Respiratory Medicine

Cite this

Systematic evaluation of genetic variants in three biological pathways on patient survival in low-stage non-small cell lung cancer. / Pankratz, V. Shane; Sun, Zhifu D; Aakre, Jeremiah; Li, Yan; Johnson, Cassandra; Garces, Yolanda Isabel; Aubry, Marie C.; Molina, Julian R; Wigle, Dennis A; Yang, Ping.

In: Journal of Thoracic Oncology, Vol. 6, No. 9, 09.2011, p. 1488-1495.

Research output: Contribution to journalArticle

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abstract = "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 -4, q = 0.06; rs1729786 in ABCC4: p = 9.25 × 10 -4, 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.",
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