Role of novel and GWAS originated PLCE1 genetic variants in susceptibility and prognosis of esophageal cancer patients in northern Indian population

Meenakshi Umar, Rohit Upadhyay, Shaleen Kumar, Uday Chand Ghoshal, Balraj Mittal

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Recent genome-wide association studies (GWAS) have identified variants in phospholipase C epsilon1 (PLCE1) as novel susceptibility markers for esophageal squamous cell carcinoma (ESCC) in Chinese population. Although few studies have replicated this findings in other populations, but results are contradictory. So, we aimed to replicate association of two previously reported non-synonymous polymorphisms (rs2274223A>G and rs3765524C>T) from haplotype block 10 and evaluated a novel variant (rs7922612C>T) from haplotype block 2 of PLCE1 with susceptibility and prognosis of ESCC in northern Indian population. The genotyping of PLCE1 variants were performed in 293 histopathologically confirmed incident ESCC cases (including 177 follow-up cases) and 314 age-, gender-, and ethnicity-matched controls using PCR RFLP. All statistical analyses were performed through SPSS version 15.0. Modeling and functional prediction of two non-synonymous variants were carried out using bioinformatics tools. PLCE1 polymorphisms were not associated with susceptibility to ESCC or its clinical phenotypes (tumor location/lymph node metastasis). No interaction with environmental risk factors was found. In silico analysis suggested negligible effect on structure of PLCE1 protein due to PLCE1 rs2274223 (H1927R) and rs3765524 (T1777I) polymorphisms. Survival analysis showed PLCE1 rs7922612CT + TT genotype conferred adverse outcome to ESCC patients. Our study for the first time suggests that GWAS originated PLCE1 variants do not have independent role in susceptibility of ESCC in northern Indian population; however, a novel haplo-tagging SNP rs7922612 may modify survival outcome of ESCC patients.

Original languageEnglish
Pages (from-to)11667-11676
Number of pages10
JournalTumor Biology
Volume35
Issue number11
DOIs
Publication statusPublished - 1 Jan 2014
Externally publishedYes

Fingerprint

Genome-Wide Association Study
Type C Phospholipases
Esophageal Neoplasms
Population
Haplotypes
Survival Analysis
Esophageal Squamous Cell Carcinoma
Computational Biology
Restriction Fragment Length Polymorphisms
Computer Simulation
Single Nucleotide Polymorphism
Lymph Nodes
Genotype
Neoplasm Metastasis
Phenotype
Polymerase Chain Reaction
Survival

Keywords

  • Esophageal cancer
  • PLCE1
  • Polymorphisms
  • Prognosis
  • RFLP

ASJC Scopus subject areas

  • Cancer Research

Cite this

Role of novel and GWAS originated PLCE1 genetic variants in susceptibility and prognosis of esophageal cancer patients in northern Indian population. / Umar, Meenakshi; Upadhyay, Rohit; Kumar, Shaleen; Ghoshal, Uday Chand; Mittal, Balraj.

In: Tumor Biology, Vol. 35, No. 11, 01.01.2014, p. 11667-11676.

Research output: Contribution to journalArticle

Umar, Meenakshi ; Upadhyay, Rohit ; Kumar, Shaleen ; Ghoshal, Uday Chand ; Mittal, Balraj. / Role of novel and GWAS originated PLCE1 genetic variants in susceptibility and prognosis of esophageal cancer patients in northern Indian population. In: Tumor Biology. 2014 ; Vol. 35, No. 11. pp. 11667-11676.
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