Identification of Gene Regulatory Variations Affecting Nasopharyngeal Carcinoma Susceptibility

Project: National Science and Technology CouncilNational Science and Technology Council Academic Grants

Project Details

Abstract

Large‐scale genome‐wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) genotyping have successfully applied in various complex diseases and thousands of significant SNPs were identified. However, how those inherited genetic variations affect disease status through influencing subsequent biological process is still unknown. The study of how genetic variations affect gene expression, also known as expression quantitative trait loci (eQTL) mapping, provides a possible answer. Compared to other marginal associated SNPs, eQTL SNPs are more likely to carry true association signals of a disease. Evidences have demonstrated genotypes of SNPs might influence downstream gene expression and the clinical outcome of cancer patients. Therefore, systematic investigation of eQTLs in combination of GWAS results will be a key component of understanding the genetic effect of tumourigenesis and may also serve as a prognostic predictor in clinical applications. Recently, we have performed a successful GWAS study in NPC. To further investigate how those inherited variations affect disease status through influence of gene expression, we propose to identify NPC susceptible eQTLs through investigation of transcriptome and whole genome sequencing in same NPC patient group while in combination of NPC susceptible information from our previous GWAS study. In addition to eQTL mapping, taking the advantage of the next generation sequencing (NGS) technology, we can also use the RNA‐Seq data to investigate splicing events and somatic mutations that cannot be achieved by traditional microarray assay. Therefore, in this proposal we intend to accomplish the following specific aims in next three years: Aim 1. To discover potential bio‐signatures in NPC through whole transcriptom analysis Aim 2. To discover mutation profiles in NPC through exon somatic mutation analysis Aim 3. To discover susceptible gene regulatory variations in NPC through eQTL analysis

Project IDs

Project ID:PC10301-1144
External Project ID:NSC101-2314-B182-051-MY3
StatusFinished
Effective start/end date01/08/1431/07/15

Keywords

  • nasopharyngeal carcinoma
  • gene regulatory variation
  • expression quantitative trait loci

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