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
External Project ID:NSC101-2314-B182-051-MY3
Status | Finished |
---|---|
Effective start/end date | 01/08/14 → 31/07/15 |
Keywords
- nasopharyngeal carcinoma
- gene regulatory variation
- expression quantitative trait loci
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