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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer.

Jun Zhong1, Ashley Jermusyk1, Lang Wu2

  • 1Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.

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This study identified novel genes and genetic locations linked to pancreatic cancer risk by analyzing gene expression and DNA data. These findings offer new targets for understanding and potentially treating pancreatic cancer.

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Area of Science:

  • Genetics
  • Oncology
  • Bioinformatics

Background:

  • Genome-wide association studies (GWAS) have identified 20 pancreatic cancer risk loci in European populations.
  • However, a significant portion of pancreatic cancer heritability remains unexplained, with responsible genes largely unknown.

Purpose of the Study:

  • To discover novel pancreatic cancer risk loci and potential causal genes.
  • To integrate genome-wide association studies (GWAS) with transcriptome-wide association studies (TWAS) for enhanced discovery.

Main Methods:

  • Performed a pancreatic cancer transcriptome-wide association study (TWAS) in Europeans using FUSION, MetaXcan, and Summary-MulTiXcan.
  • Integrated GWAS summary statistics (9,040 cases, 12,496 controls) with gene expression prediction models from normal pancreatic tissue and 48 other tissues.

Main Results:

  • Identified 25 genes significantly associated with pancreatic cancer risk (FDR < .05).
  • Discovered 14 candidate genes at 11 novel risk loci and 11 genes at six known risk loci.
  • 12 gene associations remained significant after Bonferroni correction, including CELA3B, SMC2, PNMT, TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1.

Conclusions:

  • Integrated gene expression and genotype data to identify novel pancreatic cancer risk loci.
  • Identified candidate functional genes that warrant further investigation for their role in pancreatic cancer development.