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Related Concept Videos

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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.
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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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Genome-Wide Association Analysis of Protein-Coding Variants in IgA Nephropathy.

Ming Li1,2,3, Yan-Na Wang1, Ling Wang4

  • 1Department of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.

Journal of the American Society of Nephrology : JASN
|October 3, 2023
PubMed
Summary

This study identified a rare variant in vascular endothelial growth factor A (VEGFA) significantly increasing IgA nephropathy risk. A common PKD1L3 variant was linked to lower haptoglobin levels, expanding the understanding of IgA nephropathy genetics.

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Area of Science:

  • Genetics
  • Nephrology
  • Molecular Biology

Background:

  • Genome-wide association studies (GWAS) have identified numerous IgA nephropathy (IgAN) susceptibility loci.
  • However, rare and low-frequency coding variants remain under-investigated in IgAN pathogenesis.

Purpose of the Study:

  • To investigate the role of rare and low-frequency coding variants in IgA nephropathy susceptibility.
  • To identify novel genetic variants associated with IgA nephropathy risk and progression.

Main Methods:

  • A large-scale, three-stage exome chip-based association study was conducted in Han Chinese individuals.
  • Sequencing analysis was employed to identify rare coding variants.
  • Molecular dynamic simulations were used to assess the impact of VEGFA mutations on protein structure and function.

Main Results:

  • A rare nonsynonymous variant in vascular endothelial growth factor A (VEGFA) was significantly associated with a two-fold increased risk of IgA nephropathy.
  • A common nonsynonymous variant in PKD1L3 was associated with lower haptoglobin protein levels.
  • The identified rare VEGFA variant demonstrated potential to alter protein structure and increase receptor binding, and was linked to increased IgAN progression risk.

Conclusions:

  • The study identified novel risk variants in VEGFA and PKD1L3, contributing to the understanding of IgA nephropathy genetic architecture.
  • These findings highlight the importance of investigating rare coding variants in complex diseases.