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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.
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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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Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
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Related Experiment Video

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In Vivo Modeling of the Morbid Human Genome using Danio rerio
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Decoding non-coding SNPs: systems genomics modelling dissects the heterogeneity of IBD.

Dezső Módos1,2,3,4,5, John P Thomas2,6, Johanne Brooks-Warburton3,4,7,8

  • 1Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.

Molecular Systems Biology
|November 26, 2025
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Summary
This summary is machine-generated.

This study introduces a novel systems genomics approach to understand how genetic variations influence complex immune-mediated inflammatory disorders (IMIDs). The method links non-coding single-nucleotide polymorphisms (SNPs) to disease pathways, aiding precision medicine for conditions like Crohn's disease and ulcerative colitis.

Keywords:
Inflammatory Bowel DiseaseNetwork PropagationPrecision MedicineSingle-nucleotide PolymorphismsSystems Genomics

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Area of Science:

  • Genomics
  • Systems Biology
  • Immunology

Background:

  • Genome-wide association studies (GWAS) identify genetic loci for complex diseases like immune-mediated inflammatory disorders (IMIDs).
  • Interpreting the functional impact of non-coding single-nucleotide polymorphisms (SNPs) associated with IMIDs is challenging due to low effect sizes and polygenicity.
  • Understanding the link between genetic variations and disease mechanisms is crucial for developing effective treatments.

Purpose of the Study:

  • To develop and apply a novel systems genomics approach to model the cumulative impact of non-coding SNPs on cellular signaling and gene regulatory networks.
  • To investigate the pathomechanisms of Crohn's disease (CD) and ulcerative colitis (UC), forms of inflammatory bowel disease (IBD).
  • To bridge the gap between genotype and phenotype for advancing precision medicine in complex immune-mediated inflammatory disorders.

Main Methods:

  • A systems genomics approach was developed to model the cumulative effects of non-coding SNPs.
  • The approach was applied to analyze 2,636 patient genomes for Crohn's disease and ulcerative colitis.
  • Analysis focused on how SNP signals propagate through signaling and gene regulatory networks.

Main Results:

  • Non-coding SNPs were found to propagate signals towards known and novel pathogenic pathways in Crohn's disease and ulcerative colitis.
  • SNP-propagated gene regulatory networks successfully stratified patients into distinct clusters.
  • These clusters corresponded to cell type-specific gene dysregulation and predicted potential therapeutic responses.

Conclusions:

  • The novel systems genomics approach effectively links non-coding genetic variations to complex disease pathways.
  • This method provides a framework for understanding genotype-phenotype relationships in immune-mediated inflammatory disorders.
  • The findings lay the foundation for accelerating precision medicine strategies in complex immune-mediated inflammatory disorders.