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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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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Related Experiment Video

Updated: Dec 2, 2025

Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
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Genome-Wide Search for SNP Interactions in GWAS Data: Algorithm, Feasibility, Replication Using Schizophrenia

Kwan-Yeung Lee1, Kwong-Sak Leung1, Suk Ling Ma2

  • 1Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.

Frontiers in Genetics
|November 2, 2020
PubMed
Summary

This study explored gene-gene interactions in schizophrenia susceptibility using genome-wide association study (GWAS) data. It identified novel interactions, particularly between protein-coding genes and non-coding RNAs, offering new insights into schizophrenia genetics.

Keywords:
GWASexhaustive searchgene–lncRNA interactionsschizophreniasecond order SNP–SNP interaction

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Area of Science:

  • Genetics
  • Neuroscience
  • Bioinformatics

Background:

  • Schizophrenia is a complex psychiatric disorder with a significant genetic component.
  • Understanding gene-gene interactions is crucial for elucidating schizophrenia's etiology.
  • Previous research has primarily focused on protein-protein interactions.

Purpose of the Study:

  • To identify novel single nucleotide polymorphism (SNP)-SNP interactions associated with schizophrenia susceptibility.
  • To explore gene-gene interactions beyond protein-protein interactions, including those involving non-coding RNAs.
  • To validate identified interactions using independent datasets.

Main Methods:

  • Utilized a recently developed algorithm for exhaustive SNP-SNP interaction analysis across three genome-wide association study (GWAS) datasets.
  • Screened 729,454 SNPs for pairwise interactions under dominant-dominant or recessive-recessive modes.
  • Performed replication analysis on top interaction SNP pairs in independent datasets.

Main Results:

  • Identified significant SNP-SNP interactions, with a notable proportion involving protein-coding genes partnered with non-coding RNAs (ncRNAs).
  • Confirmed enrichment of signals over noise in the top 10,000 interactions.
  • Replicated 14 SNP-pairs, including a specific interaction between FHIT and LINC00969 SNPs, both expressed in the brain.

Conclusions:

  • The study provides novel insights into genetic interactions in schizophrenia, highlighting the role of ncRNAs.
  • Identified replicable SNP-SNP interactions suggest a new avenue for understanding schizophrenia's genetic architecture.
  • This exhaustive analysis of GWAS data represents an early attempt to uncover complex genetic interactions in schizophrenia.