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Genome-wide Association Studies-GWAS01:11

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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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Sampling is a technique to select a portion (or subset) of the larger population and study that portion (the sample) to gain information about the population. The sampling method ensures that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest.
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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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Related Experiment Video

Updated: Jul 27, 2025

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Genome-wide association study stratified by

Konstantin Senkevich1,2, Sara Bandres-Ciga3, Alejandro Cisterna-García4

  • 1The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada.

Medrxiv : the Preprint Server for Health Sciences
|June 9, 2023
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Summary
This summary is machine-generated.

Researchers identified new genetic loci near EMP1 and VANGL1 associated with Parkinson's disease (PD) risk, depending on MAPT haplotype. Further studies are needed to confirm these Parkinson's disease genetic findings.

Keywords:
EMP1GWASMAPTParkinson’s diseaseVANGL1genetics

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Area of Science:

  • Neurogenetics
  • Genomics of neurodegenerative diseases

Background:

  • The MAPT locus plays a significant role in Parkinson's disease (PD) pathogenesis.
  • Genetic variations within or near MAPT can influence PD risk and progression.
  • Understanding how genetic factors modify MAPT's effect is crucial for identifying PD mechanisms.

Approach:

  • Genome-wide association studies (GWAS) were performed on stratified cohorts based on MAPT haplotypes (H1/H1 and H2).
  • Replication analyses were conducted using UK Biobank data.
  • Burden analyses investigated the association of rare variants in nominated genes with PD.

Key Points:

  • A novel locus near EMP1 was associated with PD in MAPT H1/H1 carriers (rs56312722).
  • A novel locus near VANGL1 was associated with PD in MAPT H2 carriers (rs11590278).
  • Rare EMP1 variants showed association with PD in MAPT H2 carriers, particularly the p.V11G variant.

Conclusions:

  • Identified potential novel genetic loci modifying PD risk associated with MAPT haplotypes.
  • Replication in independent cohorts is necessary to validate these findings.
  • These discoveries may offer new insights into PD genetic architecture.