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Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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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Infinium Assay for Large-scale SNP Genotyping Applications
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Genome-wide linkage analysis of 972 bipolar pedigrees using single-nucleotide polymorphisms.

J A Badner1, D Koller, T Foroud

  • 1Department of Psychiatry, University of Chicago, Chicago, IL, USA.

Molecular Psychiatry
|July 20, 2011
PubMed
Summary
This summary is machine-generated.

This study pooled genetic data from nearly 1000 families to identify Bipolar I disorder (BPI) risk loci. Genome-wide significant findings were observed on chromosomes 6q21 and 9q21, aiding future rare variant searches.

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Area of Science:

  • Genetics
  • Psychiatric Disorders
  • Genomic Analysis

Background:

  • Bipolar I disorder (BPI) linkage studies are often limited by small sample sizes and low genetic information content.
  • Microsatellite markers may be less informative in smaller pedigrees, necessitating higher density genotyping for robust genetic analysis.

Purpose of the Study:

  • To increase genetic information content in Bipolar I disorder (BPI) linkage studies by pooling resources and performing higher density genotyping.
  • To identify potential susceptibility loci for BPI and related disorders through comprehensive linkage analysis.

Main Methods:

  • Genotyped 972 informative pedigrees (European ancestry) using a dense panel of 6090 single-nucleotide polymorphisms (SNPs).
  • Analyzed linkage using parametric and non-parametric methods across three affection status models, including BPI, BPII, and recurrent major depression.
  • Applied genome-wide significance criteria and inspected parametric scores for rare variant localization.

Main Results:

  • Achieved a mean information content of 0.86 after pruning for linkage disequilibrium.
  • Identified strongest linkage signals for BPI and schizoaffective disorder at 6q21 (LOD 3.4) and 9q21 (LOD 3.4).
  • Observed 59 parametric LODs of 2 or greater in larger multiplex families, suggesting potential rare susceptibility loci.

Conclusions:

  • The study successfully enhanced genetic information content and identified suggestive linkage regions for BPI.
  • Findings provide a foundation for prioritizing rare variant discovery using whole exome or genome sequencing in BPI and related disorders.