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Related Concept Videos

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.
GWAS does not require the identification of the target gene involved in...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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,...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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%...
Heritability01:06

Heritability

Heritability is a statistical concept that measures the degree to which genetic differences among individuals contribute to trait variations within a population. It is a fundamental idea in genetics, often prone to misinterpretation. Heritability is expressed as a percentage, reflecting the proportion of variation in a specific trait across a population that can be linked to genetic differences. However, it's important to understand that heritability does not determine how "genetic" a trait is,...
Pharmacogenomics: Identification of New Drug Targets01:29

Pharmacogenomics: Identification of New Drug Targets

Advances in genomics have profoundly influenced drug discovery by increasing both the speed and accuracy of pharmaceutical development. Pharmacogenomics, which examines how genetic variation influences drug response, facilitates the identification of novel therapeutic targets and enables patient stratification for personalized treatment. These strategies contribute to improved drug efficacy, minimized adverse effects, and more efficient clinical trial design.Mapping genetic differences...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...

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Related Experiment Video

Updated: May 16, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

Improved heritability estimation from genome-wide SNPs.

Doug Speed1, Gibran Hemani, Michael R Johnson

  • 1University College London Genetics Institute, University College London, London WC1E 6BT, UK. doug.speed@ucl.ac.uk

American Journal of Human Genetics
|December 11, 2012
PubMed
Summary
This summary is machine-generated.

Estimating heritability (h²) using genome-wide SNPs is powerful but sensitive to linkage disequilibrium (LD). We developed a method to adjust for LD, reducing bias and improving heritability estimates for human traits.

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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
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Last Updated: May 16, 2026

Infinium Assay for Large-scale SNP Genotyping Applications
13:33

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Published on: November 19, 2013

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Area of Science:

  • Genetics
  • Statistical Genetics
  • Bioinformatics

Background:

  • Genome-wide SNP data enables estimation of narrow-sense heritability (h²) in unrelated individuals, offering advantages over pedigree-based methods.
  • Previous SNP-based heritability estimates attribute substantial genetic influence to common variants, yet the accuracy of underlying methods requires scrutiny.

Purpose of the Study:

  • To investigate the impact of linkage disequilibrium (LD) on SNP-based heritability estimation using mixed-model analysis.
  • To develop and validate a method for correcting biases in heritability estimates caused by uneven LD.

Main Methods:

  • Simulations were conducted to assess the robustness of mixed-model analysis to violations of key assumptions, particularly concerning LD.
  • A modified kinship matrix was developed, weighting SNPs by local LD, to correct for estimation biases.
  • The developed method, LDAK (Linkage Disequilibrium Adjusted Kinships), was applied to real-world disease data.

Main Results:

  • SNP-based heritability estimation is sensitive to uneven LD, leading to over- or underestimation of causal variant contributions.
  • The proposed LD adjustment significantly reduces bias and enhances the precision of heritability (h²) estimates.
  • Application to Wellcome Trust Case Control Consortium data showed downward revision of h² for immune-related diseases and upward revision for some non-immune diseases.

Conclusions:

  • Uneven linkage disequilibrium poses a significant challenge for accurate SNP-based heritability estimation.
  • The LDAK method provides a robust approach to correct for LD biases, improving the reliability of heritability estimates.
  • This LD-adjusted method has implications for understanding the genetic architecture of complex human traits and diseases.