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Related Concept Videos

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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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"...
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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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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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Diploid organisms have two alleles of each gene, one from each parent, in their somatic cells. Therefore, each individual contributes two alleles to the gene pool of the population. The gene pool of a population is the sum of every allele of all genes within that population and has some degree of variation. Genetic variation is typically expressed as a relative frequency, which is the percentage of the total population that has a given allele, genotype or phenotype.
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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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Infinium Assay for Large-scale SNP Genotyping Applications
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Interpreting SNP heritability in admixed populations.

Jinguo Huang1,2, Nicole Kleman3, Saonli Basu4

  • 1Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.

Genetics
|May 22, 2025
PubMed
Summary

Single-nucleotide polymorphism (SNP) heritability estimates can be biased in admixed populations due to directional linkage disequilibrium (LD). This bias affects genome-wide association studies and polygenic prediction in diverse populations.

Keywords:
GREMLHE regressionLDSCadmixturecomplex traitsheritabilitypopulation structurestatistical genetics

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Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
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Area of Science:

  • Population Genetics
  • Quantitative Genetics
  • Genomics

Background:

  • Single-nucleotide polymorphism (SNP) heritability (hsnp2) estimates the proportion of phenotypic variance explained by genotyped SNPs.
  • hsnp2 is often considered a lower bound of total heritability (h2), assuming all causal variants are genotyped.
  • Interpretation of hsnp2 and its equivalence to h2 is complex, especially in admixed populations.

Purpose of the Study:

  • To analyze the behavior of heritability (h2) and common hsnp2 estimators in admixed populations.
  • To investigate biases in hsnp2 estimates arising from admixture and directional linkage disequilibrium (LD).
  • To clarify the implications for genome-wide association studies (GWAS) and polygenic prediction in admixed groups.

Main Methods:

  • Analytical theory and simulations were employed.
  • The study focused on three random-effect estimators: genome-wide restricted maximum likelihood (GREML), Haseman-Elston regression, and LD score regression.
  • The behavior of heritability estimators was examined in the context of population admixture.

Main Results:

  • hsnp2 estimates can be biased in admixed populations, even when all causal variants are genotyped and environmental confounding is absent.
  • Admixture-induced directional LD contributes to genetic variance and heritability, which random-effect estimators may not fully capture.
  • Estimates of local ancestry heritability (h^γ2) are also biased due to directional LD.

Conclusions:

  • Admixture introduces biases in hsnp2 and h^γ2 estimates, dependent on admixture history and trait genetic architecture.
  • Understanding these biases is crucial for accurate genetic interpretation and application in diverse populations.
  • The findings have significant implications for GWAS and polygenic prediction strategies in admixed cohorts.