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Related Concept Videos

Polygenic Traits01:18

Polygenic Traits

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When more than one gene is responsible for a given phenotype, the trait is considered polygenic. Human height is a polygenic trait. Studies have uncovered hundreds of loci that influence height, and there are believed to be many more. Due to the high number of genes involved, as well as environmental and nutritional factors, height varies significantly within a given population. The distribution of height forms a bell-shaped curve, with relatively few individuals in the population at the...
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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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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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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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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Human Genetics01:28

Human Genetics

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Human genetics provides a profound framework for understanding the interplay between genetic predispositions and human psychology. At the heart of this discipline lies the study of how genes influence physical traits, behaviors, and susceptibility to diseases. Each person carries a unique genetic code that subtly or significantly shapes their psychological and behavioral landscape.
The complex relationship between genetics and psychology is observable through common biological components such...
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Heritability01:06

Heritability

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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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Related Experiment Video

Updated: Nov 29, 2025

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Genotype imputation and variability in polygenic risk score estimation.

Shang-Fu Chen1,2, Raquel Dias1,2, Doug Evans1,2

  • 1Scripps Research Translational Institute, Scripps Research, La Jolla, CA, 92037, USA.

Genome Medicine
|November 23, 2020
PubMed
Summary
This summary is machine-generated.

Genotype imputation can introduce minor variability in polygenic risk scores (PRSs), but rarely impacts individual interpretation. Using deterministic or averaged imputation methods can improve PRS stability for healthcare applications.

Keywords:
Coronary artery diseaseGenetic risk scoreGenome-wide scoreGenotype imputationGenotype phasingPRSPolygenic risk scorePolygenic score

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Polygenic risk scores (PRSs) summarize genetic predisposition for diseases/traits.
  • PRSs are increasingly used in research and commercial settings for healthcare guidance.
  • Lack of guidelines for PRS generation and updating poses challenges.

Purpose of the Study:

  • To characterize variability in PRS calculations due to genotype imputation.
  • To evaluate the impact of different imputation algorithms on PRS stability.
  • To assess PRS variability relative to a whole-genome sequencing gold standard.

Main Methods:

  • Evaluated PRS variability using 3 pre-phasing tools (Beagle, Eagle, SHAPEIT) and 2 imputation tools (Beagle, Minimac4).
  • Assessed 14 different PRSs across various disease architectures and generation methods.
  • Compared imputed PRS to a whole-genome sequencing (WGS)-based gold standard.

Main Results:

  • Genotype imputation introduces variability in individual PRSs without altering the genetic model.
  • Stochastic pre-phasing algorithms cause the most significant PRS variability.
  • Most imputation-induced PRS variability is minor (<5 percentile rank change) and does not affect score interpretation.

Conclusions:

  • Genotype imputation variability can be substantial in rare cases, impacting individual PRS interpretation.
  • Population-level PRS reproducibility masks rare individual-level variability.
  • Recommend deterministic or averaged stochastic imputation for stable PRS generation and delivery.