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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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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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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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Multiple Allele Traits01:49

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The Concept of Multiple Allelism
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Comparing Copy Number Variations and SNPs02:26

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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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Improving Translational Accuracy02:07

Improving Translational Accuracy

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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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Related Experiment Video

Updated: Jan 15, 2026

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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STREAM-PRS: a multi-tool pipeline for streamlining polygenic risk score computation.

Sara Becelaere1,2, Yasmina Abakkouy1, Deborah Sarah Jans1

  • 1Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.

Genome Medicine
|October 10, 2025
PubMed
Summary
This summary is machine-generated.

STREAM-PRS optimizes polygenic risk score (PRS) calculations by testing multiple tools, identifying the best strategy for disease prediction. This pipeline enhances PRS portability and accuracy for genetic predisposition assessments.

Keywords:
Automated multi-tool pipelineComplex diseaseInflammatory bowel diseasePolygenic risk scoresPrecision medicine

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Area of Science:

  • Genetics and Genomics
  • Computational Biology
  • Disease Risk Prediction

Background:

  • Polygenic risk scores (PRS) estimate genetic predisposition to diseases, but numerous calculation tools exist with varying strategies.
  • Challenges like population stratification and PRS portability necessitate robust methods for tool and setting selection.
  • STREAM-PRS was developed as a pipeline to systematically evaluate and select optimal PRS calculation tools.

Purpose of the Study:

  • To develop and validate STREAM-PRS, an efficient pipeline for selecting the best polygenic risk score (PRS) calculation tool and settings.
  • To address the challenge of PRS portability across different datasets and research centers.
  • To apply the pipeline to identify an optimal PRS for inflammatory bowel disease (IBD).

Main Methods:

  • STREAM-PRS calculates PRS using five popular tools (PRSice-2, PRS-CS, LDpred2, lassosum, lassosum2) with various settings.
  • The pipeline selects optimal variants in a training dataset and calculates scores in a test dataset, followed by PC correction and standardization.
  • Performance is evaluated based on variance explained (R²); applied to an in-house IBD cohort using 1000 Genomes data for training and UK Biobank data for testing.

Main Results:

  • STREAM-PRS completed 472 PRS calculations across 5 tools in approximately 20 hours.
  • For IBD, lassosum with specific shrinkage (0.7) and lambda (0.008859) values performed best, achieving R² of 0.203 and AUC of 0.75 in validation.
  • The optimized PRS effectively identified high-risk individuals (PPV=0.905) but was less reliable for excluding lower-risk individuals (NPV=0.341).

Conclusions:

  • STREAM-PRS offers an efficient framework for optimizing PRS calculation strategies and improving cross-center portability.
  • The pipeline facilitates the selection of the most suitable PRS tool and settings for specific research questions.
  • STREAM-PRS is publicly available at https://github.com/SaraBecelaere/STREAM-PRS.