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Polygenic Traits01:18

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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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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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PRSice: Polygenic Risk Score software.

Jack Euesden1, Cathryn M Lewis1, Paul F O'Reilly1

  • 1MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.

Bioinformatics (Oxford, England)
|January 1, 2015
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Summary
This summary is machine-generated.

We introduce PRSice, the first dedicated software for calculating polygenic risk scores (PRS). This tool enhances genetic studies by providing high-resolution PRS analysis, improving phenotype biomarker applications.

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Area of Science:

  • Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Polygenic risk scores (PRS) aggregate trait-associated alleles across genetic loci.
  • PRS are increasingly used to detect shared genetic etiology and act as phenotype biomarkers.

Purpose of the Study:

  • To present PRSice, the first dedicated software for calculating, applying, evaluating, and plotting PRS.
  • To provide a high-resolution analysis for optimal PRS identification and application.

Main Methods:

  • PRSice is implemented in R with bash and PLINK-1.9 wrappers for efficiency.
  • It supports high-resolution and broad P-value threshold calculations, SNP thinning, and handles genotyped/imputed data.
  • The software can incorporate ancestry-informative variables and apply PRS across multiple traits concurrently.

Main Results:

  • PRSice enables the calculation of PRS at numerous thresholds to identify the best-fit score.
  • The software was exemplified using data from schizophrenia, major depressive disorder, and smoking.
  • The importance of identifying the best-fit PRS and establishing significance thresholds was illustrated.

Conclusions:

  • PRSice is a comprehensive tool for advancing PRS analysis in genetic research.
  • The software facilitates a more nuanced understanding of genetic contributions to complex traits.
  • It supports diverse applications including clinical trial screening and biomarker development.