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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Incomplete Dominance01:43

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Gregor Mendel's work (1822 - 1884) was primarily focused on pea plants. Through his initial experiments, he determined that every gene in a diploid cell has two variants called alleles inherited from each parent. He suggested that amongst these two alleles, one allele is dominant in character and the other recessive. The combination of alleles determines the phenotype of a gene in an organism.
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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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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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Single Nucleotide Polymorphisms-SNPs01:05

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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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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Related Experiment Video

Updated: Jun 23, 2025

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Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic

Yasemin Bridges1, Vinicius de Souza2, Katherina G Cortes3

  • 1William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.

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Summary

Developing effective rare disease diagnostic tools is challenging. PhEval provides a standardized framework to benchmark variant and gene prioritization algorithms (VGPAs), improving rare disease diagnosis and patient care.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Rare disease diagnosis relies on complex computational tools like variant and gene prioritization algorithms (VGPAs).
  • Evaluating and comparing VGPAs is difficult due to a lack of standardized frameworks, reproducible data, and consistent methodologies.
  • This hinders the development and adoption of effective rare disease diagnostic pipelines.

Purpose of the Study:

  • To introduce PhEval, a novel benchmarking tool designed to standardize the evaluation of phenotype-driven VGPAs.
  • To address the limitations in reproducibility and comparability of current VGPA assessment methods.

Main Methods:

  • Development of PhEval, a benchmarking tool incorporating standardized test corpora and generation utilities.
  • Utilizing real-world patient case report data to create standardized datasets for evaluation.
  • Controlling the configuration of VGPAs during benchmarking to ensure consistency.

Main Results:

  • PhEval provides a standardized and empirical framework for evaluating VGPAs.
  • The tool includes standardized test corpora and generation tools for open benchmarking.
  • PhEval enables transparent, portable, comparable, and reproducible assessment of VGPAs.

Conclusions:

  • PhEval and its associated corpora overcome challenges in data availability and tool configuration for rare disease VGPA benchmarking.
  • This standardized approach is crucial for advancing the accuracy and reliability of rare disease diagnostic tools.
  • Improved VGPA assessment directly contributes to better patient diagnosis and care in rare genetic disorders.