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Related Concept Videos

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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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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Inheritance01:25

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Gregor Mendel's pioneering work on the principles of inheritance fundamentally transformed our understanding of how traits are transmitted from generation to generation. His experiments with pea plants laid the groundwork for the discovery of genes, discrete units within organisms that control heredity.
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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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Updated: Sep 28, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Predicting genes from phenotypes using human phenotype ontology (HPO) terms.

Anne Slavotinek1, Hannah Prasad2, Tiffany Yip3

  • 1Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA. anne.slavotinek@ucsf.edu.

Human Genetics
|March 31, 2022
PubMed
Summary

Whole exome sequencing (WES) interpretation is improved by using Human Phenotype Ontology (HPO) terms. Phen2Gene software effectively ranks causative genes, especially those linked to well-defined phenotypes and deep HPO hierarchies.

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Area of Science:

  • Genomics and Bioinformatics
  • Clinical Genetics
  • Medical Informatics

Background:

  • Interpreting genomic variants from whole exome sequencing (WES) is challenging.
  • Standardizing clinical features using Human Phenotype Ontology (HPO) terms can aid variant interpretation.
  • Predicting causative genes requires efficient prioritization methods.

Purpose of the Study:

  • To evaluate the utility of Phen2Gene software in ranking causative genes identified through WES.
  • To assess the impact of HPO term characteristics on gene prioritization.
  • To determine the effectiveness of HPO terms in identifying pathogenic variants in pediatric patients.

Main Methods:

  • Performed WES on 453 pediatric patients (<18 years).
  • Extracted HPO terms from clinical notes using PhenoDB.
  • Utilized Phen2Gene to generate gene scores and rankings based on HPO terms.

Main Results:

  • Identified 114 pathogenic/likely pathogenic variants in 112 patients.
  • Phen2Gene ranked causative genes in the top two classes (1-50) in 27.7% of cases.
  • Gene score correlated with publication age, HPO term hierarchical depth, and Online Mendelian Inheritance in Man (OMIM) terms.

Conclusions:

  • Genes associated with recognizable phenotypes and deep HPO hierarchies achieve higher Phen2Gene scores and rankings.
  • Phen2Gene, using HPO terms, is effective in prioritizing candidate genes from WES data.
  • Clinicians should consider phenotype recognizability and HPO depth for gene prioritization.