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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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 result in visible changes...

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Related Experiment Video

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Efficient and Consistent Generation of Retinal Pigment Epithelium/Choroid Flatmounts from Human Eyes for Histological Analysis
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iSyTE: integrated Systems Tool for Eye gene discovery.

Salil A Lachke1, Joshua W K Ho, Gregory V Kryukov

  • 1Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard edical School, Boston, Massachusetts, USA.

Investigative Ophthalmology & Visual Science
|February 11, 2012
PubMed
Summary

A new computational tool, iSyTE (integrated Systems Tool for Eye gene discovery), aids in identifying genes linked to congenital cataract. This bioinformatics approach effectively prioritizes candidate genes for further research, accelerating eye disease gene discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Ophthalmology

Background:

  • Identifying genes responsible for congenital cataract and other ocular defects is crucial for understanding disease mechanisms.
  • Existing methods for gene discovery can be time-consuming and may not efficiently prioritize candidate genes within complex genomic regions.

Purpose of the Study:

  • To develop and validate a computational tool, iSyTE (integrated Systems Tool for Eye gene discovery), for identifying and prioritizing genes associated with cataract and other ocular defects.
  • To utilize mouse embryonic lens gene expression data as a bioinformatics filter to select candidate genes from disease-associated genomic regions.

Main Methods:

  • Obtained microarray gene expression profiles from microdissected embryonic mouse lens at key developmental stages (E10.5-E12.5).
  • Identified differentially regulated genes by comparing lens expression profiles with whole embryo body (excluding ocular tissue) expression profiles in silico.
  • Validated iSyTE's effectiveness by assessing its ability to rank known cataract genes within top candidates in mapped human genomic intervals.

Main Results:

  • Gene set analysis confirmed that iSyTE effectively removes housekeeping genes, enabling the identification of less abundant, disease-associated genes.
  • For 24 human genomic intervals linked to congenital cataract, iSyTE ranked the causative gene within the top two candidates in approximately 88% of cases.
  • In situ hybridization confirmed the lens expression of several novel genes identified by iSyTE.

Conclusions:

  • iSyTE is a valuable, publicly available web resource for prioritizing candidate genes within genomic intervals associated with congenital cataract.
  • The iSyTE approach, when extended to other ocular tissues, holds significant potential for accelerating the discovery of genes involved in various eye diseases.