Genetic variant

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A Genetic variant may refer to:

Finding causative variants

Candidate alleles can be stratified on the basis of their predicted impact or deleteriousness, for example by giving greater weight to frameshifts, stop codons, and disruptions of canonical splice sites than to missense variants.[1] However, this approach can only be used on alleles that affect protein-coding sequences or canonical splice sites. The ultimate goal is to enrich for functional sites at which observed variants are more likely to affect phenotype.

Issues

  • Every sequenced exome presents the clinical geneticist with thousands of variants
  • Therefore the first step is to reduce the search space using various methods and strategies, for example, filtering out variants that are present in controls
  • Phenotype driven approaches leverage from biomedical ontologies such as the Human Phenotype Ontology, which links genes to diseases

Annotation tools

Free

Commercial

References

  1. Exome sequencing as a tool for Mendelian disease gene discovery http://www.nature.com/nrg/journal/v12/n11/execsumm/nrg3031.html