Exome sequencing analysis: A guide to disease variant detection

Ofer Isakov, Marie Perrone, Noam Shomron

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

14 Scopus citations


Whole exome sequencing presents a powerful tool to study rare genetic disorders. The most challenging part of using exome sequencing for the purpose of disease-causing variant detection is analyzing, interpreting, and filtering the large number of detected variants. In this chapter we provide a comprehensive description of the various steps required for such an analysis. We address strategies in selecting samples to sequence, and technical considerations involved in exome sequencing. We then discuss how to identify variants, and methods for first annotating detected variants using characteristics such as allele frequency, location in the genome, and predicted severity, and then classifying and prioritizing the detected variants based on those annotations. Finally, we review possible gene annotations that may help to establish a relationship between genes carrying high-priority variants and the phenotype in question, in order to identify the most likely causative mutations.

Original languageEnglish
Title of host publicationDeep Sequencing Data Analysis
Number of pages22
StatePublished - 2013

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Disease variants
  • Exome
  • Exome analysis
  • Exome sequencing
  • Gene annotation
  • Variant annotation
  • Variant detection
  • Variant prioritization


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