Genomic Structural Variants

Volume 838 of the series Methods in Molecular Biology pp 343-367


Characterizing and Interpreting Genetic Variation from Personal Genome Sequencing

  • Anna C. V. JohanssonAffiliated withDepartment of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University
  • , Lars FeukAffiliated withDepartment of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University Email author 

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Since the completion of the human genome project, there has been enormous progress in the development of novel technologies for DNA sequencing. The advent of next-generation sequencing technologies now makes it possible to sequence an entire human genome in one or a few experiments. As a consequence, several individual human genomes have now been fully sequenced, using different experimental strategies. Although the protocols differ between the various sequencing technologies, the challenges of analyzing the data, calling variation, and interpreting the results are similar for all platforms. Here, we give an overview of the human genome sequencing projects completed to date. The strategies for aligning sequence reads and extracting information about different types of genetic variation from the sequence data are discussed. Identification of structural variation, such as copy number variation and insertion-deletion variants, can be complex, and there are a plethora of algorithms and analysis tools available. We also give an overview of the challenge of interpreting the whole-genome sequence data both from a technical and clinical perspective.

Key words

Copy number variation Indel Personal genomics Whole-genome sequencing