Genome structural variation discovery and genotyping View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-03-01

AUTHORS

Can Alkan, Bradley P. Coe, Evan E. Eichler

ABSTRACT

Key PointsStructural variation was originally defined as insertions, deletions and inversions greater than 1 kb in size, but with the sequencing of human genomes now becoming routine, the operational spectrum of structural variants has widened to include events >50 bp in length.The main focus of structural variant (SV) studies should be accurate characterization of the copy, content and structure of genomic variants.Methods to discover and genotype structural variation can be divided into two main types: experimental and computational.Experimental methods for discovering SVs include hybridization-based approaches (SNP microarrays and array comparative genomic hybridization) and single-molecule analysis (optical mapping). In addition, PCR-based techniques can be used to genotype SVs.Computational methods use genome sequencing data to discover and genotype SVs. There are four main computational approaches: read-pair, read-depth, split-read and sequence-assembly methods.All existing platforms and methods have different biases and limitations. Accurate characterization of the full spectrum of structural variation remains a challenge. More... »

PAGES

363-376

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  • Journal

    TITLE

    Nature Reviews Genetics

    ISSUE

    5

    VOLUME

    12

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nrg2958

    DOI

    http://dx.doi.org/10.1038/nrg2958

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1004346662

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/21358748


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