Personalized copy number and segmental duplication maps using next-generation sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-10

AUTHORS

Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S Cenk Sahinalp, Richard A Gibbs, Evan E Eichler

ABSTRACT

Despite their importance in gene innovation and phenotypic variation, duplicated regions have remained largely intractable owing to difficulties in accurately resolving their structure, copy number and sequence content. We present an algorithm (mrFAST) to comprehensively map next-generation sequence reads, which allows for the prediction of absolute copy-number variation of duplicated segments and genes. We examine three human genomes and experimentally validate genome-wide copy number differences. We estimate that, on average, 73-87 genes vary in copy number between any two individuals and find that these genic differences overwhelmingly correspond to segmental duplications (odds ratio = 135; P < 2.2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology. More... »

PAGES

1061-1067

References to SciGraph publications

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  • Journal

    TITLE

    Nature Genetics

    ISSUE

    10

    VOLUME

    41

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ng.437

    DOI

    http://dx.doi.org/10.1038/ng.437

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1035989827

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19718026


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