Genetic variation and the de novo assembly of human genomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-10-07

AUTHORS

Mark J. P. Chaisson, Richard K. Wilson, Evan E. Eichler

ABSTRACT

Key PointsComplete de novo assembly of a genome is guaranteed to allow assessment of the full range of genetic variation, although the only mammalian genome assemblies completed to date are for human and mouse. Assemblies using massively parallel sequencing (MPS) have increased the diversity of draft genomes that are available but do not completely resolve genomes.When designing a de novo assembly project, the most-suitable assembly approach to use differs depending on the characteristics of the sequencing reads. MPS methods have relied on de Bruijn graphs, whereas single-molecule sequencing (SMS) reads require pairwise overlaps encoded in overlap or string graphs.A component of 'missing heritability' is missed sequence variation. Approximately 5–40 Mb of sequence are absent from any given human reference genome owing to structural polymorphism, and standard resequencing has missed detection of diseases such as medullary cystic kidney disease type 1, amyotrophic lateral sclerosis and facioscapulohumeral muscular dystrophy.Single-molecule long-read sequencing is currently driving gains in genome assembly accuracy and completeness, but new technologies are being developed to generate long-range information, such as optical maps and dilution pool sequencing, that may aid in scaffolding complex regions. More... »

PAGES

627-640

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    http://scigraph.springernature.com/pub.10.1038/nrg3933

    DOI

    http://dx.doi.org/10.1038/nrg3933

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1016840633

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26442640


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