Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-02

AUTHORS

Andreas Gnirke, Alexandre Melnikov, Jared Maguire, Peter Rogov, Emily M LeProust, William Brockman, Timothy Fennell, Georgia Giannoukos, Sheila Fisher, Carsten Russ, Stacey Gabriel, David B Jaffe, Eric S Lander, Chad Nusbaum

ABSTRACT

Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA 'baits' to fish targets out of a 'pond' of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that approximately 60% of target bases in the exonic 'catch', and approximately 80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space. More... »

PAGES

182-189

Journal

TITLE

Nature Biotechnology

ISSUE

2

VOLUME

27

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt.1523

    DOI

    http://dx.doi.org/10.1038/nbt.1523

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1040653661

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19182786


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    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt.1523'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nbt.1523'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.1523'

    RDF/XML is a standard XML format for linked data.

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