Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-08

AUTHORS

Ernest T Lam, Alex Hastie, Chin Lin, Dean Ehrlich, Somes K Das, Michael D Austin, Paru Deshpande, Han Cao, Niranjan Nagarajan, Ming Xiao, Pui-Yan Kwok

ABSTRACT

We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics. More... »

PAGES

771

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.2303

DOI

http://dx.doi.org/10.1038/nbt.2303

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1045232898

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22797562


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nbt.2303'

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.2303'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.2303'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.2303'


 

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316 https://www.grid.ac/institutes/grid.418377.e schema:alternateName Genome Institute of Singapore
317 schema:name Genome Institute of Singapore, Singapore.
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319 https://www.grid.ac/institutes/grid.470262.5 schema:alternateName BioNano Genomics (United States)
320 schema:name BioNano Genomics, San Diego, USA.
321 rdf:type schema:Organization
 




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