Haplotype-resolved genome sequencing of a Gujarati Indian individual View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-01

AUTHORS

Jacob O Kitzman, Alexandra P MacKenzie, Andrew Adey, Joseph B Hiatt, Rupali P Patwardhan, Peter H Sudmant, Sarah B Ng, Can Alkan, Ruolan Qiu, Evan E Eichler, Jay Shendure

ABSTRACT

Haplotype information is essential to the complete description and interpretation of genomes, genetic diversity and genetic ancestry. Although individual human genome sequencing is increasingly routine, nearly all such genomes are unresolved with respect to haplotype. Here we combine the throughput of massively parallel sequencing with the contiguity information provided by large-insert cloning to experimentally determine the haplotype-resolved genome of a South Asian individual. A single fosmid library was split into a modest number of pools, each providing ∼3% physical coverage of the diploid genome. Sequencing of each pool yielded reads overwhelmingly derived from only one homologous chromosome at any given location. These data were combined with whole-genome shotgun sequence to directly phase 94% of ascertained heterozygous single nucleotide polymorphisms (SNPs) into long haplotype blocks (N50 of 386 kilobases (kbp)). This method also facilitates the analysis of structural variation, for example, to anchor novel insertions to specific locations and haplotypes. More... »

PAGES

59

Journal

TITLE

Nature Biotechnology

ISSUE

1

VOLUME

29

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nbt.1740

DOI

http://dx.doi.org/10.1038/nbt.1740

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1021995395

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/21170042


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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.1740'

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.1740'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nbt.1740'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nbt.1740'


 

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