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Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device.

ABSTRACT: We show how a bird's-eye view of genomic structure can be obtained at ?1-kb resolution from long (?2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution with a commercial sequencer, thereby reconciling haplotype-phased chromosome substructure with sequence.

SUBMITTER: Marie R

PROVIDER: S-EPMC3612670 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device.

Marie Rodolphe R Pedersen Jonas N JN Bauer David L V DL Rasmussen Kristian H KH Yusuf Mohammed M Volpi Emanuela E Flyvbjerg Henrik H Kristensen Anders A Mir Kalim U KU

Proceedings of the National Academy of Sciences of the United States of America 20130311 13

We show how a bird's-eye view of genomic structure can be obtained at ∼1-kb resolution from long (∼2 Mb) DNA molecules extracted from whole chromosomes in a nanofluidic laboratory-on-a-chip. We use an improved single-molecule denaturation mapping approach to detect repetitive elements and known as well as unique structural variation. Following its mapping, a molecule of interest was rescued from the chip; amplified and localized to a chromosome by FISH; and interrogated down to 1-bp resolution w ...[more]

PMID: 23479649

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