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

Rodolphe  Marie; Jonas Nyvold Pedersen; David  L. V. Bauer; Kristian Hagsted Rasmussen; Mohammed  Yusuf; Emanuela  Volpi; Henrik Flyvbjerg; Anders Kristensen; Kalim  U. Mirb

doi:10.1073/pnas.1214570110

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

Rodolphe Marie
, Jonas Nyvold Pedersen
, David L. V. Bauer
, Kristian Hagsted Rasmussen
, Mohammed Yusuf
, Emanuela Volpi
, Henrik Flyvbjerg
, Anders Kristensen
, Kalim U. Mirb

University of Oxford

Research output: Contribution to journal › Journal article › Research › peer-review

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 laboratoryon-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 fromthe 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.

Original language	English
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	110
Issue number	13
Pages (from-to)	4893-4898
ISSN	0027-8424
DOIs	https://doi.org/10.1073/pnas.1214570110
Publication status	Published - 2013

Keywords

Physical Sciences
Biological Sciences
Applied Physical Sciences
Genetics

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10.1073/pnas.1214570110

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CELL-O-MATIC: High Throughput Systematic Single Cell Genomics using Micro/Nano-Fluidic Chips for Extracting, Pre-analysing, Selecting and Preparing Sequence-ready DNA
Kristensen, A. (Project Coordinator) & Bjerrum, A. (Project Coordinator)
01/01/2012 → 31/12/2015
Project: Research

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Marie, R., Pedersen, J. N., L. V. Bauer, D., Rasmussen, K. H., Yusuf, M., Volpi, E., Flyvbjerg, H., Kristensen, A., & U. Mirb, K. (2013). Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device. Proceedings of the National Academy of Sciences of the United States of America, 110(13), 4893-4898. https://doi.org/10.1073/pnas.1214570110

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title = "Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device",

abstract = "We show how a bird{\textquoteright}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 laboratoryon-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 fromthe 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.",

keywords = "Physical Sciences, Biological Sciences, Applied Physical Sciences, Genetics",

author = "Rodolphe Marie and Pedersen, \{Jonas Nyvold\} and \{L. V. Bauer\}, David and Rasmussen, \{Kristian Hagsted\} and Mohammed Yusuf and Emanuela Volpi and Henrik Flyvbjerg and Anders Kristensen and \{U. Mirb\}, Kalim",

year = "2013",

doi = "10.1073/pnas.1214570110",

language = "English",

volume = "110",

pages = "4893--4898",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

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Marie, R , Pedersen, JN, L. V. Bauer, D, Rasmussen, KH, Yusuf, M, Volpi, E, Flyvbjerg, H, Kristensen, A & U. Mirb, K 2013, 'Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 13, pp. 4893-4898. https://doi.org/10.1073/pnas.1214570110

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device. / Marie, Rodolphe ; Pedersen, Jonas Nyvold; L. V. Bauer, David et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 13, 2013, p. 4893-4898.

Research output: Contribution to journal › Journal article › Research › peer-review

TY - JOUR

T1 - Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device

AU - Marie, Rodolphe

AU - Pedersen, Jonas Nyvold

AU - L. V. Bauer, David

AU - Rasmussen, Kristian Hagsted

AU - Yusuf, Mohammed

AU - Volpi, Emanuela

AU - Flyvbjerg, Henrik

AU - Kristensen, Anders

AU - U. Mirb, Kalim

PY - 2013

Y1 - 2013

N2 - 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 laboratoryon-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 fromthe 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.

AB - 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 laboratoryon-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 fromthe 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.

KW - Physical Sciences

KW - Biological Sciences

KW - Applied Physical Sciences

KW - Genetics

U2 - 10.1073/pnas.1214570110

DO - 10.1073/pnas.1214570110

M3 - Journal article

C2 - 23479649

SN - 0027-8424

VL - 110

SP - 4893

EP - 4898

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 13

ER -

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

Abstract

Keywords

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Projects

CELL-O-MATIC: High Throughput Systematic Single Cell Genomics using Micro/Nano-Fluidic Chips for Extracting, Pre-analysing, Selecting and Preparing Sequence-ready DNA

Cite this