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

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 w...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 110; no. 13; pp. 4893 - 4898
Main Authors Marie, Rodolphe, Pedersen, Jonas N., Bauer, David L. V., Rasmussen, Kristian H., Yusuf, Mohammed, Volpi, Emanuela, Flyvbjerg, Henrik, Kristensen, Anders, Mir, Kalim U.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 26.03.2013
National Acad Sciences
Subjects
Bar codes
Biological Sciences
Chromosome Mapping - instrumentation
Chromosome Mapping - methods
Chromosomes
Chromosomes, Human - chemistry
Chromosomes, Human - genetics
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA mapping
Genetic variation
Genome, Human
Genomes
Genomics
Humans
In Situ Hybridization, Fluorescence - instrumentation
In Situ Hybridization, Fluorescence - methods
Male
Microfluidic Analytical Techniques - instrumentation
Microfluidic Analytical Techniques - methods
Molecules
Physical Sciences
Sequencing
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Summary: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.
Bibliography:http://dx.doi.org/10.1073/pnas.1214570110
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Author contributions: R.M., J.N.P., D.L.V.B., M.Y., H.F., A.K., and K.U.M. designed research; R.M., J.N.P., D.L.V.B., M.Y., H.F., and K.U.M. performed research; R.M., J.N.P., D.L.V.B., K.H.R., and H.F. contributed new reagents/analytic tools; R.M., J.N.P., D.L.V.B., M.Y., and E.V. analyzed data; and R.M., J.N.P., D.L.V.B., M.Y., E.V., H.F., A.K., and K.U.M. wrote the paper.
4Present address: Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115.
2Present address: Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
Edited* by Robert H. Austin, Princeton University, Princeton, NJ, and approved February 1, 2013 (received for review August 27, 2012)
1J.N.P. and D.L.V.B. contributed equally to this work.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1214570110