Optical mapping and nanocoding approaches to whole-genome analysis

Aditya Gupta; Kristy L. Kounovsky-Shafer; Prabu Ravindran; David C. Schwartz

doi:10.1007/s10404-015-1685-y

Optical mapping and nanocoding approaches to whole-genome analysis

Aditya Gupta, Kristy L. Kounovsky-Shafer, Prabu Ravindran, David C. Schwartz

Chemistry

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

11 Scopus citations

Abstract

Recent application of microfluidic and nanofluidic approaches to genomics has enabled rapid analysis of whole human and other large genomes. Here, we present a review of optical mapping and nanocoding, two single-molecule whole-genome analysis systems, which are used for physical mapping of genomes. Optical mapping employs a microfluidic device, fabricated using soft lithography approaches, to achieve DNA presentation via DNA flow in microchannels. On the other hand, nanocoding leverages DNA confinement in nanoscale devices to achieve DNA presentation. In this review, we focus on the physical principles underlying DNA presentation in both of these systems and the application of these approaches towards better understanding of genomic structure and structural variation.

Original language	English (US)
Article number	44
Pages (from-to)	1-14
Number of pages	14
Journal	Microfluidics and Nanofluidics
Volume	20
Issue number	3
DOIs	https://doi.org/10.1007/s10404-015-1685-y
State	Published - Mar 1 2016

Keywords

DNA presentation
Microfluidics
Nanocoding
Nanoconfinement
Optical mapping

ASJC Scopus subject areas

Electronic, Optical and Magnetic Materials
Condensed Matter Physics
Materials Chemistry

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10.1007/s10404-015-1685-y

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title = "Optical mapping and nanocoding approaches to whole-genome analysis",

abstract = "Recent application of microfluidic and nanofluidic approaches to genomics has enabled rapid analysis of whole human and other large genomes. Here, we present a review of optical mapping and nanocoding, two single-molecule whole-genome analysis systems, which are used for physical mapping of genomes. Optical mapping employs a microfluidic device, fabricated using soft lithography approaches, to achieve DNA presentation via DNA flow in microchannels. On the other hand, nanocoding leverages DNA confinement in nanoscale devices to achieve DNA presentation. In this review, we focus on the physical principles underlying DNA presentation in both of these systems and the application of these approaches towards better understanding of genomic structure and structural variation.",

keywords = "DNA presentation, Microfluidics, Nanocoding, Nanoconfinement, Optical mapping",

author = "Aditya Gupta and Kounovsky-Shafer, {Kristy L.} and Prabu Ravindran and Schwartz, {David C.}",

note = "Funding Information: We thank all the members of the Laboratory for Molecular and Computational Genomics (LMCG) for helpful discussions and research efforts directed towards the development of these systems. We also thank National Human Genome Research Institute (NHGRI R01HG000225) and National Science Foundation (NSF) for supporting our research efforts over the years. Publisher Copyright: {\textcopyright} 2016, Springer-Verlag Berlin Heidelberg.",

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doi = "10.1007/s10404-015-1685-y",

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AU - Gupta, Aditya

AU - Kounovsky-Shafer, Kristy L.

AU - Ravindran, Prabu

AU - Schwartz, David C.

N1 - Funding Information: We thank all the members of the Laboratory for Molecular and Computational Genomics (LMCG) for helpful discussions and research efforts directed towards the development of these systems. We also thank National Human Genome Research Institute (NHGRI R01HG000225) and National Science Foundation (NSF) for supporting our research efforts over the years. Publisher Copyright: © 2016, Springer-Verlag Berlin Heidelberg.

PY - 2016/3/1

Y1 - 2016/3/1

N2 - Recent application of microfluidic and nanofluidic approaches to genomics has enabled rapid analysis of whole human and other large genomes. Here, we present a review of optical mapping and nanocoding, two single-molecule whole-genome analysis systems, which are used for physical mapping of genomes. Optical mapping employs a microfluidic device, fabricated using soft lithography approaches, to achieve DNA presentation via DNA flow in microchannels. On the other hand, nanocoding leverages DNA confinement in nanoscale devices to achieve DNA presentation. In this review, we focus on the physical principles underlying DNA presentation in both of these systems and the application of these approaches towards better understanding of genomic structure and structural variation.

AB - Recent application of microfluidic and nanofluidic approaches to genomics has enabled rapid analysis of whole human and other large genomes. Here, we present a review of optical mapping and nanocoding, two single-molecule whole-genome analysis systems, which are used for physical mapping of genomes. Optical mapping employs a microfluidic device, fabricated using soft lithography approaches, to achieve DNA presentation via DNA flow in microchannels. On the other hand, nanocoding leverages DNA confinement in nanoscale devices to achieve DNA presentation. In this review, we focus on the physical principles underlying DNA presentation in both of these systems and the application of these approaches towards better understanding of genomic structure and structural variation.

KW - DNA presentation

KW - Microfluidics

KW - Nanocoding

KW - Nanoconfinement

KW - Optical mapping

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ER -

Optical mapping and nanocoding approaches to whole-genome analysis

Abstract

Keywords

ASJC Scopus subject areas

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