Optical mapping and nanocoding approaches to whole-genome analysis

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

Research output: Contribution to journalReview article

8 Citations (Scopus)

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 languageEnglish (US)
Article number44
Pages (from-to)1-14
Number of pages14
JournalMicrofluidics and Nanofluidics
Volume20
Issue number3
DOIs
StatePublished - Mar 1 2016

Fingerprint

genome
DNA
deoxyribonucleic acid
Genes
Microfluidics
Nanofluidics
microfluidic devices
systems analysis
microchannels
Microchannels
Lithography
lithography
Molecules
molecules

Keywords

  • DNA presentation
  • Microfluidics
  • Nanocoding
  • Nanoconfinement
  • Optical mapping

ASJC Scopus subject areas

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Materials Chemistry

Cite this

Optical mapping and nanocoding approaches to whole-genome analysis. / Gupta, Aditya; Kounovsky-Shafer, Kristy L.; Ravindran, Prabu; Schwartz, David C.

In: Microfluidics and Nanofluidics, Vol. 20, No. 3, 44, 01.03.2016, p. 1-14.

Research output: Contribution to journalReview article

Gupta, Aditya ; Kounovsky-Shafer, Kristy L. ; Ravindran, Prabu ; Schwartz, David C. / Optical mapping and nanocoding approaches to whole-genome analysis. In: Microfluidics and Nanofluidics. 2016 ; Vol. 20, No. 3. pp. 1-14.
@article{34330c73c1f74c5f83b4485b4584b9dd,
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.}",
year = "2016",
month = "3",
day = "1",
doi = "10.1007/s10404-015-1685-y",
language = "English (US)",
volume = "20",
pages = "1--14",
journal = "Microfluidics and Nanofluidics",
issn = "1613-4982",
publisher = "Springer Verlag",
number = "3",

}

TY - JOUR

T1 - Optical mapping and nanocoding approaches to whole-genome analysis

AU - Gupta, Aditya

AU - Kounovsky-Shafer, Kristy L.

AU - Ravindran, Prabu

AU - Schwartz, David C.

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

UR - http://www.scopus.com/inward/record.url?scp=84975780689&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84975780689&partnerID=8YFLogxK

U2 - 10.1007/s10404-015-1685-y

DO - 10.1007/s10404-015-1685-y

M3 - Review article

AN - SCOPUS:84975780689

VL - 20

SP - 1

EP - 14

JO - Microfluidics and Nanofluidics

JF - Microfluidics and Nanofluidics

SN - 1613-4982

IS - 3

M1 - 44

ER -