Literature DB >> 23479649

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

Rodolphe Marie1, Jonas N Pedersen, David L V Bauer, Kristian H Rasmussen, Mohammed Yusuf, Emanuela Volpi, Henrik Flyvbjerg, Anders Kristensen, Kalim U Mir.   

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.

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Year:  2013        PMID： 23479649      PMCID： PMC3612670          DOI： 10.1073/pnas.1214570110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  37 in total

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Journal:  Biopolymers       Date:  2003-10       Impact factor: 2.505

3.  From the Cover: The dynamics of genomic-length DNA molecules in 100-nm channels.

Authors:  Jonas O Tegenfeldt; Christelle Prinz; Han Cao; Steven Chou; Walter W Reisner; Robert Riehn; Yan Mei Wang; Edward C Cox; James C Sturm; Pascal Silberzan; Robert H Austin
Journal:  Proc Natl Acad Sci U S A       Date:  2004-07-13       Impact factor: 11.205

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Journal:  Nucleic Acids Res       Date:  1998-07-15       Impact factor: 16.971

5.  Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping.

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Journal:  Science       Date:  1993-10-01       Impact factor: 47.728

Review 6.  The functional impact of structural variation in humans.

Authors:  Matthew E Hurles; Emmanouil T Dermitzakis; Chris Tyler-Smith
Journal:  Trends Genet       Date:  2008-04-02       Impact factor: 11.639

7.  Rapid DNA mapping by fluorescent single molecule detection.

Authors:  Ming Xiao; Angie Phong; Connie Ha; Ting-Fung Chan; Dongmei Cai; Lucinda Leung; Eunice Wan; Amy L Kistler; Joseph L DeRisi; Paul R Selvin; Pui-Yan Kwok
Journal:  Nucleic Acids Res       Date:  2006-12-14       Impact factor: 16.971

8.  The diploid genome sequence of an individual human.

Authors:  Samuel Levy; Granger Sutton; Pauline C Ng; Lars Feuk; Aaron L Halpern; Brian P Walenz; Nelson Axelrod; Jiaqi Huang; Ewen F Kirkness; Gennady Denisov; Yuan Lin; Jeffrey R MacDonald; Andy Wing Chun Pang; Mary Shago; Timothy B Stockwell; Alexia Tsiamouri; Vineet Bafna; Vikas Bansal; Saul A Kravitz; Dana A Busam; Karen Y Beeson; Tina C McIntosh; Karin A Remington; Josep F Abril; John Gill; Jon Borman; Yu-Hui Rogers; Marvin E Frazier; Stephen W Scherer; Robert L Strausberg; J Craig Venter
Journal:  PLoS Biol       Date:  2007-09-04       Impact factor: 8.029

9.  Mapping and sequencing of structural variation from eight human genomes.

Authors:  Jeffrey M Kidd; Gregory M Cooper; William F Donahue; Hillary S Hayden; Nick Sampas; Tina Graves; Nancy Hansen; Brian Teague; Can Alkan; Francesca Antonacci; Eric Haugen; Troy Zerr; N Alice Yamada; Peter Tsang; Tera L Newman; Eray Tüzün; Ze Cheng; Heather M Ebling; Nadeem Tusneem; Robert David; Will Gillett; Karen A Phelps; Molly Weaver; David Saranga; Adrianne Brand; Wei Tao; Erik Gustafson; Kevin McKernan; Lin Chen; Maika Malig; Joshua D Smith; Joshua M Korn; Steven A McCarroll; David A Altshuler; Daniel A Peiffer; Michael Dorschner; John Stamatoyannopoulos; David Schwartz; Deborah A Nickerson; James C Mullikin; Richard K Wilson; Laurakay Bruhn; Maynard V Olson; Rajinder Kaul; Douglas R Smith; Evan E Eichler
Journal:  Nature       Date:  2008-05-01       Impact factor: 49.962

10.  Validation of rice genome sequence by optical mapping.

Authors:  Shiguo Zhou; Michael C Bechner; Michael Place; Chris P Churas; Louise Pape; Sally A Leong; Rod Runnheim; Dan K Forrest; Steve Goldstein; Miron Livny; David C Schwartz
Journal:  BMC Genomics       Date:  2007-08-15       Impact factor: 3.969
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  23 in total

1.  Visualizing the entire DNA from a chromosome in a single frame.

Authors:  C Freitag; C Noble; J Fritzsche; F Persson; M Reiter-Schad; A N Nilsson; A Granéli; T Ambjörnsson; K U Mir; J O Tegenfeldt
Journal:  Biomicrofluidics       Date:  2015-08-05       Impact factor: 2.800

2.  Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.

Authors:  Jia-Wei Yeh; Kylan Szeto
Journal:  Biomicrofluidics       Date:  2017-07-25       Impact factor: 2.800

3.  How to get into that "room at the bottom".

Authors:  Henrik Flyvbjerg
Journal:  Proc Natl Acad Sci U S A       Date:  2014-09-03       Impact factor: 11.205

4.  Mixed confinement regimes during equilibrium confinement spectroscopy of DNA.

Authors:  Damini Gupta; Julian Sheats; Abhiram Muralidhar; Jeremy J Miller; Derek E Huang; Sara Mahshid; Kevin D Dorfman; Walter Reisner
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

Review 5.  Flow of DNA in micro/nanofluidics: From fundamentals to applications.

Authors:  Lea Rems; Durgesh Kawale; L James Lee; Pouyan E Boukany
Journal:  Biomicrofluidics       Date:  2016-07-20       Impact factor: 2.800

6.  Toward single-molecule optical mapping of the epigenome.

Authors:  Michal Levy-Sakin; Assaf Grunwald; Soohong Kim; Natalie R Gassman; Anna Gottfried; Josh Antelman; Younggyu Kim; Sam O Ho; Robin Samuel; Xavier Michalet; Ron R Lin; Thomas Dertinger; Andrew S Kim; Sangyoon Chung; Ryan A Colyer; Elmar Weinhold; Shimon Weiss; Yuval Ebenstein
Journal:  ACS Nano       Date:  2013-12-20       Impact factor: 15.881

Review 7.  Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Authors:  Carlos A Aguilar; Harold G Craighead
Journal:  Nat Nanotechnol       Date:  2013-10       Impact factor: 39.213

8.  Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.

Authors:  Adam N Nilsson; Gustav Emilsson; Lena K Nyberg; Charleston Noble; Liselott Svensson Stadler; Joachim Fritzsche; Edward R B Moore; Jonas O Tegenfeldt; Tobias Ambjörnsson; Fredrik Westerlund
Journal:  Nucleic Acids Res       Date:  2014-07-10       Impact factor: 16.971

Review 9.  Analysis of single nucleic acid molecules in micro- and nano-fluidics.

Authors:  Sarah M Friedrich; Helena C Zec; Tza-Huei Wang
Journal:  Lab Chip       Date:  2016-03-07       Impact factor: 6.799

10.  Single-molecule DNA-mapping and whole-genome sequencing of individual cells.

Authors:  Rodolphe Marie; Jonas N Pedersen; Loic Bærlocher; Kamila Koprowska; Marie Pødenphant; Céline Sabatel; Maksim Zalkovskij; Andrej Mironov; Brian Bilenberg; Neil Ashley; Henrik Flyvbjerg; Walter F Bodmer; Anders Kristensen; Kalim U Mir
Journal:  Proc Natl Acad Sci U S A       Date:  2018-10-15       Impact factor: 11.205
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