High-resolution human genome structure by single-molecule analysis

被引：131

作者：

Teague, Brian ^{[1
,2
]}

Waterman, Michael S. ^{[3
]}

Goldstein, Steven ^{[1
,2
]}

Potamousis, Konstantinos ^{[1
,2
]}

Zhou, Shiguo ^{[1
,2
]}

Reslewic, Susan ^{[1
,2
]}

Sarkar, Deepayan ^{[4
]}

Valouev, Anton ^{[3
]}

Churas, Christopher ^{[1
,2
]}

Kidd, Jeffrey M. ^{[5
]}

Kohn, Scott ^{[1
,2
]}

Runnheim, Rodney ^{[1
,2
]}

Lamers, Casey ^{[1
,2
]}

Forrest, Dan ^{[1
,2
]}

Newton, Michael A. ^{[4
,6
]}

Eichler, Evan E. ^{[5
]}

Kent-First, Marijo ^{[7
]}

Surti, Urvashi ^{[8
]}

Livny, Miron ^{[9
]}

Schwartz, David C. ^{[1
,2
]}

机构：

[1] Univ Wisconsin, Dept Chem, Lab Mol & Computat Genom, Genet Lab, Madison, WI 53706 USA

[2] Univ Wisconsin, Ctr Biotechnol, Madison, WI 53706 USA

[3] Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA

[4] Univ Wisconsin, Dept Stat, Madison, WI 53706 USA

[5] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

[6] Univ Wisconsin, Dept Biostat & Med Informat, Madison, WI 53706 USA

[7] Mississippi State Univ, Dept Biol Sci, Dept Anim Sci, Mississippi State, MS 39762 USA

[8] Univ Pittsburgh, Dept Pathol, Pittsburgh, PA 15213 USA

[9] Univ Wisconsin, Dept Comp Sci, Madison, WI 53706 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2010年 / 107卷 / 24期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

structural variation; copy number variation; optical mapping; single-molecule genomics; genome assembly; COPY-NUMBER VARIATION; ORDERED RESTRICTION MAPS; SEGMENTAL DUPLICATIONS; OPTICAL MAP; SEQUENCE; SYSTEM; POLYMORPHISM; NANOSLITS;

D O I：

10.1073/pnas.0914638107

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Variation in genome structure is an important source of human genetic polymorphism: It affects a large proportion of the genome and has a variety of phenotypic consequences relevant to health and disease. In spite of this, human genome structure variation is incompletely characterized due to a lack of approaches for discovering a broad range of structural variants in a global, comprehensive fashion. We addressed this gap with Optical Mapping, a high-throughput, high-resolution single-molecule system for studying genome structure. We used Optical Mapping to create genome-wide restriction maps of a complete hydatidiform mole and three lymphoblast-derived cell lines, and we validated the approach by demonstrating a strong concordance with existing methods. We also describe thousands of new variants with sizes ranging from kb to Mb.

引用

页码：10848 / 10853

页数：6

共 44 条

[1] Optical mapping discerns genome wide DNA methylation profiles [J].

Ananiev, Gene E. ;

Goldstein, Steve ;

Runnheim, Rod ;

Forrest, Dan K. ;

Zhou, Shiguo ;

Potamousis, Konstantinos ;

Churas, Chris P. ;

Bergendahl, Veit ;

Thomson, James A. ;

Schwartz, David C. .

BMC MOLECULAR BIOLOGY, 2008, 9

[2]

Anantharaman T, 1999, Proc Int Conf Intell Syst Mol Biol, P18

[3] Primate segmental duplications: crucibles of evolution, diversity and disease [J].

Bailey, Jeffrey A. ;

Eichler, Evan E. .

NATURE REVIEWS GENETICS, 2006, 7 (07) :552-564

[4]

BOTSTEIN D, 1980, AM J HUM GENET, V32, P314

[5] Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse [J].

Church, Deanna M. ;

Goodstadt, Leo ;

Hillier, LaDeana W. ;

Zody, Michael C. ;

Goldstein, Steve ;

She, Xinwe ;

Bult, Carol J. ;

Agarwala, Richa ;

Cherry, Joshua L. ;

DiCuccio, Michael ;

Hlavina, Wratko ;

Kapustin, Yuri ;

Meric, Peter ;

Maglott, Donna ;

Birtle, Zoe ;

Marques, Ana C. ;

Graves, Tina ;

Zhou, Shiguo ;

Teague, Brian ;

Potamousis, Konstantinos ;

Churas, Christopher ;

Place, Michael ;

Herschleb, Jill ;

Runnheim, Ron ;

Forrest, Daniel ;

Amos-Landgraf, James ;

Schwartz, David C. ;

Cheng, Ze ;

Lindblad-Toh, Kerstin ;

Eichler, Evan E. ;

Ponting, Chris P. .

PLOS BIOLOGY, 2009, 7 (05)

[6] Finishing the euchromatic sequence of the human genome [J].

Collins, FS ;

Lander, ES ;

Rogers, J ;

Waterston, RH .

NATURE, 2004, 431 (7011) :931-945

[7] A high-resolution survey of deletion polymorphism in the human genome [J].

Conrad, DF ;

Andrews, TD ;

Carter, NP ;

Hurles, ME ;

Pritchard, JK .

NATURE GENETICS, 2006, 38 (01) :75-81

[8] Origins and functional impact of copy number variation in the human genome [J].

Conrad, Donald F. ;

Pinto, Dalila ;

Redon, Richard ;

Feuk, Lars ;

Gokcumen, Omer ;

Zhang, Yujun ;

Aerts, Jan ;

Andrews, T. Daniel ;

Barnes, Chris ;

Campbell, Peter ;

Fitzgerald, Tomas ;

Hu, Min ;

Ihm, Chun Hwa ;

Kristiansson, Kati ;

MacArthur, Daniel G. ;

MacDonald, Jeffrey R. ;

Onyiah, Ifejinelo ;

Pang, Andy Wing Chun ;

Robson, Sam ;

Stirrups, Kathy ;

Valsesia, Armand ;

Walter, Klaudia ;

Wei, John ;

Tyler-Smith, Chris ;

Carter, Nigel P. ;

Lee, Charles ;

Scherer, Stephen W. ;

Hurles, Matthew E. .

NATURE, 2010, 464 (7289) :704-712

[9] A microfluidic system for large DNA molecule arrays [J].

Dimalanta, ET ;

Lim, A ;

Runnheim, R ;

Lamers, C ;

Churas, C ;

Forrest, DK ;

de Pablo, JJ ;

Graham, MD ;

Coppersmith, SN ;

Goldstein, S ;

Schwartz, DC .

ANALYTICAL CHEMISTRY, 2004, 76 (18) :5293-5301

[10] MECHANISM OF ORIGIN OF COMPLETE HYDATIDIFORM MOLES [J].

JACOBS, PA ;

WILSON, CM ;

SPRENKLE, JA ;

ROSENSHEIN, NB ;

MIGEON, BR .

NATURE, 1980, 286 (5774) :714-716

← 1 2 3 4 5 →