Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells

被引:173
作者
Gole, Jeff [1 ,2 ]
Gore, Athurva [1 ,2 ]
Richards, Andrew [1 ,2 ]
Chiu, Yu-Jui [3 ]
Fung, Ho-Lim [1 ,2 ]
Bushman, Diane [4 ]
Chiang, Hsin-I [1 ,2 ]
Chun, Jerold [4 ]
Lo, Yu-Hwa [5 ]
Zhang, Kun [1 ,2 ]
机构
[1] Univ Calif San Diego, Dept Bioengn, Inst Genom Med, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Inst Engn Med, La Jolla, CA 92093 USA
[3] Univ Calif San Diego, Mat Sci & Engn Program, La Jolla, CA 92093 USA
[4] Scripps Res Inst, Dorris Neurosci Ctr, Dept Mol & Cellular Neurosci, La Jolla, CA 92037 USA
[5] Univ Calif San Diego, Dept Elect & Comp Engn, La Jolla, CA 92093 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
SPERM CELLS; ANEUPLOIDY; RECOMBINATION; AMPLIFICATION; NUCLEOTIDE; MOSAICISM; EVOLUTION; RARE;
D O I
10.1038/nbt.2720
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Genome sequencing of single cells has a variety of applications, including characterizing difficult-to-culture microorganisms and identifying somatic mutations in single cells from mammalian tissues. A major hurdle in this process is the bias in amplifying the genetic material from a single cell, a procedure known as polymerase cloning. Here we describe the microwell displacement amplification system (MIDAS), a massively parallel polymerase cloning method in which single cells are randomly distributed into hundreds to thousands of nanoliter wells and their genetic material is simultaneously amplified for shotgun sequencing. MIDAS reduces amplification bias because polymerase cloning occurs in physically separated, nanoliter-scale reactors, facilitating the de novo assembly of near-complete microbial genomes from single Escherichia coli cells. In addition, MIDAS allowed us to detect single-copy number changes in primary human adult neurons at 1- to 2-Mb resolution. MIDAS can potentially further the characterization of genomic diversity in many heterogeneous cell populations.
引用
收藏
页码:1126 / +
页数:9
相关论文
共 39 条
[1]   Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing [J].
Adey, Andrew ;
Shendure, Jay .
GENOME RESEARCH, 2012, 22 (06) :1139-1143
[2]   Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes [J].
Albertsen, Mads ;
Hugenholtz, Philip ;
Skarshewski, Adam ;
Nielsen, Kare L. ;
Tyson, Gene W. ;
Nielsen, Per H. .
NATURE BIOTECHNOLOGY, 2013, 31 (06) :533-+
[3]   An integrated map of genetic variation from 1,092 human genomes [J].
Altshuler, David M. ;
Durbin, Richard M. ;
Abecasis, Goncalo R. ;
Bentley, David R. ;
Chakravarti, Aravinda ;
Clark, Andrew G. ;
Donnelly, Peter ;
Eichler, Evan E. ;
Flicek, Paul ;
Gabriel, Stacey B. ;
Gibbs, Richard A. ;
Green, Eric D. ;
Hurles, Matthew E. ;
Knoppers, Bartha M. ;
Korbel, Jan O. ;
Lander, Eric S. ;
Lee, Charles ;
Lehrach, Hans ;
Mardis, Elaine R. ;
Marth, Gabor T. ;
McVean, Gil A. ;
Nickerson, Deborah A. ;
Schmidt, Jeanette P. ;
Sherry, Stephen T. ;
Wang, Jun ;
Wilson, Richard K. ;
Gibbs, Richard A. ;
Dinh, Huyen ;
Kovar, Christie ;
Lee, Sandra ;
Lewis, Lora ;
Muzny, Donna ;
Reid, Jeff ;
Wang, Min ;
Wang, Jun ;
Fang, Xiaodong ;
Guo, Xiaosen ;
Jian, Min ;
Jiang, Hui ;
Jin, Xin ;
Li, Guoqing ;
Li, Jingxiang ;
Li, Yingrui ;
Li, Zhuo ;
Liu, Xiao ;
Lu, Yao ;
Ma, Xuedi ;
Su, Zhe ;
Tai, Shuaishuai ;
Tang, Meifang .
NATURE, 2012, 491 (7422) :56-65
[4]   The RAST server: Rapid annotations using subsystems technology [J].
Aziz, Ramy K. ;
Bartels, Daniela ;
Best, Aaron A. ;
DeJongh, Matthew ;
Disz, Terrence ;
Edwards, Robert A. ;
Formsma, Kevin ;
Gerdes, Svetlana ;
Glass, Elizabeth M. ;
Kubal, Michael ;
Meyer, Folker ;
Olsen, Gary J. ;
Olson, Robert ;
Osterman, Andrei L. ;
Overbeek, Ross A. ;
McNeil, Leslie K. ;
Paarmann, Daniel ;
Paczian, Tobias ;
Parrello, Bruce ;
Pusch, Gordon D. ;
Reich, Claudia ;
Stevens, Rick ;
Vassieva, Olga ;
Vonstein, Veronika ;
Wilke, Andreas ;
Zagnitko, Olga .
BMC GENOMICS, 2008, 9 (1)
[5]   SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].
Bankevich, Anton ;
Nurk, Sergey ;
Antipov, Dmitry ;
Gurevich, Alexey A. ;
Dvorkin, Mikhail ;
Kulikov, Alexander S. ;
Lesin, Valery M. ;
Nikolenko, Sergey I. ;
Son Pham ;
Prjibelski, Andrey D. ;
Pyshkin, Alexey V. ;
Sirotkin, Alexander V. ;
Vyahhi, Nikolay ;
Tesler, Glenn ;
Alekseyev, Max A. ;
Pevzner, Pavel A. .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477
[6]   Genome-wide copy number analysis of single cells [J].
Baslan, Timour ;
Kendall, Jude ;
Rodgers, Linda ;
Cox, Hilary ;
Riggs, Mike ;
Stepansky, Asya ;
Troge, Jennifer ;
Ravi, Kandasamy ;
Esposito, Diane ;
Lakshmi, B. ;
Wigler, Michael ;
Navin, Nicholas ;
Hicks, James .
NATURE PROTOCOLS, 2012, 7 (06) :1024-1041
[7]   Digital MDA for enumeration of total nucleic acid contamination [J].
Blainey, Paul C. ;
Quake, Stephen R. .
NUCLEIC ACIDS RESEARCH, 2011, 39 (04) :e19
[8]   Efficient de novo assembly of single-cell bacterial genomes from short-read data sets [J].
Chitsaz, Hamidreza ;
Yee-Greenbaum, Joyclyn L. ;
Tesler, Glenn ;
Lombardo, Mary-Jane ;
Dupont, Christopher L. ;
Badger, Jonathan H. ;
Novotny, Mark ;
Rusch, Douglas B. ;
Fraser, Louise J. ;
Gormley, Niall A. ;
Schulz-Trieglaff, Ole ;
Smith, Geoffrey P. ;
Evers, Dirk J. ;
Pevzner, Pavel A. ;
Lasken, Roger S. .
NATURE BIOTECHNOLOGY, 2011, 29 (10) :915-U214
[9]   Whole-genome molecular haplotyping of single cells [J].
Fan, H. Christina ;
Wang, Jianbin ;
Potanina, Anastasia ;
Quake, Stephen R. .
NATURE BIOTECHNOLOGY, 2011, 29 (01) :51-+
[10]   Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome [J].
Fitzsimons, Michael S. ;
Novotny, Mark ;
Lo, Chien-Chi ;
Dichosa, Armand E. K. ;
Yee-Greenbaum, Joyclyn L. ;
Snook, Jeremy P. ;
Gu, Wei ;
Chertkov, Olga ;
Davenport, Karen W. ;
McMurry, Kim ;
Reitenga, Krista G. ;
Daughton, Ashlynn R. ;
He, Jian ;
Johnson, Shannon L. ;
Gleasner, Cheryl D. ;
Wills, Patti L. ;
Parson-Quintana, Beverly ;
Chain, Patrick S. ;
Detter, John C. ;
Lasken, Roger S. ;
Han, Cliff S. .
GENOME RESEARCH, 2013, 23 (05) :878-888