Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

被引：788

作者：

Rohland, Nadin ^{[1
]}

Reich, David

机构：

[1] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

来源：

GENOME RESEARCH | 2012年 / 22卷 / 05期

关键词：

FULLY AUTOMATED PROCESS; GENOMIC ENRICHMENT; CONSTRUCTION; DISCOVERY; SELECTION;

D O I：

10.1101/gr.128124.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about $15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.

引用

页码：939 / 946

页数：8

共 30 条

[1] Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition [J].

Adey, Andrew ;

Morrison, Hilary G. ;

Asan ;

Xun, Xu ;

Kitzman, Jacob O. ;

Turner, Emily H. ;

Stackhouse, Bethany ;

MacKenzie, Alexandra P. ;

Caruccio, Nicholas C. ;

Zhang, Xiuqing ;

Shendure, Jay .

GENOME BIOLOGY, 2010, 11 (12)

[2] Direct selection of human genomic loci by microarray hybridization [J].

Albert, Thomas J. ;

Molla, Michael N. ;

Muzny, Donna M. ;

Nazareth, Lynne ;

Wheeler, David ;

Song, Xingzhi ;

Richmond, Todd A. ;

Middle, Chris M. ;

Rodesch, Matthew J. ;

Packard, Charles J. ;

Weinstock, George M. ;

Gibbs, Richard A. .

NATURE METHODS, 2007, 4 (11) :903-905

[3] Hundreds of variants clustered in genomic loci and biological pathways affect human height [J].

Allen, Hana Lango ;

Estrada, Karol ;

Lettre, Guillaume ;

Berndt, Sonja I. ;

Weedon, Michael N. ;

Rivadeneira, Fernando ;

Willer, Cristen J. ;

Jackson, Anne U. ;

Vedantam, Sailaja ;

Raychaudhuri, Soumya ;

Ferreira, Teresa ;

Wood, Andrew R. ;

Weyant, Robert J. ;

Segre, Ayellet V. ;

Speliotes, Elizabeth K. ;

Wheeler, Eleanor ;

Soranzo, Nicole ;

Park, Ju-Hyun ;

Yang, Jian ;

Gudbjartsson, Daniel ;

Heard-Costa, Nancy L. ;

Randall, Joshua C. ;

Qi, Lu ;

Smith, Albert Vernon ;

Maegi, Reedik ;

Pastinen, Tomi ;

Liang, Liming ;

Heid, Iris M. ;

Luan, Jian'an ;

Thorleifsson, Gudmar ;

Winkler, Thomas W. ;

Goddard, Michael E. ;

Lo, Ken Sin ;

Palmer, Cameron ;

Workalemahu, Tsegaselassie ;

Aulchenko, Yurii S. ;

Johansson, Asa ;

Zillikens, M. Carola ;

Feitosa, Mary F. ;

Esko, Tonu ;

Johnson, Toby ;

Ketkar, Shamika ;

Kraft, Peter ;

Mangino, Massimo ;

Prokopenko, Inga ;

Absher, Devin ;

Albrecht, Eva ;

Ernst, Florian ;

Glazer, Nicole L. ;

Hayward, Caroline .

NATURE, 2010, 467 (7317) :832-838

[4] A map of human genome variation from population-scale sequencing [J].

Altshuler, David ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Collins, Francis S. ;

De la Vega, Francisco M. ;

Donnelly, Peter ;

Egholm, Michael ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Knoppers, Bartha M. ;

Lander, Eric S. ;

Lehrach, Hans ;

Mardis, Elaine R. ;

McVean, Gil A. ;

Nickerson, DebbieA. ;

Peltonen, Leena ;

Schafer, Alan J. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Deiros, David ;

Metzker, Mike ;

Muzny, Donna ;

Reid, Jeff ;

Wheeler, David ;

Wang, Jun ;

Li, Jingxiang ;

Jian, Min ;

Li, Guoqing ;

Li, Ruiqiang ;

Liang, Huiqing ;

Tian, Geng ;

Wang, Bo ;

Wang, Jian ;

Wang, Wei ;

Yang, Huanming ;

Zhang, Xiuqing ;

Zheng, Huisong ;

Lander, Eric S. ;

Altshuler, David L. ;

Ambrogio, Lauren ;

Bloom, Toby ;

Cibulskis, Kristian ;

Fennell, Tim J. ;

Gabriel, Stacey B. .

NATURE, 2010, 467 (7319) :1061-1073

[5] Large Scale Library Generation for High Throughput Sequencing Authors and Affiliations [J].

Borgstrom, Erik ;

Lundin, Sverker ;

Lundeberg, Joakim .

PLOS ONE, 2011, 6 (04)

[6] Performance comparison of exome DNA sequencing technologies [J].

Clark, Michael J. ;

Chen, Rui ;

Lam, Hugo Y. K. ;

Karczewski, Konrad J. ;

Chen, Rong ;

Euskirchen, Ghia ;

Butte, Atul J. ;

Snyder, Michael .

NATURE BIOTECHNOLOGY, 2011, 29 (10) :908-U206

[7]

Craig DW, 2008, NAT METHODS, V5, P887, DOI [10.1038/nmeth.1251, 10.1038/NMETH.1251]

[8] Combining target enrichment with barcode multiplexing for high throughput SNP discovery [J].

Cummings, Nik ;

King, Rob ;

Rickers, Andre ;

Kaspi, Antony ;

Lunke, Sebastian ;

Haviv, Izhak ;

Jowett, Jeremy B. M. .

BMC GENOMICS, 2010, 11

[9] SOLID-PHASE REVERSIBLE IMMOBILIZATION FOR THE ISOLATION OF PCR PRODUCTS [J].

DEANGELIS, MM ;

WANG, DG ;

HAWKINS, TL .

NUCLEIC ACIDS RESEARCH, 1995, 23 (22) :4742-4743

[10] Semi-Automated Library Preparation for High-Throughput DNA Sequencing Platforms [J].

Farias-Hesson, Eveline ;

Erikson, Jonathan ;

Atkins, Alexander ;

Shen, Peidong ;

Davis, Ronald W. ;

Scharfe, Curt ;

Pourmand, Nader .

JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, 2010,

← 1 2 3 →