A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

被引：321

作者：

Fisher, Sheila ^{[2
]}

Barry, Andrew ^{[2
]}

Abreu, Justin ^{[2
]}

Minie, Brian ^{[2
]}

Nolan, Jillian ^{[2
]}

Delorey, Toni M. ^{[2
]}

Young, Geneva ^{[2
]}

Fennell, Timothy J. ^{[2
]}

Allen, Alexander ^{[2
]}

Ambrogio, Lauren ^{[2
]}

Berlin, Aaron M. ^{[1
,2
]}

Blumenstiel, Brendan ^{[2
]}

Cibulskis, Kristian ^{[2
]}

Friedrich, Dennis ^{[2
]}

Johnson, Ryan ^{[2
]}

Juhn, Frank ^{[3
]}

Reilly, Brian ^{[2
]}

Shammas, Ramy ^{[2
]}

Stalker, John ^{[2
]}

Sykes, Sean M. ^{[1
,2
]}

Thompson, Jon ^{[2
]}

Walsh, John ^{[2
]}

Zimmer, Andrew ^{[2
]}

Zwirko, Zac ^{[2
,3
]}

Gabriel, Stacey ^{[1
,2
]}

Nicol, Robert ^{[2
]}

Nusbaum, Chad ^{[1
,2
]}

机构：

[1] MIT, Genome Sequencing & Anal Program, Broad Inst, Cambridge, MA 02141 USA

[2] Harvard Univ, Cambridge, MA 02141 USA

[3] Fdn Med, Cambridge, MA 02139 USA

来源：

GENOME BIOLOGY | 2011年 / 12卷 / 01期

关键词：

HUMAN GENOME; DNA; MUTATIONS; DISCOVERY;

D O I：

10.1186/gb-2011-12-1-r1

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 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Genome targeting methods enable cost-effective capture of specific subsets of the genome for sequencing. We present here an automated, highly scalable method for carrying out the Solution Hybrid Selection capture approach that provides a dramatic increase in scale and throughput of sequence-ready libraries produced. Significant process improvements and a series of in-process quality control checkpoints are also added. These process improvements can also be used in a manual version of the protocol.

引用

页数：15

共 31 条

[1]

Whole exome capture in solution with 3 Gbp of data [J].

Bainbridge, Matthew N. ;

Wang, Min ;

Burgess, Daniel L. ;

Kovar, Christie ;

Rodesch, Matthew J. ;

D'Ascenzo, Mark ;

Kitzman, Jacob ;

Wu, Yuan-Qing ;

Newsham, Irene ;

Richmond, Todd A. ;

Jeddeloh, Jeffrey A. ;

Muzny, Donna ;

Albert, Thomas J. ;

Gibbs, Richard A. .

GENOME BIOLOGY, 2010, 11 (06)

[2]

Accurate whole human genome sequencing using reversible terminator chemistry [J].

Bentley, David R. ;

Balasubramanian, Shankar ;

Swerdlow, Harold P. ;

Smith, Geoffrey P. ;

Milton, John ;

Brown, Clive G. ;

Hall, Kevin P. ;

Evers, Dirk J. ;

Barnes, Colin L. ;

Bignell, Helen R. ;

Boutell, Jonathan M. ;

Bryant, Jason ;

Carter, Richard J. ;

Cheetham, R. Keira ;

Cox, Anthony J. ;

Ellis, Darren J. ;

Flatbush, Michael R. ;

Gormley, Niall A. ;

Humphray, Sean J. ;

Irving, Leslie J. ;

Karbelashvili, Mirian S. ;

Kirk, Scott M. ;

Li, Heng ;

Liu, Xiaohai ;

Maisinger, Klaus S. ;

Murray, Lisa J. ;

Obradovic, Bojan ;

Ost, Tobias ;

Parkinson, Michael L. ;

Pratt, Mark R. ;

Rasolonjatovo, Isabelle M. J. ;

Reed, Mark T. ;

Rigatti, Roberto ;

Rodighiero, Chiara ;

Ross, Mark T. ;

Sabot, Andrea ;

Sankar, Subramanian V. ;

Scally, Aylwyn ;

Schroth, Gary P. ;

Smith, Mark E. ;

Smith, Vincent P. ;

Spiridou, Anastassia ;

Torrance, Peta E. ;

Tzonev, Svilen S. ;

Vermaas, Eric H. ;

Walter, Klaudia ;

Wu, Xiaolin ;

Zhang, Lu ;

Alam, Mohammed D. ;

Anastasi, Carole .

NATURE, 2008, 456 (7218) :53-59

[3]

BLEEKER LG, 2010, NAT GENET, V42, P13

[4]

Genetic diagnosis by whole exome capture and massively parallel DNA sequencing [J].

Choi, Murim ;

Scholl, Ute I. ;

Ji, Weizhen ;

Liu, Tiewen ;

Tikhonova, Irina R. ;

Zumbo, Paul ;

Nayir, Ahmet ;

Bakkaloglu, Aysin ;

Ozen, Seza ;

Sanjad, Sami ;

Nelson-Williams, Carol ;

Farhi, Anita ;

Mane, Shrikant ;

Lifton, Richard P. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) :19096-19101

[5]

Targeted High-Throughput DNA Sequencing for Gene Discovery in Retinitis Pigmentosa [J].

Daiger, Stephen P. ;

Sullivan, Lori S. ;

Bowne, Sara J. ;

Birch, David G. ;

Heckenlively, John R. ;

Pierce, Eric A. ;

Weinstock, George M. .

RETINAL DEGENERATIVE DISEASES: LABORATORY AND THERAPEUTIC INVESTIGATIONS, 2010, 664 :325-331

[6]

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays [J].

Drmanac, Radoje ;

Sparks, Andrew B. ;

Callow, Matthew J. ;

Halpern, Aaron L. ;

Burns, Norman L. ;

Kermani, Bahram G. ;

Carnevali, Paolo ;

Nazarenko, Igor ;

Nilsen, Geoffrey B. ;

Yeung, George ;

Dahl, Fredrik ;

Fernandez, Andres ;

Staker, Bryan ;

Pant, Krishna P. ;

Baccash, Jonathan ;

Borcherding, Adam P. ;

Brownley, Anushka ;

Cedeno, Ryan ;

Chen, Linsu ;

Chernikoff, Dan ;

Cheung, Alex ;

Chirita, Razvan ;

Curson, Benjamin ;

Ebert, Jessica C. ;

Hacker, Coleen R. ;

Hartlage, Robert ;

Hauser, Brian ;

Huang, Steve ;

Jiang, Yuan ;

Karpinchyk, Vitali ;

Koenig, Mark ;

Kong, Calvin ;

Landers, Tom ;

Le, Catherine ;

Liu, Jia ;

McBride, Celeste E. ;

Morenzoni, Matt ;

Morey, Robert E. ;

Mutch, Karl ;

Perazich, Helena ;

Perry, Kimberly ;

Peters, Brock A. ;

Peterson, Joe ;

Pethiyagoda, Charit L. ;

Pothuraju, Kaliprasad ;

Richter, Claudia ;

Rosenbaum, Abraham M. ;

Roy, Shaunak ;

Shafto, Jay ;

Sharanhovich, Uladzislau .

SCIENCE, 2010, 327 (5961) :78-81

[7]

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing [J].

Gnirke, Andreas ;

Melnikov, Alexandre ;

Maguire, Jared ;

Rogov, Peter ;

LeProust, Emily M. ;

Brockman, William ;

Fennell, Timothy ;

Giannoukos, Georgia ;

Fisher, Sheila ;

Russ, Carsten ;

Gabriel, Stacey ;

Jaffe, David B. ;

Lander, Eric S. ;

Nusbaum, Chad .

NATURE BIOTECHNOLOGY, 2009, 27 (02) :182-189

[8]

DNA PURIFICATION AND ISOLATION USING A SOLID-PHASE [J].

HAWKINS, TL ;

OCONNORMORIN, T ;

ROY, A ;

SANTILLAN, C .

NUCLEIC ACIDS RESEARCH, 1994, 22 (21) :4543-4544

[9]

Exome Sequencing of a Multigenerational Human Pedigree [J].

Hedges, Dale ;

Burges, Dan ;

Powell, Eric ;

Almonte, Cherylyn ;

Huang, Jia ;

Young, Stuart ;

Boese, Benjamin ;

Schmidt, Mike ;

Pericak-Vance, Margaret A. ;

Martin, Eden ;

Zhang, Xinmin ;

Harkins, Timothy T. ;

Zuechner, Stephan .

PLOS ONE, 2009, 4 (12)

[10]

Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection [J].

Herman, Daniel S. ;

Hovingh, G. Kees ;

Iartchouk, Oleg ;

Rehm, Heidi L. ;

Kucherlapati, Raju ;

Seidman, J. G. ;

Seidman, Christine E. .

NATURE METHODS, 2009, 6 (07) :507-U57

← 1 2 3 4 →