Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications

被引：230

作者：

Gu, W. ^{[1
,3
,4
]}

Crawford, E. D. ^{[2
]}

O'Donovan, B. D. ^{[5
]}

Wilson, M. R. ^{[6
]}

Chow, E. D. ^{[7
]}

Retallack, H. ^{[8
]}

DeRisi, J. L. ^{[1
,2
]}

机构：

[1] Univ Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94143 USA

[2] Howard Hughes Med Inst, Chevy Chase, MD USA

[3] Univ Calif San Francisco, Dept Pathol, San Francisco, CA 94143 USA

[4] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 USA

[5] Univ Calif San Francisco, Integrat Program Quantitat Biol Bioinformat, San Francisco, CA 94143 USA

[6] Univ Calif San Francisco, Dept Neurol, San Francisco, CA 94143 USA

[7] Univ Calif San Francisco, Dept Biochem & Biophys, Ctr Adv Technol, San Francisco, CA 94143 USA

[8] Univ Calif San Francisco, Biomed Sci Grad Program, Med Scientist Training Program, San Francisco, CA 94143 USA

来源：

GENOME BIOLOGY | 2016年 / 17卷

关键词：

Cas9; CRISPR; Depletion; Sequencing; RNA-Seq; Infectious Disease; Cancer; Diagnostics; RNA-GUIDED ENDONUCLEASE; CD-HIT; DNA; MUTATIONS; MULTIPLEX; SYSTEM; GENOME; CANCER; QUANTIFICATION; DIAGNOSIS;

D O I：

10.1186/s13059-016-0904-5

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：

Next-generation sequencing has generated a need for a broadly applicable method to remove unwanted high-abundance species prior to sequencing. We introduce DASH ( Depletion of Abundant Sequences by Hybridization). Sequencing libraries are 'DASHed' with recombinant Cas9 protein complexed with a library of guide RNAs targeting unwanted species for cleavage, thus preventing them from consuming sequencing space. We demonstrate a more than 99 % reduction of mitochondrial rRNA in HeLa cells, and enrichment of pathogen sequences in patient samples. We also demonstrate an application of DASH in cancer. This simple method can be adapted for any sample type and increases sequencing yield without additional cost.

引用

页数：13

共 55 条

[1] Comparative analysis of RNA sequencing methods for degraded or low-input samples [J].

Adiconis, Xian ;

Borges-Rivera, Diego ;

Satija, Rahul ;

DeLuca, David S. ;

Busby, Michele A. ;

Berlin, Aaron M. ;

Sivachenko, Andrey ;

Thompson, Dawn Anne ;

Wysoker, Alec ;

Fennell, Timothy ;

Gnirke, Andreas ;

Pochet, Nathalie ;

Regev, Aviv ;

Levin, Joshua Z. .

NATURE METHODS, 2013, 10 (07) :623-+

[2] Connector Inversion Probe Technology: A Powerful One-Primer Multiplex DNA Amplification System for Numerous Scientific Applications [J].

Akhras, Michael S. ;

Unemo, Magnus ;

Thiyagarajan, Sreedevi ;

Nyren, Pal ;

Davis, Ronald W. ;

Fire, Andrew Z. ;

Pourmand, Nader .

PLOS ONE, 2007, 2 (09)

[3] Signatures of mutational processes in human cancer [J].

Alexandrov, Ludmil B. ;

Nik-Zainal, Serena ;

Wedge, David C. ;

Aparicio, Samuel A. J. R. ;

Behjati, Sam ;

Biankin, Andrew V. ;

Bignell, Graham R. ;

Bolli, Niccolo ;

Borg, Ake ;

Borresen-Dale, Anne-Lise ;

Boyault, Sandrine ;

Burkhardt, Birgit ;

Butler, Adam P. ;

Caldas, Carlos ;

Davies, Helen R. ;

Desmedt, Christine ;

Eils, Roland ;

Eyfjord, Jorunn Erla ;

Foekens, John A. ;

Greaves, Mel ;

Hosoda, Fumie ;

Hutter, Barbara ;

Ilicic, Tomislav ;

Imbeaud, Sandrine ;

Imielinsk, Marcin ;

Jaeger, Natalie ;

Jones, David T. W. ;

Jones, David ;

Knappskog, Stian ;

Kool, Marcel ;

Lakhani, Sunil R. ;

Lopez-Otin, Carlos ;

Martin, Sancha ;

Munshi, Nikhil C. ;

Nakamura, Hiromi ;

Northcott, Paul A. ;

Pajic, Marina ;

Papaemmanuil, Elli ;

Paradiso, Angelo ;

Pearson, John V. ;

Puente, Xose S. ;

Raine, Keiran ;

Ramakrishna, Manasa ;

Richardson, Andrea L. ;

Richter, Julia ;

Rosenstiel, Philip ;

Schlesner, Matthias ;

Schumacher, Ton N. ;

Span, Paul N. ;

Teague, Jon W. .

NATURE, 2013, 500 (7463) :415-+

[4] MOST HUMAN CARCINOMAS OF THE EXOCRINE PANCREAS CONTAIN MUTANT C-K-RAS GENES [J].

ALMOGUERA, C ;

SHIBATA, D ;

FORRESTER, K ;

MARTIN, J ;

ARNHEIM, N ;

PERUCHO, M .

CELL, 1988, 53 (04) :549-554

[5] Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies [J].

Bettegowda, Chetan ;

Sausen, Mark ;

Leary, Rebecca J. ;

Kinde, Isaac ;

Wang, Yuxuan ;

Agrawal, Nishant ;

Bartlett, Bjarne R. ;

Wang, Hao ;

Luber, Brandon ;

Alani, Rhoda M. ;

Antonarakis, Emmanuel S. ;

Azad, Nilofer S. ;

Bardelli, Alberto ;

Brem, Henry ;

Cameron, John L. ;

Lee, Clarence C. ;

Fecher, Leslie A. ;

Gallia, Gary L. ;

Gibbs, Peter ;

Le, Dung ;

Giuntoli, Robert L. ;

Goggins, Michael ;

Hogarty, Michael D. ;

Holdhoff, Matthias ;

Hong, Seung-Mo ;

Jiao, Yuchen ;

Juhl, Hartmut H. ;

Kim, Jenny J. ;

Siravegna, Giulia ;

Laheru, Daniel A. ;

Lauricella, Calogero ;

Lim, Michael ;

Lipson, Evan J. ;

Marie, Suely Kazue Nagahashi ;

Netto, George J. ;

Oliner, Kelly S. ;

Olivi, Alessandro ;

Olsson, Louise ;

Riggins, Gregory J. ;

Sartore-Bianchi, Andrea ;

Schmidt, Kerstin ;

Shih, Ie-Ming ;

Oba-Shinjo, Sueli Mieko ;

Siena, Salvatore ;

Theodorescu, Dan ;

Tie, Jeanne ;

Harkins, Timothy T. ;

Veronese, Silvio ;

Wang, Tian-Li ;

Weingart, Jon D. .

SCIENCE TRANSLATIONAL MEDICINE, 2014, 6 (224)

[6] Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis [J].

Briese, Thomas ;

Kapoor, Amit ;

Mishra, Nischay ;

Jain, Komal ;

Kumar, Arvind ;

Jabado, Omar J. ;

Lipkin, W. Ian .

MBIO, 2015, 6 (05)

[7] MUTATIONS IN THE KRAS2 ONCOGENE DURING PROGRESSIVE STAGES OF HUMAN-COLON CARCINOMA [J].

BURMER, GC ;

LOEB, LA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1989, 86 (07) :2403-2407

[8] Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System [J].

Chen, Baohui ;

Gilbert, Luke A. ;

Cimini, Beth A. ;

Schnitzbauer, Joerg ;

Zhang, Wei ;

Li, Gene-Wei ;

Park, Jason ;

Blackburn, Elizabeth H. ;

Weissman, Jonathan S. ;

Qi, Lei S. ;

Huang, Bo .

CELL, 2013, 155 (07) :1479-1491

[9] 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

[10] Multiplex Genome Engineering Using CRISPR/Cas Systems [J].

Cong, Le ;

Ran, F. Ann ;

Cox, David ;

Lin, Shuailiang ;

Barretto, Robert ;

Habib, Naomi ;

Hsu, Patrick D. ;

Wu, Xuebing ;

Jiang, Wenyan ;

Marraffini, Luciano A. ;

Zhang, Feng .

SCIENCE, 2013, 339 (6121) :819-823

← 1 2 3 4 5 6 →