Targeted single molecule mutation detection with massively parallel sequencing.
作者： Mark T. Gregory , Jessica A. Bertout , Nolan G. Ericson , Sean D. Taylor , Rithun Mukherjee
DOI: 10.1093/NAR/GKV915
关键词: Shotgun sequencing 、 Biology 、 Cancer genome sequencing 、 Genetics 、 Deep sequencing 、 Massive parallel sequencing 、 DNA sequencing 、 Sequencing by ligation 、 Exome sequencing 、 DNA nanoball sequencing
摘要: Next-generation sequencing (NGS) technologies have transformed genomic research and the potential to revolutionize clinical medicine. However, background error rates of instruments limitations in targeted read coverage precluded detection rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding correction rolling circle amplification (RCA)-based target enrichment vastly improve NGS-based variant detection. The CypherSeq methodology involves ligation sample into circular vectors, contain barcodes for computational adapters library preparation sequencing. is capable detecting mutations genome-wide as well those within specific genes via RCA-based enrichment. We demonstrate that correcting errors incurred during reproducibly detect down frequency 2.4 × 10(-7) per base pair, report spectra spontaneous ethyl methanesulfonate-induced across Saccharomyces cerevisiae genome.
oup.com
paperity.org
oxfordjournals.org参考文章(37)
Hidetaka Uramoto, Fumihiro Tanaka, Recurrence after surgery in patients with NSCLC Translational lung cancer research. ,vol. 3, pp. 242- 249 ,(2014) , 10.3978/J.ISSN.2218-6751.2013.12.05
Matthew T. Laurie, Jessica A. Bertout, Sean D. Taylor, Joshua N. Burton, Jay A. Shendure, Jason H. Bielas, Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries. BioTechniques. ,vol. 55, pp. 61- 67 ,(2013) , 10.2144/000114063
Jef D. Boeke, Joshua Trueheart, Georges Natsoulis, Gerald R. Fink, 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods in Enzymology. ,vol. 154, pp. 164- 175 ,(1987) , 10.1016/0076-6879(87)54076-9
C Schlötterer, R Kofler, E Versace, R Tobler, S U Franssen, Combining Experimental Evolution With Next-Generation Sequencing: A Powerful Tool to Study Adaptation From Standing Genetic Variation Heredity. ,vol. 114, pp. 431- 440 ,(2015) , 10.1038/HDY.2014.86
Aaron M Newman, Scott V Bratman, Jacqueline To, Jacob F Wynne, Neville C W Eclov, Leslie A Modlin, Chih Long Liu, Joel W Neal, Heather A Wakelee, Robert E Merritt, Joseph B Shrager, Billy W Loo, Ash A Alizadeh, Maximilian Diehn, An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage Nature Medicine. ,vol. 20, pp. 548- 554 ,(2014) , 10.1038/NM.3519
Yiping He, Jian Wu, Devin C. Dressman, Christine Iacobuzio-Donahue, Sanford D. Markowitz, Victor E. Velculescu, Luis A. Diaz Jr, Kenneth W. Kinzler, Bert Vogelstein, Nickolas Papadopoulos, Heteroplasmic mitochondrial DNA mutations in normal and tumour cells Nature. ,vol. 464, pp. 610- 614 ,(2010) , 10.1038/NATURE08802
Peter M Power, Stephen D Bentley, Julian Parkhill, E Moxon, Derek W Hood, Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants BMC Microbiology. ,vol. 12, pp. 273- 273 ,(2012) , 10.1186/1471-2180-12-273
Christian Schlötterer, Raymond Tobler, Robert Kofler, Viola Nolte, Sequencing pools of individuals — mining genome-wide polymorphism data without big funding Nature Reviews Genetics. ,vol. 15, pp. 749- 763 ,(2014) , 10.1038/NRG3803
Ramin Nazarian, Hubing Shi, Qi Wang, Xiangju Kong, Richard C. Koya, Hane Lee, Zugen Chen, Mi-Kyung Lee, Narsis Attar, Hooman Sazegar, Thinle Chodon, Stanley F. Nelson, Grant McArthur, Jeffrey A. Sosman, Antoni Ribas, Roger S. Lo, Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation Nature. ,vol. 468, pp. 973- 977 ,(2010) , 10.1038/NATURE09626
Michael A Quail, Iwanka Kozarewa, Frances Smith, Aylwyn Scally, Philip J Stephens, Richard Durbin, Harold Swerdlow, Daniel J Turner, A large genome center's improvements to the Illumina sequencing system Nature Methods. ,vol. 5, pp. 1005- 1010 ,(2008) , 10.1038/NMETH.1270