Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection.
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TLDR
This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations.Abstract:
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced ...read more
Citations
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RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.
Liangjun Chen,Weiyong Liu,Qi Zhang,Ke Xu,Guangming Ye,Weichen Wu,Ziyong Sun,Fang Liu,Kailang Wu,Bo Zhong,Mei Yi,Wenxia Zhang,Yu Chen,Yirong Li,Mang Shi,Ke Lan,Yingle Liu +16 more
TL;DR: Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), and Evolutionary analysis based on ORF1a/1b, S, and N genes suggests2019-n coV is more likely a novel CoV independently introduced from animals to humans.
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Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
Steve Miller,Samia N. Naccache,Samia N. Naccache,Erik Samayoa,Kevin Messacar,Shaun Arevalo,Scot Federman,Doug Stryke,Elizabeth Pham,Becky Fung,William J. Bolosky,Danielle Ingebrigtsen,Walter Lorizio,Sandra M. Paff,John A. Leake,Rick L. Pesano,Roberta L. DeBiasi,Samuel R. Dominguez,Charles Y. Chiu +18 more
TL;DR: The analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF, is demonstrated.
Journal ArticleDOI
Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.
Wei Gu,Xianding Deng,Marco Lee,Yasemin D. Sucu,Shaun Arevalo,Doug Stryke,Scot Federman,Allan Gopez,Kevin Reyes,Kelsey C. Zorn,Hannah A. Sample,Guixia Yu,Gurpreet Ishpuniani,Benjamin Briggs,Eric D. Chow,Amy C. Berger,Michael R. Wilson,Candace Wang,Elaine Hsu,Steve Miller,Joseph L. DeRisi,Charles Y. Chiu +21 more
TL;DR: A universal method enables high-specificity, unbiased pathogen detection from diverse body fluids using metagenomic sequencing and may accelerate clinical decisions.
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Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Xianding Deng,Wei Gu,Scot Federman,Louis du Plessis,Oliver G. Pybus,Oliver G. Pybus,Nuno R. Faria,Nuno R. Faria,Candace Wang,Guixia Yu,Brian Bushnell,Chao Yang Pan,Hugo Guevara,Alicia Sotomayor-Gonzalez,Kelsey C. Zorn,Allan Gopez,Venice Servellita,Elaine Hsu,Steve Miller,Trevor Bedford,Alexander L. Greninger,Alexander L. Greninger,Pavitra Roychoudhury,Pavitra Roychoudhury,Lea M. Starita,Michael Famulare,Helen Y. Chu,Jay Shendure,Keith R. Jerome,Keith R. Jerome,Catie Anderson,Karthik Gangavarapu,Mark Zeller,Emily Spencer,Kristian G. Andersen,Duncan MacCannell,Clinton R. Paden,Yan Li,Jing Zhang,Suxiang Tong,Gregory L. Armstrong,Scott Morrow,Matthew Willis,Bela T. Matyas,Sundari Mase,Olivia Kasirye,Maggie Park,Godfred Masinde,Curtis Chan,Alexander T. Yu,Shua J. Chai,Shua J. Chai,Elsa Villarino,Brandon Bonin,Debra A. Wadford,Charles Y. Chiu +55 more
TL;DR: The genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020 is investigated, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship to support contact tracing, social distancing, and travel restrictions to contain the spread of the virus.
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IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.
Katrina Kalantar,Tiago Carvalho,Charles F. A. de Bourcy,Boris Dimitrov,Greg Dingle,Rebecca Egger,Julie Han,Olivia B. Holmes,Yun Fang Juan,Ryan King,Andrey Kislyuk,Michael F. Lin,Maria Mariano,Todd Morse,Lucia V. Reynoso,David Rissato Cruz,Jonathan Sheu,Jennifer Tang,James H.-C. Wang,Mark A. Zhang,Emily Zhong,Vida Ahyong,Sreyngim Lay,Sophana Chea,Jennifer A. Bohl,Jessica E. Manning,Cristina M. Tato,Joseph L. DeRisi +27 more
TL;DR: Novel virus detection capability is benchmarked using both synthetically evolved viral sequences and real-world samples, including IDseq analysis of a nasopharyngeal swab sample acquired and processed locally in Cambodia from a tourist infected with the recently emergent SARS-CoV-2.
References
More filters
Journal ArticleDOI
Trimmomatic: a flexible trimmer for Illumina sequence data
TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Journal ArticleDOI
Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease.
TL;DR: In this article, the rat pancreas RNA was used as a source for the purification of alpha-amylase messenger ribonucleic acid (RBA) using 2-mercaptoethanol.
Journal ArticleDOI
Accurate whole human genome sequencing using reversible terminator chemistry
David R. Bentley,Shankar Balasubramanian,Harold Swerdlow,Harold Swerdlow,Geoffrey Paul Smith,John Milton,John Milton,Clive Gavin Brown,Clive Gavin Brown,Kevin Hall,Dirk J. Evers,Colin Barnes,Colin Barnes,Helen Bignell,Jonathan Mark Boutell,Jason Bryant,Richard J. Carter,R. Keira Cheetham,Anthony J. Cox,Darren James Ellis,Michael R. Flatbush,Niall Anthony Gormley,Sean Humphray,Leslie J. Irving,Mirian S. Karbelashvili,Scott M. Kirk,Heng Li,Xiaohai Liu,Xiaohai Liu,Klaus Maisinger,Lisa Murray,Bojan Obradovic,Tobias William Barr Ost,Michael Lawrence Parkinson,M. R. Pratt,Isabelle Rasolonjatovo,Mark T. Reed,Roberto Rigatti,Chiara Rodighiero,Mark T. Ross,Andrea Sabot,Subramanian V. Sankar,Aylwyn Scally,Gary P. Schroth,Mark Smith,Vincent Peter Smith,Anastassia Spiridou,Peta E. Torrance,Svilen S. Tzonev,Eric Vermaas,Klaudia Walter,Wu Xiaolin,Lu Zhang,Mohammed D. Alam,Carole Anastasi,Ify C. Aniebo,David Mark Dunstan Bailey,Iain R. Bancarz,Saibal Banerjee,Selena G. Barbour,Primo Baybayan,Vincent A. Benoit,Kevin Benson,Claire Bevis,Phillip J. Black,Asha Boodhun,Joe S. Brennan,John Bridgham,Rob C. Brown,Andrew A. Brown,Dale Buermann,Abass A. Bundu,James C. Burrows,Nigel P. Carter,Nestor Castillo,Maria Chiara E. Catenazzi,Simon Chang,R. Neil Cooley,Natasha R. Crake,Olubunmi O. Dada,Konstantinos D. Diakoumakos,Belen Dominguez-Fernandez,David James Earnshaw,David James Earnshaw,Ugonna C. Egbujor,David W. Elmore,Sergey Etchin,Mark R. Ewan,Milan Fedurco,Louise Fraser,Karin Fuentes Fajardo,W. Scott Furey,David George,Kimberley J. Gietzen,Colin P. Goddard,George Stefan Golda,Philip A. Granieri,David E. Green,David L. Gustafson,Nancy F. Hansen,Kevin Harnish,Christian D. Haudenschild,Narinder I. Heyer,Matthew M. Hims,Johnny T. Ho,Adrian Horgan,Katya Hoschler,Steve Hurwitz,Denis V. Ivanov,Maria Q. Johnson,Terena James,T. A. Huw Jones,Gyoung-Dong Kang,Tzvetana H. Kerelska,Alan D. Kersey,Irina Khrebtukova,Alex P. Kindwall,Zoya Kingsbury,Paula Kokko-Gonzales,Anil Kumar,Marc Laurent,Cindy Lawley,Sarah E. Lee,Xavier Lee,Arnold Liao,Jennifer A. Loch,Mitch Lok,Shujun Luo,Radhika M. Mammen,John W. Martin,Patrick Mccauley,Paul McNitt,Parul Mehta,Keith W. Moon,Joe W. Mullens,Taksina Newington,Zemin Ning,Bee Ling Ng,Sonia M. Novo,Michael J. O'Neill,Mark A. Osborne,Mark A. Osborne,Andrew Osnowski,Omead Ostadan,Lambros L. Paraschos,Lea Pickering,Andrew C. Pike,Alger C. Pike,D. Chris Pinkard,Daniel P. Pliskin,Joe Podhasky,Victor J. Quijano,Come Raczy,Vicki H. Rae,Stephen Rawlings,Ana Chiva Rodriguez,Phyllida M. Roe,John Rogers,Maria Candelaria Rogert Bacigalupo,Nikolai Romanov,Anthony Romieu,Rithy K. Roth,Natalie J. Rourke,Silke Ruediger,Eli Rusman,Raquel Maria Sanches-Kuiper,Martin R. Schenker,Josefina M. Seoane,Richard Shaw,Mitch K. Shiver,Steven W. Short,Ning Sizto,Johannes P. Sluis,Melanie Anne Smith,Jean Ernest Sohna Sohna,Eric J. Spence,Kim B. Stevens,Neil Sutton,Lukasz Szajkowski,Carolyn Tregidgo,Gerardo Turcatti,Stephanie Vandevondele,Yuli Verhovsky,Selene M. Virk,Suzanne Wakelin,Gregory C. Walcott,Jingwen Wang,Graham John Worsley,Juying Yan,Ling Yau,Mike Zuerlein,Jane Rogers,James C. Mullikin,Matthew E. Hurles,Nick J. McCooke,Nick J. McCooke,John Stephen West,Frank L. Oaks,Peter Lundberg,David Klenerman,Richard Durbin,Anthony J. Smith +201 more
TL;DR: An approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost is reported, effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
Journal ArticleDOI
Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies
Chetan Bettegowda,Chetan Bettegowda,Mark Sausen,Rebecca J. Leary,Isaac Kinde,Yuxuan Wang,Nishant Agrawal,Nishant Agrawal,Bjarne Bartlett,Bjarne Bartlett,Hao Wang,Brandon Luber,Rhoda M. Alani,Emmanuel S. Antonarakis,Nilofer S. Azad,Alberto Bardelli,Henry Brem,John L. Cameron,Clarence Lee,Leslie A. Fecher,Leslie A. Fecher,Gary L. Gallia,Peter Gibbs,Dung T. Le,Dung T. Le,Robert L. Giuntoli,Michael Goggins,Michael D. Hogarty,Matthias Holdhoff,Seung-Mo Hong,Seung-Mo Hong,Yuchen Jiao,Hartmut Juhl,Jenny J. Kim,Giulia Siravegna,Daniel A. Laheru,Calogero Lauricella,Michael Lim,Evan J. Lipson,Suely Kazue Nagahashi Marie,George J. Netto,Kelly S. Oliner,Alessandro Olivi,Louise Olsson,Gregory J. Riggins,Andrea Sartore-Bianchi,Kerstin Schmidt,le-Ming Shih,Sueli Mieko Oba-Shinjo,Salvatore Siena,Dan Theodorescu,Jeanne Tie,Timothy T. Harkins,Silvio Veronese,Tian Li Wang,Jon D. Weingart,Christopher L. Wolfgang,Laura D. Wood,Dongmei Xing,Ralph H. Hruban,Jian Wu,Peter J. Allen,C. Max Schmidt,Michael A. Choti,Victor E. Velculescu,Kenneth W. Kinzler,Bert Vogelstein,Nickolas Papadopoulos,Luis A. Diaz,Luis A. Diaz +69 more
TL;DR: The ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types was evaluated and suggested that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes.
Journal ArticleDOI
Kraken: ultrafast metagenomic sequence classification using exact alignments
TL;DR: Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences that achieves classification accuracy comparable to the fastest BLAST program.
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