Literature DB >> 31626891

An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients.

Thidathip Wongsurawat1, Mayumi Nakagawa2, Omar Atiq3, Hannah N Coleman2, Piroon Jenjaroenpun1, James I Allred4, Angela Trammel4, Pantakan Puengrang5, David W Ussery6, Intawat Nookaew7.   

Abstract

Gut metagenome profiling using the Oxford Nanopore Technologies (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species. IT better detected low-abundance species through amplification, when material was limited.
Copyright © 2019 Elsevier B.V. All rights reserved.

Entities:  

Keywords:  Head and neck cancer; Microbiome; Next-generation sequencing; Shotgun metagenome sequencing; Third-generation sequencing

Year:  2019        PMID： 31626891      PMCID： PMC6956648          DOI： 10.1016/j.mimet.2019.105739

Source DB:  PubMed          Journal:  J Microbiol Methods        ISSN： 0167-7012            Impact factor:   2.363


  25 in total

1.  Oral microbiome, periodontitis and risk of head and neck cancer.

Authors:  Leonardo Victor Galvão-Moreira; Maria Carmen Fontoura Nogueira da Cruz
Journal:  Oral Oncol       Date:  2015-12-10       Impact factor: 5.337

2.  The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients.

Authors:  Vyara Matson; Jessica Fessler; Riyue Bao; Tara Chongsuwat; Yuanyuan Zha; Maria-Luisa Alegre; Jason J Luke; Thomas F Gajewski
Journal:  Science       Date:  2018-01-05       Impact factor: 47.728

Review 3.  Shotgun metagenomics, from sampling to analysis.

Authors:  Christopher Quince; Alan W Walker; Jared T Simpson; Nicholas J Loman; Nicola Segata
Journal:  Nat Biotechnol       Date:  2017-09-12       Impact factor: 54.908

4.  Human papillomavirus type 16 viral load is decreased following a therapeutic vaccination.

Authors:  Hannah N Coleman; William W Greenfield; Shawna L Stratton; Rita Vaughn; Alexander Kieber; Andrea M Moerman-Herzog; Horace J Spencer; Wilbur C Hitt; Charles Matthew Quick; Laura F Hutchins; Samuel G Mackintosh; Ricky D Edmondson; Stephen W Erickson; Mayumi Nakagawa
Journal:  Cancer Immunol Immunother       Date:  2016-03-15       Impact factor: 6.968

Review 5.  Update on Head and Neck Cancer: Current Knowledge on Epidemiology, Risk Factors, Molecular Features and Novel Therapies.

Authors:  Francesca Pezzuto; Luigi Buonaguro; Francesco Caponigro; Franco Ionna; Noemy Starita; Clorinda Annunziata; Franco M Buonaguro; Maria Lina Tornesello
Journal:  Oncology       Date:  2015-05-08       Impact factor: 2.935

6.  Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.

Authors:  V Gopalakrishnan; C N Spencer; L Nezi; A Reuben; M C Andrews; T V Karpinets; P A Prieto; D Vicente; K Hoffman; S C Wei; A P Cogdill; L Zhao; C W Hudgens; D S Hutchinson; T Manzo; M Petaccia de Macedo; T Cotechini; T Kumar; W S Chen; S M Reddy; R Szczepaniak Sloane; J Galloway-Pena; H Jiang; P L Chen; E J Shpall; K Rezvani; A M Alousi; R F Chemaly; S Shelburne; L M Vence; P C Okhuysen; V B Jensen; A G Swennes; F McAllister; E Marcelo Riquelme Sanchez; Y Zhang; E Le Chatelier; L Zitvogel; N Pons; J L Austin-Breneman; L E Haydu; E M Burton; J M Gardner; E Sirmans; J Hu; A J Lazar; T Tsujikawa; A Diab; H Tawbi; I C Glitza; W J Hwu; S P Patel; S E Woodman; R N Amaria; M A Davies; J E Gershenwald; P Hwu; J E Lee; J Zhang; L M Coussens; Z A Cooper; P A Futreal; C R Daniel; N J Ajami; J F Petrosino; M T Tetzlaff; P Sharma; J P Allison; R R Jenq; J A Wargo
Journal:  Science       Date:  2017-11-02       Impact factor: 47.728

7.  An integrated catalog of reference genes in the human gut microbiome.

Authors:  Junhua Li; Huijue Jia; Xianghang Cai; Huanzi Zhong; Qiang Feng; Shinichi Sunagawa; Manimozhiyan Arumugam; Jens Roat Kultima; Edi Prifti; Trine Nielsen; Agnieszka Sierakowska Juncker; Chaysavanh Manichanh; Bing Chen; Wenwei Zhang; Florence Levenez; Juan Wang; Xun Xu; Liang Xiao; Suisha Liang; Dongya Zhang; Zhaoxi Zhang; Weineng Chen; Hailong Zhao; Jumana Yousuf Al-Aama; Sherif Edris; Huanming Yang; Jian Wang; Torben Hansen; Henrik Bjørn Nielsen; Søren Brunak; Karsten Kristiansen; Francisco Guarner; Oluf Pedersen; Joel Doré; S Dusko Ehrlich; Peer Bork; Jun Wang
Journal:  Nat Biotechnol       Date:  2014-07-06       Impact factor: 54.908

8.  The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers.

Authors:  Yenkai Lim; Naoki Fukuma; Makrina Totsika; Liz Kenny; Mark Morrison; Chamindie Punyadeera
Journal:  Front Cell Infect Microbiol       Date:  2018-08-03       Impact factor: 5.293

9.  Trimmomatic: a flexible trimmer for Illumina sequence data.

Authors:  Anthony M Bolger; Marc Lohse; Bjoern Usadel
Journal:  Bioinformatics       Date:  2014-04-01       Impact factor: 6.937

10.  The salivary microbiome as an indicator of carcinogenesis in patients with oropharyngeal squamous cell carcinoma: A pilot study.

Authors:  Axel Wolf; Christine Moissl-Eichinger; Alexandra Perras; Kaisa Koskinen; Peter V Tomazic; Dietmar Thurnher
Journal:  Sci Rep       Date:  2017-07-19       Impact factor: 4.379
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  4 in total

1.  MinION Sequencing of colorectal cancer tumour microbiomes-A comparison with amplicon-based and RNA-Sequencing.

Authors:  William S Taylor; John Pearson; Allison Miller; Sebastian Schmeier; Frank A Frizelle; Rachel V Purcell
Journal:  PLoS One       Date:  2020-05-20       Impact factor: 3.240

2.  Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa.

Authors:  Irina Kurina; Anna Popenko; Natalia Klimenko; Stanislav Koshechkin; Liubov Chuprikova; Maxim Filipenko; Alexander Tyakht; Dmitry Alexeev
Journal:  Mol Cell Probes       Date:  2020-04-15       Impact factor: 2.365

3.  Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota.

Authors:  Takeo Shibata; Mayumi Nakagawa; Hannah N Coleman; Sarah M Owens; William W Greenfield; Toshiyuki Sasagawa; Michael S Robeson
Journal:  PLoS One       Date:  2021-08-30       Impact factor: 3.240

4.  Recovery of human gut microbiota genomes with third-generation sequencing.

Authors:  Yanfei Li; Yueling Jin; Jianming Zhang; Haoying Pan; Lan Wu; Dingsheng Liu; Jinlong Liu; Jing Hu; Junwei Shen
Journal:  Cell Death Dis       Date:  2021-06-02       Impact factor: 8.469
  4 in total

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