Literature DB >> 30084865

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application.

Gaye Lightbody1, Valeriia Haberland2, Fiona Browne1, Laura Taggart3, Huiru Zheng1, Eileen Parkes4, Jaine K Blayney4.   

Abstract

There has been an exponential growth in the performance and output of sequencing technologies (omics data) with full genome sequencing now producing gigabases of reads on a daily basis. These data may hold the promise of personalized medicine, leading to routinely available sequencing tests that can guide patient treatment decisions. In the era of high-throughput sequencing (HTS), computational considerations, data governance and clinical translation are the greatest rate-limiting steps. To ensure that the analysis, management and interpretation of such extensive omics data is exploited to its full potential, key factors, including sample sourcing, technology selection and computational expertise and resources, need to be considered, leading to an integrated set of high-performance tools and systems. This article provides an up-to-date overview of the evolution of HTS and the accompanying tools, infrastructure and data management approaches that are emerging in this space, which, if used within in a multidisciplinary context, may ultimately facilitate the development of personalized medicine.
© The Author(s) 2018. Published by Oxford University Press.

Entities:  

Keywords:  clinical translation; cloud computing; grid computing; high-performance computing; high-throughput sequencing; personalized medicine; translational research

Year:  2019        PMID: 30084865      PMCID: PMC6917217          DOI: 10.1093/bib/bby051

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  157 in total

1.  Ethical and practical challenges of sharing data from genome-wide association studies: the eMERGE Consortium experience.

Authors:  Amy L McGuire; Melissa Basford; Lynn G Dressler; Stephanie M Fullerton; Barbara A Koenig; Rongling Li; Cathy A McCarty; Erin Ramos; Maureen E Smith; Carol P Somkin; Carol Waudby; Wendy A Wolf; Ellen Wright Clayton
Journal:  Genome Res       Date:  2011-06-01       Impact factor: 9.043

2.  Use of mass spectrometry to identify protein biomarkers of disease severity in the synovial fluid and serum of patients with rheumatoid arthritis.

Authors:  Hua Liao; Jiang Wu; Eric Kuhn; Wendy Chin; Betty Chang; Michael D Jones; Steve O'Neil; Karl R Clauser; Johann Karl; Fritz Hasler; Ronenn Roubenoff; Werner Zolg; Brad C Guild
Journal:  Arthritis Rheum       Date:  2004-12

3.  A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer.

Authors:  Soonmyung Paik; Steven Shak; Gong Tang; Chungyeul Kim; Joffre Baker; Maureen Cronin; Frederick L Baehner; Michael G Walker; Drew Watson; Taesung Park; William Hiller; Edwin R Fisher; D Lawrence Wickerham; John Bryant; Norman Wolmark
Journal:  N Engl J Med       Date:  2004-12-10       Impact factor: 91.245

Review 4.  Pharmacologically active drug metabolites: impact on drug discovery and pharmacotherapy.

Authors:  R Scott Obach
Journal:  Pharmacol Rev       Date:  2013-02-13       Impact factor: 25.468

5.  Why the US Centers for Medicare and Medicaid Services (CMS) should have required a randomized trial of Foundation Medicine (F1CDx) before paying for it.

Authors:  V Prasad
Journal:  Ann Oncol       Date:  2018-02-01       Impact factor: 32.976

6.  The real cost of sequencing: higher than you think!

Authors:  Andrea Sboner; Xinmeng Jasmine Mu; Dov Greenbaum; Raymond K Auerbach; Mark B Gerstein
Journal:  Genome Biol       Date:  2011-08-25       Impact factor: 13.583

7.  Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Authors:  Nick Craddock; Matthew E Hurles; Niall Cardin; Richard D Pearson; Vincent Plagnol; Samuel Robson; Damjan Vukcevic; Chris Barnes; Donald F Conrad; Eleni Giannoulatou; Chris Holmes; Jonathan L Marchini; Kathy Stirrups; Martin D Tobin; Louise V Wain; Chris Yau; Jan Aerts; Tariq Ahmad; T Daniel Andrews; Hazel Arbury; Anthony Attwood; Adam Auton; Stephen G Ball; Anthony J Balmforth; Jeffrey C Barrett; Inês Barroso; Anne Barton; Amanda J Bennett; Sanjeev Bhaskar; Katarzyna Blaszczyk; John Bowes; Oliver J Brand; Peter S Braund; Francesca Bredin; Gerome Breen; Morris J Brown; Ian N Bruce; Jaswinder Bull; Oliver S Burren; John Burton; Jake Byrnes; Sian Caesar; Chris M Clee; Alison J Coffey; John M C Connell; Jason D Cooper; Anna F Dominiczak; Kate Downes; Hazel E Drummond; Darshna Dudakia; Andrew Dunham; Bernadette Ebbs; Diana Eccles; Sarah Edkins; Cathryn Edwards; Anna Elliot; Paul Emery; David M Evans; Gareth Evans; Steve Eyre; Anne Farmer; I Nicol Ferrier; Lars Feuk; Tomas Fitzgerald; Edward Flynn; Alistair Forbes; Liz Forty; Jayne A Franklyn; Rachel M Freathy; Polly Gibbs; Paul Gilbert; Omer Gokumen; Katherine Gordon-Smith; Emma Gray; Elaine Green; Chris J Groves; Detelina Grozeva; Rhian Gwilliam; Anita Hall; Naomi Hammond; Matt Hardy; Pile Harrison; Neelam Hassanali; Husam Hebaishi; Sarah Hines; Anne Hinks; Graham A Hitman; Lynne Hocking; Eleanor Howard; Philip Howard; Joanna M M Howson; Debbie Hughes; Sarah Hunt; John D Isaacs; Mahim Jain; Derek P Jewell; Toby Johnson; Jennifer D Jolley; Ian R Jones; Lisa A Jones; George Kirov; Cordelia F Langford; Hana Lango-Allen; G Mark Lathrop; James Lee; Kate L Lee; Charlie Lees; Kevin Lewis; Cecilia M Lindgren; Meeta Maisuria-Armer; Julian Maller; John Mansfield; Paul Martin; Dunecan C O Massey; Wendy L McArdle; Peter McGuffin; Kirsten E McLay; Alex Mentzer; Michael L Mimmack; Ann E Morgan; Andrew P Morris; Craig Mowat; Simon Myers; William Newman; Elaine R Nimmo; Michael C O'Donovan; Abiodun Onipinla; Ifejinelo Onyiah; Nigel R Ovington; Michael J Owen; Kimmo Palin; Kirstie Parnell; David Pernet; John R B Perry; Anne Phillips; Dalila Pinto; Natalie J Prescott; Inga Prokopenko; Michael A Quail; Suzanne Rafelt; Nigel W Rayner; Richard Redon; David M Reid; Susan M Ring; Neil Robertson; Ellie Russell; David St Clair; Jennifer G Sambrook; Jeremy D Sanderson; Helen Schuilenburg; Carol E Scott; Richard Scott; Sheila Seal; Sue Shaw-Hawkins; Beverley M Shields; Matthew J Simmonds; Debbie J Smyth; Elilan Somaskantharajah; Katarina Spanova; Sophia Steer; Jonathan Stephens; Helen E Stevens; Millicent A Stone; Zhan Su; Deborah P M Symmons; John R Thompson; Wendy Thomson; Mary E Travers; Clare Turnbull; Armand Valsesia; Mark Walker; Neil M Walker; Chris Wallace; Margaret Warren-Perry; Nicholas A Watkins; John Webster; Michael N Weedon; Anthony G Wilson; Matthew Woodburn; B Paul Wordsworth; Allan H Young; Eleftheria Zeggini; Nigel P Carter; Timothy M Frayling; Charles Lee; Gil McVean; Patricia B Munroe; Aarno Palotie; Stephen J Sawcer; Stephen W Scherer; David P Strachan; Chris Tyler-Smith; Matthew A Brown; Paul R Burton; Mark J Caulfield; Alastair Compston; Martin Farrall; Stephen C L Gough; Alistair S Hall; Andrew T Hattersley; Adrian V S Hill; Christopher G Mathew; Marcus Pembrey; Jack Satsangi; Michael R Stratton; Jane Worthington; Panos Deloukas; Audrey Duncanson; Dominic P Kwiatkowski; Mark I McCarthy; Willem Ouwehand; Miles Parkes; Nazneen Rahman; John A Todd; Nilesh J Samani; Peter Donnelly
Journal:  Nature       Date:  2010-04-01       Impact factor: 49.962

8.  Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Authors:  Wenqian Zhang; Ying Yu; Falk Hertwig; Jean Thierry-Mieg; Wenwei Zhang; Danielle Thierry-Mieg; Jian Wang; Cesare Furlanello; Viswanath Devanarayan; Jie Cheng; Youping Deng; Barbara Hero; Huixiao Hong; Meiwen Jia; Li Li; Simon M Lin; Yuri Nikolsky; André Oberthuer; Tao Qing; Zhenqiang Su; Ruth Volland; Charles Wang; May D Wang; Junmei Ai; Davide Albanese; Shahab Asgharzadeh; Smadar Avigad; Wenjun Bao; Marina Bessarabova; Murray H Brilliant; Benedikt Brors; Marco Chierici; Tzu-Ming Chu; Jibin Zhang; Richard G Grundy; Min Max He; Scott Hebbring; Howard L Kaufman; Samir Lababidi; Lee J Lancashire; Yan Li; Xin X Lu; Heng Luo; Xiwen Ma; Baitang Ning; Rosa Noguera; Martin Peifer; John H Phan; Frederik Roels; Carolina Rosswog; Susan Shao; Jie Shen; Jessica Theissen; Gian Paolo Tonini; Jo Vandesompele; Po-Yen Wu; Wenzhong Xiao; Joshua Xu; Weihong Xu; Jiekun Xuan; Yong Yang; Zhan Ye; Zirui Dong; Ke K Zhang; Ye Yin; Chen Zhao; Yuanting Zheng; Russell D Wolfinger; Tieliu Shi; Linda H Malkas; Frank Berthold; Jun Wang; Weida Tong; Leming Shi; Zhiyu Peng; Matthias Fischer
Journal:  Genome Biol       Date:  2015-06-25       Impact factor: 13.583

9.  Searching for SNPs with cloud computing.

Authors:  Ben Langmead; Michael C Schatz; Jimmy Lin; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-11-20       Impact factor: 13.583

10.  Embracing an integromic approach to tissue biomarker research in cancer: Perspectives and lessons learned.

Authors:  Gerald Li; Peter Bankhead; Philip D Dunne; Paul G O'Reilly; Jacqueline A James; Manuel Salto-Tellez; Peter W Hamilton; Darragh G McArt
Journal:  Brief Bioinform       Date:  2017-07-01       Impact factor: 11.622

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  34 in total

Review 1.  Application of the conventional and novel methods in testing EGFR variants for NSCLC patients in the last 10 years through different regions: a systematic review.

Authors:  Jasmina Obradovic; Jovana Todosijevic; Vladimir Jurisic
Journal:  Mol Biol Rep       Date:  2021-05-10       Impact factor: 2.316

2.  MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules.

Authors:  Paolo Martini; Monica Chiogna; Enrica Calura; Chiara Romualdi
Journal:  Nucleic Acids Res       Date:  2019-08-22       Impact factor: 16.971

3.  Message in a Bottle-Metabarcoding enables biodiversity comparisons across ecoregions.

Authors:  D Steinke; S L deWaard; J E Sones; N V Ivanova; S W J Prosser; K Perez; T W A Braukmann; M Milton; E V Zakharov; J R deWaard; S Ratnasingham; P D N Hebert
Journal:  Gigascience       Date:  2022-04-28       Impact factor: 7.658

4.  QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing.

Authors:  Frédéric Jarlier; Nicolas Joly; Nicolas Fedy; Thomas Magalhaes; Leonor Sirotti; Paul Paganiban; Firmin Martin; Michael McManus; Philippe Hupé
Journal:  F1000Res       Date:  2020-04-06

5.  MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets.

Authors:  Urminder Singh; Manhoi Hur; Karin Dorman; Eve Syrkin Wurtele
Journal:  Nucleic Acids Res       Date:  2020-02-28       Impact factor: 16.971

Review 6.  Fabrication approaches for high-throughput and biomimetic disease modeling.

Authors:  Mackenzie L Grubb; Steven R Caliari
Journal:  Acta Biomater       Date:  2021-03-11       Impact factor: 10.633

7.  RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars.

Authors:  Saranya Chandrasekar; Purushothaman Natarajan; Priyank Hanuman Mhatre; Mahesh Mahajan; Sundararaj Nivitha; Venkatasalam E Palanisamy; Umesh K Reddy; Palanisamy Sundararaj
Journal:  Plants (Basel)       Date:  2022-04-07

8.  Robustness of differential gene expression analysis of RNA-seq.

Authors:  A Stupnikov; C E McInerney; K I Savage; S A McIntosh; F Emmert-Streib; R Kennedy; M Salto-Tellez; K M Prise; D G McArt
Journal:  Comput Struct Biotechnol J       Date:  2021-05-26       Impact factor: 7.271

9.  A Molecular Signature Response Classifier to Predict Inadequate Response to Tumor Necrosis Factor-α Inhibitors: The NETWORK-004 Prospective Observational Study.

Authors:  Stanley Cohen; Alvin F Wells; Jeffrey R Curtis; Rajat Dhar; Theodore Mellors; Lixia Zhang; Johanna B Withers; Alex Jones; Susan D Ghiassian; Mengran Wang; Erin Connolly-Strong; Sarah Rapisardo; Zoran Gatalica; Dimitrios A Pappas; Joel M Kremer; Alif Saleh; Viatcheslav R Akmaev
Journal:  Rheumatol Ther       Date:  2021-06-19

10.  BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization.

Authors:  Federico Taverna; Jermaine Goveia; Tobias K Karakach; Shawez Khan; Katerina Rohlenova; Lucas Treps; Abhishek Subramanian; Luc Schoonjans; Mieke Dewerchin; Guy Eelen; Peter Carmeliet
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

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