Literature DB >> 26000024

The road from next-generation sequencing to personalized medicine.

Manuel L Gonzalez-Garay1.   

Abstract

Moving from a traditional medical model of treating pathologies to an individualized predictive and preventive model of personalized medicine promises to reduce the healthcare cost on an overburdened and overwhelmed system. Next-generation sequencing (NGS) has the potential to accelerate the early detection of disorders and the identification of pharmacogenetics markers to customize treatments. This review explains the historical facts that led to the development of NGS along with the strengths and weakness of NGS, with a special emphasis on the analytical aspects used to process NGS data. There are solutions to all the steps necessary for performing NGS in the clinical context where the majority of them are very efficient, but there are some crucial steps in the process that need immediate attention.

Entities:  

Keywords:  CADD; GWAVA; NGS; functional prediction program; genomics; personalized medicine; workflow management system

Year:  2014        PMID: 26000024      PMCID: PMC4437232          DOI: 10.2217/pme.14.34

Source DB:  PubMed          Journal:  Per Med        ISSN: 1741-0541            Impact factor:   2.512


  127 in total

1.  SOAP2: an improved ultrafast tool for short read alignment.

Authors:  Ruiqiang Li; Chang Yu; Yingrui Li; Tak-Wah Lam; Siu-Ming Yiu; Karsten Kristiansen; Jun Wang
Journal:  Bioinformatics       Date:  2009-06-03       Impact factor: 6.937

2.  Mapping short DNA sequencing reads and calling variants using mapping quality scores.

Authors:  Heng Li; Jue Ruan; Richard Durbin
Journal:  Genome Res       Date:  2008-08-19       Impact factor: 9.043

Review 3.  What can exome sequencing do for you?

Authors:  Jacek Majewski; Jeremy Schwartzentruber; Emilie Lalonde; Alexandre Montpetit; Nada Jabado
Journal:  J Med Genet       Date:  2011-07-05       Impact factor: 6.318

4.  VariBench: a benchmark database for variations.

Authors:  Preethy Sasidharan Nair; Mauno Vihinen
Journal:  Hum Mutat       Date:  2012-10-11       Impact factor: 4.878

Review 5.  Molecular modelling and simulations in cancer research.

Authors:  Ran Friedman; Kjetil Boye; Kjersti Flatmark
Journal:  Biochim Biophys Acta       Date:  2013-02-14

6.  Performance of mutation pathogenicity prediction methods on missense variants.

Authors:  Janita Thusberg; Ayodeji Olatubosun; Mauno Vihinen
Journal:  Hum Mutat       Date:  2011-02-22       Impact factor: 4.878

7.  dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.

Authors:  Xiaoming Liu; Xueqiu Jian; Eric Boerwinkle
Journal:  Hum Mutat       Date:  2013-07-10       Impact factor: 4.878

8.  VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Authors:  Hao Hu; Chad D Huff; Barry Moore; Steven Flygare; Martin G Reese; Mark Yandell
Journal:  Genet Epidemiol       Date:  2013-07-08       Impact factor: 2.135

9.  SNAP: predict effect of non-synonymous polymorphisms on function.

Authors:  Yana Bromberg; Burkhard Rost
Journal:  Nucleic Acids Res       Date:  2007-05-25       Impact factor: 16.971

10.  An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Authors:  Catherine A Brownstein; Alan H Beggs; Nils Homer; Barry Merriman; Timothy W Yu; Katherine C Flannery; Elizabeth T DeChene; Meghan C Towne; Sarah K Savage; Emily N Price; Ingrid A Holm; Lovelace J Luquette; Elaine Lyon; Joseph Majzoub; Peter Neupert; David McCallie; Peter Szolovits; Huntington F Willard; Nancy J Mendelsohn; Renee Temme; Richard S Finkel; Sabrina W Yum; Livija Medne; Shamil R Sunyaev; Ivan Adzhubey; Christopher A Cassa; Paul I W de Bakker; Hatice Duzkale; Piotr Dworzyński; William Fairbrother; Laurent Francioli; Birgit H Funke; Monica A Giovanni; Robert E Handsaker; Kasper Lage; Matthew S Lebo; Monkol Lek; Ignaty Leshchiner; Daniel G MacArthur; Heather M McLaughlin; Michael F Murray; Tune H Pers; Paz P Polak; Soumya Raychaudhuri; Heidi L Rehm; Rachel Soemedi; Nathan O Stitziel; Sara Vestecka; Jochen Supper; Claudia Gugenmus; Bernward Klocke; Alexander Hahn; Max Schubach; Mortiz Menzel; Saskia Biskup; Peter Freisinger; Mario Deng; Martin Braun; Sven Perner; Richard J H Smith; Janeen L Andorf; Jian Huang; Kelli Ryckman; Val C Sheffield; Edwin M Stone; Thomas Bair; E Ann Black-Ziegelbein; Terry A Braun; Benjamin Darbro; Adam P DeLuca; Diana L Kolbe; Todd E Scheetz; Aiden E Shearer; Rama Sompallae; Kai Wang; Alexander G Bassuk; Erik Edens; Katherine Mathews; Steven A Moore; Oleg A Shchelochkov; Pamela Trapane; Aaron Bossler; Colleen A Campbell; Jonathan W Heusel; Anne Kwitek; Tara Maga; Karin Panzer; Thomas Wassink; Douglas Van Daele; Hela Azaiez; Kevin Booth; Nic Meyer; Michael M Segal; Marc S Williams; Gerard Tromp; Peter White; Donald Corsmeier; Sara Fitzgerald-Butt; Gail Herman; Devon Lamb-Thrush; Kim L McBride; David Newsom; Christopher R Pierson; Alexander T Rakowsky; Aleš Maver; Luca Lovrečić; Anja Palandačić; Borut Peterlin; Ali Torkamani; Anna Wedell; Mikael Huss; Andrey Alexeyenko; Jessica M Lindvall; Måns Magnusson; Daniel Nilsson; Henrik Stranneheim; Fulya Taylan; Christian Gilissen; Alexander Hoischen; Bregje van Bon; Helger Yntema; Marcel Nelen; Weidong Zhang; Jason Sager; Lu Zhang; Kathryn Blair; Deniz Kural; Michael Cariaso; Greg G Lennon; Asif Javed; Saloni Agrawal; Pauline C Ng; Komal S Sandhu; Shuba Krishna; Vamsi Veeramachaneni; Ofer Isakov; Eran Halperin; Eitan Friedman; Noam Shomron; Gustavo Glusman; Jared C Roach; Juan Caballero; Hannah C Cox; Denise Mauldin; Seth A Ament; Lee Rowen; Daniel R Richards; F Anthony San Lucas; Manuel L Gonzalez-Garay; C Thomas Caskey; Yu Bai; Ying Huang; Fang Fang; Yan Zhang; Zhengyuan Wang; Jorge Barrera; Juan M Garcia-Lobo; Domingo González-Lamuño; Javier Llorca; Maria C Rodriguez; Ignacio Varela; Martin G Reese; Francisco M De La Vega; Edward Kiruluta; Michele Cargill; Reece K Hart; Jon M Sorenson; Gholson J Lyon; David A Stevenson; Bruce E Bray; Barry M Moore; Karen Eilbeck; Mark Yandell; Hongyu Zhao; Lin Hou; Xiaowei Chen; Xiting Yan; Mengjie Chen; Cong Li; Can Yang; Murat Gunel; Peining Li; Yong Kong; Austin C Alexander; Zayed I Albertyn; Kym M Boycott; Dennis E Bulman; Paul M K Gordon; A Micheil Innes; Bartha M Knoppers; Jacek Majewski; Christian R Marshall; Jillian S Parboosingh; Sarah L Sawyer; Mark E Samuels; Jeremy Schwartzentruber; Isaac S Kohane; David M Margulies
Journal:  Genome Biol       Date:  2014-03-25       Impact factor: 13.583

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  9 in total

1.  Machine Learning Predictability of Clinical Next Generation Sequencing for Hematologic Malignancies to Guide High-Value Precision Medicine.

Authors:  Grace Y E Kim; Morteza Noshad; Henning Stehr; Rebecca Rojansky; Dita Gratzinger; Jean Oak; Rondeep Brar; David Iberri; Christina Kong; James Zehnder; Jonathan H Chen
Journal:  AMIA Annu Symp Proc       Date:  2022-02-21

2.  The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation.

Authors:  Lin Sun; Yang Liu; Thomas Lehnert; Martin A M Gijs; Songjing Li
Journal:  Biomicrofluidics       Date:  2022-07-28       Impact factor: 3.258

3.  Ultrasensitive detection of SARS-CoV-2 RNA and antigen using single-molecule optofluidic chip.

Authors:  G G Meena; A M Stambaugh; V Ganjalizadeh; M A Stott; A R Hawkins; H Schmidt
Journal:  APL Photonics       Date:  2021-06-01

4.  Prospective Decision Analysis Study of Clinical Genomic Testing in Metastatic Breast Cancer: Impact on Outcomes and Patient Perceptions.

Authors:  Daniel G Stover; Raquel E Reinbolt; Elizabeth J Adams; Sarah Asad; Katlyn Tolliver; Mahmoud Abdel-Rasoul; Cynthia D Timmers; Susan Gillespie; James L Chen; Siraj Mahamed Ali; Katharine A Collier; Mathew A Cherian; Anne M Noonan; Sagar Sardesai; Jeffrey VanDeusen; Robert Wesolowski; Nicole Williams; Clara N Lee; Charles L Shapiro; Erin R Macrae; Bhuvaneswari Ramaswamy; Maryam B Lustberg
Journal:  JCO Precis Oncol       Date:  2019-11-18

5.  Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath.

Authors:  Sandeep K Kasoji; Samantha G Pattenden; Ewa P Malc; Chatura N Jayakody; James K Tsuruta; Piotr A Mieczkowski; William P Janzen; Paul A Dayton
Journal:  PLoS One       Date:  2015-07-17       Impact factor: 3.240

Review 6.  A Comprehensive Review of Performance of Next-Generation Sequencing Platforms.

Authors:  Muhammad Tariq Pervez; Mirza Jawad Ul Hasnain; Syed Hassan Abbas; Mahmoud F Moustafa; Naeem Aslam; Syed Shah Muhammad Shah
Journal:  Biomed Res Int       Date:  2022-09-29       Impact factor: 3.246

7.  DGIdb 2.0: mining clinically relevant drug-gene interactions.

Authors:  Alex H Wagner; Adam C Coffman; Benjamin J Ainscough; Nicholas C Spies; Zachary L Skidmore; Katie M Campbell; Kilannin Krysiak; Deng Pan; Joshua F McMichael; James M Eldred; Jason R Walker; Richard K Wilson; Elaine R Mardis; Malachi Griffith; Obi L Griffith
Journal:  Nucleic Acids Res       Date:  2015-11-03       Impact factor: 16.971

8.  SVIM: structural variant identification using mapped long reads.

Authors:  David Heller; Martin Vingron
Journal:  Bioinformatics       Date:  2019-09-01       Impact factor: 6.937

Review 9.  Clinical Application of Next-Generation Sequencing as A Liquid Biopsy Technique in Advanced Colorectal Cancer: A Trick or A Treat?

Authors:  Myrto Kastrisiou; George Zarkavelis; George Pentheroudakis; Angeliki Magklara
Journal:  Cancers (Basel)       Date:  2019-10-16       Impact factor: 6.639

  9 in total

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