Literature DB >> 30323017

Next-Generation Sequencing Strategies.

Shawn E Levy1, Braden E Boone1.   

Abstract

More than a decade ago, the term "next-generation" sequencing was coined to describe what was, at the time, revolutionary new methods to sequence RNA and DNA at a faster pace and cheaper cost than could be performed by standard bench-top protocols. Since then, the field of DNA sequencing has evolved at a rapid pace, with new breakthroughs allowing capacity to exponentially increase and cost to dramatically decrease. As genome-scale sequencing has become routine, a paradigm shift is occurring in genomics, which uses the power of high-throughput, rapid sequencing power with large-scale studies. These new approaches to genetic discovery will provide direct impact to fields such as personalized medicine, evolution, and biodiversity. This work reviews recent technology advances and methods in next-generation sequencing and highlights current large-scale sequencing efforts driving the evolution of the genomics space.
Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved.

Mesh:

Year:  2019        PMID: 30323017      PMCID: PMC6601457          DOI: 10.1101/cshperspect.a025791

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Med        ISSN: 2157-1422            Impact factor:   6.915


  72 in total

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Authors:  Li Ding; Matthew H Bailey; Eduard Porta-Pardo; Vesteinn Thorsson; Antonio Colaprico; Denis Bertrand; David L Gibbs; Amila Weerasinghe; Kuan-Lin Huang; Collin Tokheim; Isidro Cortés-Ciriano; Reyka Jayasinghe; Feng Chen; Lihua Yu; Sam Sun; Catharina Olsen; Jaegil Kim; Alison M Taylor; Andrew D Cherniack; Rehan Akbani; Chayaporn Suphavilai; Niranjan Nagarajan; Joshua M Stuart; Gordon B Mills; Matthew A Wyczalkowski; Benjamin G Vincent; Carolyn M Hutter; Jean Claude Zenklusen; Katherine A Hoadley; Michael C Wendl; Llya Shmulevich; Alexander J Lazar; David A Wheeler; Gad Getz
Journal:  Cell       Date:  2018-04-05       Impact factor: 41.582

2.  A new method for sequencing DNA.

Authors:  A M Maxam; W Gilbert
Journal:  Proc Natl Acad Sci U S A       Date:  1977-02       Impact factor: 11.205

3.  Light-generated oligonucleotide arrays for rapid DNA sequence analysis.

Authors:  A C Pease; D Solas; E J Sullivan; M T Cronin; C P Holmes; S P Fodor
Journal:  Proc Natl Acad Sci U S A       Date:  1994-05-24       Impact factor: 11.205

4.  Population genomics: laying the groundwork for genetic disease modeling and targeting.

Authors:  J Gulcher; K Stefansson
Journal:  Clin Chem Lab Med       Date:  1998-08       Impact factor: 3.694

5.  Reconstructing complex regions of genomes using long-read sequencing technology.

Authors:  John Huddleston; Swati Ranade; Maika Malig; Francesca Antonacci; Mark Chaisson; Lawrence Hon; Peter H Sudmant; Tina A Graves; Can Alkan; Megan Y Dennis; Richard K Wilson; Stephen W Turner; Jonas Korlach; Evan E Eichler
Journal:  Genome Res       Date:  2014-01-13       Impact factor: 9.043

6.  Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

Authors:  Amanda M Hulse-Kemp; Shamoni Maheshwari; Kevin Stoffel; Theresa A Hill; David Jaffe; Stephen R Williams; Neil Weisenfeld; Srividya Ramakrishnan; Vijay Kumar; Preyas Shah; Michael C Schatz; Deanna M Church; Allen Van Deynze
Journal:  Hortic Res       Date:  2018-01-12       Impact factor: 6.793

7.  Reproductive fitness and genetic risk of psychiatric disorders in the general population.

Authors:  Niamh Mullins; Andrés Ingason; Heather Porter; Jack Euesden; Alexandra Gillett; Sigurgeir Ólafsson; Daniel F Gudbjartsson; Cathryn M Lewis; Engilbert Sigurdsson; Evald Saemundsen; Ólafur Ó Gudmundsson; Michael L Frigge; Augustine Kong; Agnar Helgason; G Bragi Walters; Omar Gustafsson; Hreinn Stefansson; Kari Stefansson
Journal:  Nat Commun       Date:  2017-06-13       Impact factor: 14.919

8.  The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.

Authors: 
Journal:  Microbiome       Date:  2016-06-03       Impact factor: 14.650

9.  Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.

Authors:  Assaf Rotem; Oren Ram; Noam Shoresh; Ralph A Sperling; Alon Goren; David A Weitz; Bradley E Bernstein
Journal:  Nat Biotechnol       Date:  2015-10-12       Impact factor: 54.908

10.  The cumulative burden of surviving childhood cancer: an initial report from the St Jude Lifetime Cohort Study (SJLIFE).

Authors:  Nickhill Bhakta; Qi Liu; Kirsten K Ness; Malek Baassiri; Hesham Eissa; Frederick Yeo; Wassim Chemaitilly; Matthew J Ehrhardt; Johnnie Bass; Michael W Bishop; Kyla Shelton; Lu Lu; Sujuan Huang; Zhenghong Li; Eric Caron; Jennifer Lanctot; Carrie Howell; Timothy Folse; Vijaya Joshi; Daniel M Green; Daniel A Mulrooney; Gregory T Armstrong; Kevin R Krull; Tara M Brinkman; Raja B Khan; Deo K Srivastava; Melissa M Hudson; Yutaka Yasui; Leslie L Robison
Journal:  Lancet       Date:  2017-09-08       Impact factor: 79.321

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  11 in total

Review 1.  Pharmacogenomics of Pain Management: The Impact of Specific Biological Polymorphisms on Drugs and Metabolism.

Authors:  Elyse M Cornett; Michelle A Carroll Turpin; Allison Pinner; Pankaj Thakur; Tamizh Selvan Gnana Sekaran; Harish Siddaiah; Jasmine Rivas; Anna Yates; G Jason Huang; Anitha Senthil; Narjeet Khurmi; Jenna L Miller; Cain W Stark; Richard D Urman; Alan David Kaye
Journal:  Curr Oncol Rep       Date:  2020-02-06       Impact factor: 5.075

2.  A novel mutation of RPGR in a Chinese family with X-linked retinitis pigmentosa.

Authors:  Hui-Hui Sun; Jing-Cong Zhao; Su-Ling Yang; Jin-Dou Shi; Yun-Shuo Wei; Jian-Cang Wang; Feng Gu; Lu Chen
Journal:  Int J Ophthalmol       Date:  2022-09-18       Impact factor: 1.645

Review 3.  Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine.

Authors:  Habiba Abdelhalim; Asude Berber; Mudassir Lodi; Rihi Jain; Achuth Nair; Anirudh Pappu; Kush Patel; Vignesh Venkat; Cynthia Venkatesan; Raghu Wable; Matthew Dinatale; Allyson Fu; Vikram Iyer; Ishan Kalove; Marc Kleyman; Joseph Koutsoutis; David Menna; Mayank Paliwal; Nishi Patel; Thirth Patel; Zara Rafique; Rothela Samadi; Roshan Varadhan; Shreyas Bolla; Sreya Vadapalli; Zeeshan Ahmed
Journal:  Front Genet       Date:  2022-07-06       Impact factor: 4.772

4.  Application of Artificial Intelligence for Medical Research.

Authors:  Ryuji Hamamoto
Journal:  Biomolecules       Date:  2021-01-12

5.  The Application of Whole-Exome Sequencing in Patients With FUO.

Authors:  Wanru Guo; Xuewen Feng; Ming Hu; Yanwan Shangguan; Jiafeng Xia; Wenjuan Hu; Xiaomeng Li; Zunjing Zhang; Yunzhen Shi; Kaijin Xu
Journal:  Front Cell Infect Microbiol       Date:  2022-01-12       Impact factor: 5.293

6.  Identification of the Potential Key Genes and Pathways Involved in Lens Changes of High Myopia.

Authors:  Weixia Lai; Xixi Wu; Hao Liang
Journal:  Int J Gen Med       Date:  2022-03-10

Review 7.  The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems.

Authors:  Behzad Imanian; John Donaghy; Tim Jackson; Sanjay Gummalla; Balasubramanian Ganesan; Robert C Baker; Matthew Henderson; Emily K Butler; Yingying Hong; Brendan Ring; Clare Thorp; Ramin Khaksar; Mansour Samadpour; Kahlil A Lawless; Iain MacLaren-Lee; Heather A Carleton; Renmao Tian; Wei Zhang; Jason Wan
Journal:  NPJ Sci Food       Date:  2022-08-16

8.  Integrated analysis of bulk and single-cell RNA sequencing reveals the interaction of PKP1 and tumor-infiltrating B cells and their therapeutic potential for nasopharyngeal carcinoma.

Authors:  Yu-Mei Huang; Lin-Qian Wang; Ying Liu; Fa-Qing Tang; Wen-Ling Zhang
Journal:  Front Genet       Date:  2022-09-14       Impact factor: 4.772

9.  Integrative Analysis of Incongruous Cancer Genomics and Proteomics Datasets.

Authors:  Karla Cervantes-Gracia; Richard Chahwan; Holger Husi
Journal:  Methods Mol Biol       Date:  2021

10.  Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses.

Authors:  Solomon Maina; Linda Zheng; Brendan C Rodoni
Journal:  Viruses       Date:  2021-03-30       Impact factor: 5.048

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