Literature DB >> 33654981

Preparing Single-cell DNA Library Using Nextera for Detection of CNV.

Larry Xi1, Patrick Leong1, Aleksandar Mihajlovic1.   

Abstract

Single-cell DNA sequencing is a powerful tool to evaluate the state of heterogeneity of heterogeneous tissues like cancer in a quantitative manner that bulk sequencing can never achieve. DOP-PCR (Degenerate Oligonucleotide-Primed Polymerase Chain Reaction), MDA (Multiple Displacement Amplification), MALBAC (Multiple Annealing and Looping-Based Amplification Cycles), LIANTI (Linear Amplification via Transposon Insertion) and TnBC (Transposon Barcoded) have been the primary choices to prepare single-cell libraries. TnBC library prep method is a simple and versatile methodology, to detect copy number variations or to obtain the absolute copy numbers of genes per cell.
Copyright © 2019 The Authors; exclusive licensee Bio-protocol LLC.

Entities:  

Keywords:  Copy number variation; Nextera; Shallow sequencing; Single-cell; Transposon

Year:  2019        PMID: 33654981      PMCID: PMC7854077          DOI: 10.21769/BioProtoc.3175

Source DB:  PubMed          Journal:  Bio Protoc        ISSN: 2331-8325


  12 in total

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Authors:  Timour Baslan; James Hicks
Journal:  Curr Opin Genet Dev       Date:  2014-07-10       Impact factor: 5.578

2.  Whole-genome molecular haplotyping of single cells.

Authors:  H Christina Fan; Jianbin Wang; Anastasia Potanina; Stephen R Quake
Journal:  Nat Biotechnol       Date:  2010-12-19       Impact factor: 54.908

3.  Delineating cancer evolution with single-cell sequencing.

Authors:  Nicholas E Navin
Journal:  Sci Transl Med       Date:  2015-07-15       Impact factor: 17.956

4.  Genome-wide detection of single-nucleotide and copy-number variations of a single human cell.

Authors:  Chenghang Zong; Sijia Lu; Alec R Chapman; X Sunney Xie
Journal:  Science       Date:  2012-12-21       Impact factor: 47.728

5.  EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing.

Authors:  Joshua M Francis; Cheng-Zhong Zhang; Cecile L Maire; Joonil Jung; Veronica E Manzo; Viktor A Adalsteinsson; Heather Homer; Sam Haidar; Brendan Blumenstiel; Chandra Sekhar Pedamallu; Azra H Ligon; J Christopher Love; Matthew Meyerson; Keith L Ligon
Journal:  Cancer Discov       Date:  2014-06-03       Impact factor: 39.397

6.  Diverse mechanisms of somatic structural variations in human cancer genomes.

Authors:  Lixing Yang; Lovelace J Luquette; Nils Gehlenborg; Ruibin Xi; Psalm S Haseley; Chih-Heng Hsieh; Chengsheng Zhang; Xiaojia Ren; Alexei Protopopov; Lynda Chin; Raju Kucherlapati; Charles Lee; Peter J Park
Journal:  Cell       Date:  2013-05-09       Impact factor: 41.582

7.  Assessment of megabase-scale somatic copy number variation using single-cell sequencing.

Authors:  Kristin A Knouse; Jie Wu; Angelika Amon
Journal:  Genome Res       Date:  2016-01-15       Impact factor: 9.043

8.  Detection of Copy Number Alterations Using Single Cell Sequencing.

Authors:  Kristin A Knouse; Jie Wu; Austin Hendricks
Journal:  J Vis Exp       Date:  2017-02-17       Impact factor: 1.355

9.  A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Authors:  Tyler S Alioto; Ivo Buchhalter; Sophia Derdak; Barbara Hutter; Matthew D Eldridge; Eivind Hovig; Lawrence E Heisler; Timothy A Beck; Jared T Simpson; Laurie Tonon; Anne-Sophie Sertier; Ann-Marie Patch; Natalie Jäger; Philip Ginsbach; Ruben Drews; Nagarajan Paramasivam; Rolf Kabbe; Sasithorn Chotewutmontri; Nicolle Diessl; Christopher Previti; Sabine Schmidt; Benedikt Brors; Lars Feuerbach; Michael Heinold; Susanne Gröbner; Andrey Korshunov; Patrick S Tarpey; Adam P Butler; Jonathan Hinton; David Jones; Andrew Menzies; Keiran Raine; Rebecca Shepherd; Lucy Stebbings; Jon W Teague; Paolo Ribeca; Francesc Castro Giner; Sergi Beltran; Emanuele Raineri; Marc Dabad; Simon C Heath; Marta Gut; Robert E Denroche; Nicholas J Harding; Takafumi N Yamaguchi; Akihiro Fujimoto; Hidewaki Nakagawa; Víctor Quesada; Rafael Valdés-Mas; Sigve Nakken; Daniel Vodák; Lawrence Bower; Andrew G Lynch; Charlotte L Anderson; Nicola Waddell; John V Pearson; Sean M Grimmond; Myron Peto; Paul Spellman; Minghui He; Cyriac Kandoth; Semin Lee; John Zhang; Louis Létourneau; Singer Ma; Sahil Seth; David Torrents; Liu Xi; David A Wheeler; Carlos López-Otín; Elías Campo; Peter J Campbell; Paul C Boutros; Xose S Puente; Daniela S Gerhard; Stefan M Pfister; John D McPherson; Thomas J Hudson; Matthias Schlesner; Peter Lichter; Roland Eils; David T W Jones; Ivo G Gut
Journal:  Nat Commun       Date:  2015-12-09       Impact factor: 14.919

10.  New library construction method for single-cell genomes.

Authors:  Larry Xi; Alexander Belyaev; Sandra Spurgeon; Xiaohui Wang; Haibiao Gong; Robert Aboukhalil; Richard Fekete
Journal:  PLoS One       Date:  2017-07-19       Impact factor: 3.240

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  1 in total

1.  Reconstructing and counting genomic fragments through tagmentation-based haploid phasing.

Authors:  Patrick P T Leong; Aleksandar Mihajlović; Nadežda Bogdanović; Luka Breberina; Larry Xi
Journal:  Sci Rep       Date:  2021-09-23       Impact factor: 4.379

  1 in total

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