Literature DB >> 25849638

Sequencing small genomic targets with high efficiency and extreme accuracy.

Michael W Schmitt1, Edward J Fox2, Marc J Prindle2, Kate S Reid-Bayliss2, Lawrence D True2, Jerald P Radich3, Lawrence A Loeb2.   

Abstract

The detection of minority variants in mixed samples requires methods for enrichment and accurate sequencing of small genomic intervals. We describe an efficient approach based on sequential rounds of hybridization with biotinylated oligonucleotides that enables more than 1-million-fold enrichment of genomic regions of interest. In conjunction with error-correcting double-stranded molecular tags, our approach enables the quantification of mutations in individual DNA molecules.

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Year:  2015        PMID: 25849638      PMCID: PMC4414912          DOI: 10.1038/nmeth.3351

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  20 in total

1.  Multiplexed genotyping with sequence-tagged molecular inversion probes.

Authors:  Paul Hardenbol; Johan Banér; Maneesh Jain; Mats Nilsson; Eugeni A Namsaraev; George A Karlin-Neumann; Hossein Fakhrai-Rad; Mostafa Ronaghi; Thomas D Willis; Ulf Landegren; Ronald W Davis
Journal:  Nat Biotechnol       Date:  2003-05-05       Impact factor: 54.908

Review 2.  DNA replication fidelity.

Authors:  Thomas A Kunkel
Journal:  J Biol Chem       Date:  2004-02-26       Impact factor: 5.157

3.  Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID.

Authors:  Cassandra B Jabara; Corbin D Jones; Jeffrey Roach; Jeffrey A Anderson; Ronald Swanstrom
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-30       Impact factor: 11.205

Review 4.  Target-enrichment strategies for next-generation sequencing.

Authors:  Lira Mamanova; Alison J Coffey; Carol E Scott; Iwanka Kozarewa; Emily H Turner; Akash Kumar; Eleanor Howard; Jay Shendure; Daniel J Turner
Journal:  Nat Methods       Date:  2010-02       Impact factor: 28.547

5.  Bias and artifacts in multitemplate polymerase chain reactions (PCR).

Authors:  Takahiro Kanagawa
Journal:  J Biosci Bioeng       Date:  2003       Impact factor: 2.894

6.  High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.

Authors:  Dianne I Lou; Jeffrey A Hussmann; Ross M McBee; Ashley Acevedo; Raul Andino; William H Press; Sara L Sawyer
Journal:  Proc Natl Acad Sci U S A       Date:  2013-11-15       Impact factor: 11.205

7.  Field guide to next-generation DNA sequencers.

Authors:  Travis C Glenn
Journal:  Mol Ecol Resour       Date:  2011-05-19       Impact factor: 7.090

8.  Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation.

Authors:  Joseph B Hiatt; Colin C Pritchard; Stephen J Salipante; Brian J O'Roak; Jay Shendure
Journal:  Genome Res       Date:  2013-02-04       Impact factor: 9.043

9.  Detection of ultra-rare mutations by next-generation sequencing.

Authors:  Michael W Schmitt; Scott R Kennedy; Jesse J Salk; Edward J Fox; Joseph B Hiatt; Lawrence A Loeb
Journal:  Proc Natl Acad Sci U S A       Date:  2012-08-01       Impact factor: 11.205

10.  Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage.

Authors:  Scott R Kennedy; Jesse J Salk; Michael W Schmitt; Lawrence A Loeb
Journal:  PLoS Genet       Date:  2013-09-26       Impact factor: 5.917

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  60 in total

Review 1.  The influence of subclonal resistance mutations on targeted cancer therapy.

Authors:  Michael W Schmitt; Lawrence A Loeb; Jesse J Salk
Journal:  Nat Rev Clin Oncol       Date:  2015-10-20       Impact factor: 66.675

Review 2.  Liquid biopsy and its role in an advanced clinical trial for lung cancer.

Authors:  Donald J Johann; Mathew Steliga; Ik J Shin; Donghoon Yoon; Konstantinos Arnaoutakis; Laura Hutchins; Meeiyueh Liu; Jason Liem; Karl Walker; Andy Pereira; Mary Yang; Susanne K Jeffus; Erich Peterson; Joshua Xu
Journal:  Exp Biol Med (Maywood)       Date:  2018-02

3.  Single-Molecule Sequencing Reveals Patterns of Preexisting Drug Resistance That Suggest Treatment Strategies in Philadelphia-Positive Leukemias.

Authors:  Michael W Schmitt; Justin R Pritchard; Scott M Leighow; Bella I Aminov; Lan Beppu; Daniel S Kim; J Graeme Hodgson; Victor M Rivera; Lawrence A Loeb; Jerald P Radich
Journal:  Clin Cancer Res       Date:  2018-07-24       Impact factor: 12.531

4.  Family reunion via error correction: an efficient analysis of duplex sequencing data.

Authors:  Nicholas Stoler; Barbara Arbeithuber; Gundula Povysil; Monika Heinzl; Renato Salazar; Kateryna D Makova; Irene Tiemann-Boege; Anton Nekrutenko
Journal:  BMC Bioinformatics       Date:  2020-03-04       Impact factor: 3.169

5.  Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing.

Authors:  Margaret L Hoang; Isaac Kinde; Cristian Tomasetti; K Wyatt McMahon; Thomas A Rosenquist; Arthur P Grollman; Kenneth W Kinzler; Bert Vogelstein; Nickolas Papadopoulos
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-15       Impact factor: 11.205

6.  Cancer: hunting rare somatic mutations.

Authors:  Vivien Marx
Journal:  Nat Methods       Date:  2016-03-30       Impact factor: 28.547

Review 7.  Genome-wide mapping and analysis of chromosome architecture.

Authors:  Anthony D Schmitt; Ming Hu; Bing Ren
Journal:  Nat Rev Mol Cell Biol       Date:  2016-09-01       Impact factor: 94.444

Review 8.  Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.

Authors:  Daniel B Sloan; Amanda K Broz; Joel Sharbrough; Zhiqiang Wu
Journal:  Trends Biotechnol       Date:  2018-03-14       Impact factor: 19.536

Review 9.  Current developments in molecular monitoring in chronic myeloid leukemia.

Authors:  Justine Ellen Marum; Susan Branford
Journal:  Ther Adv Hematol       Date:  2016-07-15

10.  Decreased Mitochondrial Mutagenesis during Transformation of Human Breast Stem Cells into Tumorigenic Cells.

Authors:  Eun Hyun Ahn; Seung Hyuk Lee; Joon Yup Kim; Chia-Cheng Chang; Lawrence A Loeb
Journal:  Cancer Res       Date:  2016-05-17       Impact factor: 12.701

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