Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing.

Proceedings of the National Academy of Sciences of the United States of America
Peter J CampbellMichael R Stratton

Abstract

During the clonal expansion of cancer from an ancestral cell with an initiating oncogenic mutation to symptomatic neoplasm, the occurrence of somatic mutations (both driver and passenger) can be used to track the on-going evolution of the neoplasm. All subclones within a cancer are phylogenetically related, with the prevalence of each subclone determined by its evolutionary fitness and the timing of its origin relative to other subclones. Recently developed massively parallel sequencing platforms promise the ability to detect rare subclones of genetic variants without a priori knowledge of the mutations involved. We used ultra-deep pyrosequencing to investigate intraclonal diversification at the Ig heavy chain locus in 22 patients with B-cell chronic lymphocytic leukemia. Analysis of a non-polymorphic control locus revealed artifactual insertions and deletions resulting from sequencing errors and base substitutions caused by polymerase misincorporation during PCR amplification. We developed an algorithm to differentiate genuine haplotypes of somatic hypermutations from such artifacts. This proved capable of detecting multiple rare subclones with frequencies as low as 1 in 5000 copies and allowed the characterization of phylogen...Continue Reading

References

Apr 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·P D EnnisP Parham
Nov 11, 1988·Nucleic Acids Research·A M DunningS E Humphries
Jan 8, 1999·The Journal of General Virology·M A BrachoE Barrio
Oct 25, 2000·The Journal of Immunology : Official Journal of the American Association of Immunologists·I S LossosR Levy
Sep 3, 2003·Nature Reviews. Cancer·Mel F Greaves, Joe Wiemels
Feb 16, 2005·The Journal of Clinical Investigation·Bradley T MessmerNicholas Chiorazzi
Feb 25, 2005·The New England Journal of Medicine·Susumu KobayashiBalázs Halmos
Sep 6, 2005·Cancer Research·Helen DaviesP Andrew Futreal
Sep 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Amelia CimminoCarlo M Croce
Oct 28, 2005·The New England Journal of Medicine·George Adrian CalinCarlo M Croce
Mar 4, 2006·British Journal of Haematology·Davide BagnaraFranco Fais
Apr 18, 2006·Seminars in Oncology·Paolo Ghia, Federico Caligaris-Cappio
Jun 24, 2006·Methods in Enzymology·Patricia L Foster
Sep 9, 2006·Science·Tobias SjöblomVictor E Velculescu
Mar 9, 2007·Nature·Christopher GreenmanMichael R Stratton
Jun 20, 2007·Nucleic Acids Research·Christian HoffmannFrederic D Bushman
Jan 15, 2008·Nature Methods·Aaron R QuinlanGábor T Marth

❮ Previous
Next ❯

Citations

May 13, 2010·EMBO Molecular Medicine·Vessela Kristensen, Anne-Lise Borresen-Dale
Jan 26, 2010·Human Genetics·Bruce GottliebMark A Trifiro
Apr 11, 2009·Nature·Michael R StrattonP Andrew Futreal
Oct 29, 2010·Nature·Peter J CampbellP Andrew Futreal
Jan 20, 2012·Nature·Mel Greaves, Carlo C Maley
May 1, 2012·Nature Biotechnology·Scott L CarterGad Getz
Jul 12, 2012·Nature Biotechnology·Bissan Al-LazikaniPaul Workman
May 3, 2012·Nature Communications·Moritz GerstungNiko Beerenwinkel
Apr 2, 2009·Nature Genetics·Peter J Campbell
May 20, 2011·Nature Reviews. Cancer·Lawrence A Loeb
Oct 10, 2012·Nature Reviews. Genetics·Lucy R Yates, Peter J Campbell
Jun 1, 2012·Nature Reviews. Rheumatology·Holden T MaeckerC Garrison Fathman
Oct 15, 2011·The New England Journal of Medicine·E PapaemmanuilUNKNOWN Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium
Mar 9, 2012·The New England Journal of Medicine·Marco GerlingerCharles Swanton
Feb 11, 2012·Proceedings of the National Academy of Sciences of the United States of America·Nicholas J SzerlipCameron W Brennan
Dec 14, 2011·Proceedings of the National Academy of Sciences of the United States of America·Aaron C LoganDavid B Miklos
Aug 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Michael W SchmittLawrence A Loeb
Jun 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Adam HumphriesTrevor A Graham
Jun 15, 2011·The Journal of Experimental Medicine·Giulia FabbriGianluca Gaidano
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Osvaldo ZagordiNiko Beerenwinkel
Nov 8, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Raheleh SalariSerafim Batzoglou
Feb 16, 2011·Omics : a Journal of Integrative Biology·Mones S Abu-AsabHakima Amri
Apr 30, 2010·Briefings in Bioinformatics·Keith Robison
Sep 26, 2013·Bioinformatics·Elizabeth PurdomPaul Spellman
Jan 27, 2012·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Kazushi IzawaOsamu Ohara
May 1, 2013·Nucleic Acids Research·Thierry VoetPeter J Campbell
Aug 15, 2009·Genome Research·Heinrich Magnus Manske, Dominic P Kwiatkowski
Sep 25, 2009·Cold Spring Harbor Symposia on Quantitative Biology·J E Barrick, R E Lenski
Mar 26, 2011·Science·Michael R Stratton
Mar 31, 2012·Science Translational Medicine·Timothy A YapCharles Swanton
Mar 23, 2011·Biochemistry. Biokhimii︠a︡·E V Chetverina, A B Chetverin
Jun 11, 2009·Cancer Research·Edward J FoxLawrence A Loeb
Jun 7, 2012·Transfusion Medicine and Hemotherapy : Offizielles Organ Der Deutschen Gesellschaft Fur̈ Transfusionsmedizin Und Immunham̈atologie·Christian GabrielJohannes Pröll
May 20, 2011·BMC Genomics·André GillesJean-François Martin
Aug 28, 2013·Journal of Clinical Bioinformatics·Miri MichaeliRamit Mehr

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