Abstract
High-throughput sequencing (HTS) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing our approach to leukaemia both at diagnosis and during follow-up. As part of an immunoglobulin/T cell receptor-based minimal residual disease (MRD) assessment of acute lymphoblastic leukaemia patients, we assessed the performance and feasibility of the replacement of the first steps of the approach based on DNA isolation and Sanger sequencing, using a HTS protocol combined with bioinformatics analysis and visualization using the Vidjil software. We prospectively analysed the diagnostic and relapse samples of 34 paediatric patients, thus identifying 125 leukaemic clones with recombinations on multiple loci (TRG, TRD, IGH and IGK), including Dd2/Dd3 and Intron/KDE rearrangements. Sequencing failures were halved (14% vs. 34%, P = 0.0007), enabling more patients to be monitored. Furthermore, more markers per patient could be monitored, reducing the probability of false negative MRD results. The whole analysis, from sample receipt to clinical validation, was shorter than our current diagnostic protocol, with equal resources. V(D)J recombination was successfully assigned by the software, ...Continue Reading
References
Apr 14, 1983·Nature·S Tonegawa
Aug 27, 1998·The New England Journal of Medicine·H CavéE Vilmer
Oct 14, 2003·PLoS Biology·Eleonora Market, F Nina Papavasiliou
Dec 13, 2003·Leukemia·J J M van DongenE A Macintyre
Jul 21, 2004·Bioinformatics·Mehdi Yousfi MonodMarie-Paule Lefranc
Mar 10, 2005·British Journal of Haematology·Gunter KerstPeter Bader
May 27, 2008·Nucleic Acids Research·Xavier BrochetVéronique Giudicelli
Jan 13, 2009·Bioinformatics·René L WarrenRobert A Holt
May 9, 2009·Science·Joshua A WeinsteinStephen R Quake
Jun 23, 2009·Genome Research·J Douglas FreemanRobert A Holt
Feb 18, 2010·Science Translational Medicine·Scott D BoydAndrew Z Fire
May 25, 2010·The Journal of Immunology : Official Journal of the American Association of Immunologists·Scott D BoydAndrew M Collins
Feb 12, 2011·BMC Systems Biology·Rotem Ben-Hamo, Sol Efroni
Feb 26, 2011·Genome Research·René L WarrenRobert A Holt
Jun 3, 2011·Cold Spring Harbor Protocols·Marie-Paule Lefranc
Aug 11, 2011·PloS One·Ramy ArnaoutSergei B Koralov
Nov 3, 2011·Immunology·Jennifer BenichouSol Efroni
Dec 14, 2011·Proceedings of the National Academy of Sciences of the United States of America·Aaron C LoganDavid B Miklos
May 18, 2012·Science Translational Medicine·David WuHarlan Robins
Aug 31, 2012·Blood·Charles GawadNorman Lacayo
Oct 4, 2012·Blood·Monika BrüggemannMichael Kneba
Oct 18, 2012·Blood·Malek FahamDario Campana
Jan 11, 2013·Bioinformatics·Niclas ThomasBenjamin Chain
Jan 18, 2013·PLoS Pathogens·Rosario CastroPierre Boudinot
Feb 20, 2013·Leukemia·A C LoganD B Miklos
May 15, 2013·Nucleic Acids Research·Jian YeJames M Ostell
May 31, 2013·Genome Biology·Michael G RossDavid B Jaffe
Jul 31, 2013·Nature Methods·Dmitriy A BolotinDmitriy M Chudakov
Dec 7, 2013·Science Translational Medicine·Wen-Kai WengYoun H Kim
Feb 1, 2014·British Journal of Haematology·Virginie GandemerPierre Bordigoni
Mar 13, 2014·Cellular Immunology·Norbert NiklasChristian Gabriel
Mar 19, 2014·Proceedings of the National Academy of Sciences of the United States of America·Uri LasersonGeorge M Church
Apr 29, 2014·Biology of Blood and Marrow Transplantation : Journal of the American Society for Blood and Marrow Transplantation·Aaron C LoganDavid B Miklos
Jun 3, 2014·BMC Genomics·Mathieu GiraudMartin Figeac
Apr 30, 2015·Nature Methods·Dmitriy A BolotinDmitriy M Chudakov
May 20, 2015·Bioinformatics·Leon KuchenbeckerPeter N Robinson
May 23, 2015·Blood·Jacques J M van DongenAlberto Orfao
Citations
Nov 12, 2016·PloS One·Marc DuezFlorian Thonier
Apr 30, 2019·Pediatric Blood & Cancer·Gary WrightStuart P Adams
Jun 13, 2019·International Journal of Molecular Sciences·Ricardo SánchezJoaquín Martínez-López
Apr 30, 2017·Molecular Diagnosis & Therapy·Michaela KotrovaMonika Brüggemann
Jul 16, 2020·Medicine·Zhifang MaYujun Chen
Jan 13, 2017·Briefings in Bioinformatics·James M HeatherBenny Chain
Dec 1, 2019·Blood Cancer Journal·Udo Zur StadtMartin A Horstmann
Jan 5, 2021·International Journal of Laboratory Hematology·Rodolfo P CorreiaPaulo V Campregher
Dec 9, 2016·Leukemia Research·Mikaël SalsonClaude Preudhomme
Jul 4, 2020··Yujia ChenWen Li