Literature DB >> 35622325

Immunoglobulin/T Cell Receptor Capture Strategy for Comprehensive Immunogenetics.

James Peter Stewart1, Jana Gazdova1, Shambhavi Srivastava1, Julia Revolta1, Louise Harewood1, Manisha Maurya1, Nikos Darzentas2, David Gonzalez3.   

Abstract

In the era of genomic medicine, targeted next generation sequencing strategies (NGS) are becoming increasingly adopted by clinical molecular diagnostic laboratories to identify genetic diagnostic and prognostic biomarkers in hemato-oncology. We describe the EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay, which is designed to simultaneously detect B and T cell clonal rearrangements, translocations, copy number alterations, and sequence variants. The accompanying validated bioinformatics pipeline enables production of an integrated report. The combination of the laboratory protocol and bioinformatics pipeline in the EuroClonality-NDC minimizes the potential for human error, reduces economic costs compared to current molecular testing strategies, and should improve diagnostic outcomes.
© 2022. The Author(s).

Entities:  

Keywords:  BIOMED-2; Copy number alteration; EuroClonality; Immunoglobulin; Lymphoma; Next generation sequencing; T cell receptor; Translocation

Mesh：

Substances：

Year:  2022        PMID： 35622325     DOI： 10.1007/978-1-0716-2115-8_9

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  15 in total

1.  Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing.

Authors:  Julia Richter; Matthias Schlesner; Steve Hoffmann; Markus Kreuz; Ellen Leich; Birgit Burkhardt; Maciej Rosolowski; Ole Ammerpohl; Rabea Wagener; Stephan H Bernhart; Dido Lenze; Monika Szczepanowski; Maren Paulsen; Simone Lipinski; Robert B Russell; Sabine Adam-Klages; Gordana Apic; Alexander Claviez; Dirk Hasenclever; Volker Hovestadt; Nadine Hornig; Jan O Korbel; Dieter Kube; David Langenberger; Chris Lawerenz; Jasmin Lisfeld; Katharina Meyer; Simone Picelli; Jordan Pischimarov; Bernhard Radlwimmer; Tobias Rausch; Marius Rohde; Markus Schilhabel; René Scholtysik; Rainer Spang; Heiko Trautmann; Thorsten Zenz; Arndt Borkhardt; Hans G Drexler; Peter Möller; Roderick A F MacLeod; Christiane Pott; Stefan Schreiber; Lorenz Trümper; Markus Loeffler; Peter F Stadler; Peter Lichter; Roland Eils; Ralf Küppers; Michael Hummel; Wolfram Klapper; Philip Rosenstiel; Andreas Rosenwald; Benedikt Brors; Reiner Siebert
Journal:  Nat Genet       Date:  2012-11-11       Impact factor: 38.330

Review 2.  The 2016 revision of the World Health Organization classification of lymphoid neoplasms.

Authors:  Steven H Swerdlow; Elias Campo; Stefano A Pileri; Nancy Lee Harris; Harald Stein; Reiner Siebert; Ranjana Advani; Michele Ghielmini; Gilles A Salles; Andrew D Zelenetz; Elaine S Jaffe
Journal:  Blood       Date:  2016-03-15       Impact factor: 22.113

3.  Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.

Authors:  Donavan T Cheng; Talia N Mitchell; Ahmet Zehir; Ronak H Shah; Ryma Benayed; Aijazuddin Syed; Raghu Chandramohan; Zhen Yu Liu; Helen H Won; Sasinya N Scott; A Rose Brannon; Catherine O'Reilly; Justyna Sadowska; Jacklyn Casanova; Angela Yannes; Jaclyn F Hechtman; Jinjuan Yao; Wei Song; Dara S Ross; Alifya Oultache; Snjezana Dogan; Laetitia Borsu; Meera Hameed; Khedoudja Nafa; Maria E Arcila; Marc Ladanyi; Michael F Berger
Journal:  J Mol Diagn       Date:  2015-03-20       Impact factor: 5.568

Review 4.  Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq.

Authors:  Scott V Bratman; Aaron M Newman; Ash A Alizadeh; Maximilian Diehn
Journal:  Expert Rev Mol Diagn       Date:  2015-03-16       Impact factor: 5.225

Review 5.  Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.

Authors:  J J M van Dongen; A W Langerak; M Brüggemann; P A S Evans; M Hummel; F L Lavender; E Delabesse; F Davi; E Schuuring; R García-Sanz; J H J M van Krieken; J Droese; D González; C Bastard; H E White; M Spaargaren; M González; A Parreira; J L Smith; G J Morgan; M Kneba; E A Macintyre
Journal:  Leukemia       Date:  2003-12       Impact factor: 11.528

6.  Mutational status of the TP53 gene as a predictor of response and survival in patients with chronic lymphocytic leukemia: results from the LRF CLL4 trial.

Authors:  David Gonzalez; Pilar Martinez; Rachel Wade; Sarah Hockley; David Oscier; Estella Matutes; Claire E Dearden; Sue M Richards; Daniel Catovsky; Gareth J Morgan
Journal:  J Clin Oncol       Date:  2011-04-11       Impact factor: 44.544

7.  Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets.

Authors:  K Karube; A Enjuanes; I Dlouhy; P Jares; D Martin-Garcia; F Nadeu; G R Ordóñez; J Rovira; G Clot; C Royo; A Navarro; B Gonzalez-Farre; A Vaghefi; G Castellano; C Rubio-Perez; D Tamborero; J Briones; A Salar; J M Sancho; S Mercadal; E Gonzalez-Barca; L Escoda; H Miyoshi; K Ohshima; K Miyawaki; K Kato; K Akashi; A Mozos; L Colomo; M Alcoceba; A Valera; A Carrió; D Costa; N Lopez-Bigas; R Schmitz; L M Staudt; I Salaverria; A López-Guillermo; E Campo
Journal:  Leukemia       Date:  2017-08-14       Impact factor: 11.528

8.  Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.

Authors:  Cristina López; Kortine Kleinheinz; Sietse M Aukema; Marius Rohde; Stephan H Bernhart; Daniel Hübschmann; Rabea Wagener; Umut H Toprak; Francesco Raimondi; Markus Kreuz; Sebastian M Waszak; Zhiqin Huang; Lina Sieverling; Nagarajan Paramasivam; Julian Seufert; Stephanie Sungalee; Robert B Russell; Julia Bausinger; Helene Kretzmer; Ole Ammerpohl; Anke K Bergmann; Hans Binder; Arndt Borkhardt; Benedikt Brors; Alexander Claviez; Gero Doose; Lars Feuerbach; Andrea Haake; Martin-Leo Hansmann; Jessica Hoell; Michael Hummel; Jan O Korbel; Chris Lawerenz; Dido Lenze; Bernhard Radlwimmer; Julia Richter; Philip Rosenstiel; Andreas Rosenwald; Markus B Schilhabel; Harald Stein; Stephan Stilgenbauer; Peter F Stadler; Monika Szczepanowski; Marc A Weniger; Marc Zapatka; Roland Eils; Peter Lichter; Markus Loeffler; Peter Möller; Lorenz Trümper; Wolfram Klapper; Steve Hoffmann; Ralf Küppers; Birgit Burkhardt; Matthias Schlesner; Reiner Siebert
Journal:  Nat Commun       Date:  2019-03-29       Impact factor: 14.919

9.  Use of an Integrated Pan-Cancer Oncology Enrichment Next-Generation Sequencing Assay to Measure Tumour Mutational Burden and Detect Clinically Actionable Variants.

Authors:  Valerie Pestinger; Matthew Smith; Toju Sillo; John M Findlay; Jean-Francois Laes; Gerald Martin; Gary Middleton; Phillipe Taniere; Andrew D Beggs
Journal:  Mol Diagn Ther       Date:  2020-06       Impact factor: 4.074

Review 10.  EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations.

Authors:  A W Langerak; P J T A Groenen; M Brüggemann; K Beldjord; C Bellan; L Bonello; E Boone; G I Carter; M Catherwood; F Davi; M-H Delfau-Larue; T Diss; P A S Evans; P Gameiro; R Garcia Sanz; D Gonzalez; D Grand; A Håkansson; M Hummel; H Liu; L Lombardia; E A Macintyre; B J Milner; S Montes-Moreno; E Schuuring; M Spaargaren; E Hodges; J J M van Dongen
Journal:  Leukemia       Date:  2012-08-24       Impact factor: 11.528
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