Literature DB >> 28600338

The relative utilities of genome-wide, gene panel, and individual gene sequencing in clinical practice.

Frank C Kuo1,2,3, Brenton G Mar2,4,5, R Coleman Lindsley6,7, Neal I Lindeman1,2,3.   

Abstract

Advances in technology that have transpired over the past 2 decades have enabled the analysis of cancer samples for genomic alterations to understand their biologic function and to translate that knowledge into clinical practice. With the power to analyze entire genomes in a clinically relevant time frame and with manageable costs comes the question of whether we ought to and when. This review focuses on the relative merits of 3 approaches to molecular diagnostics in hematologic malignancies: indication-specific single gene assays, gene panel assays that test for genes selected for their roles in cancer, and genome-wide assays that broadly analyze the tumor exomes or genomes. After addressing these in general terms, we review specific use cases in myeloid and lymphoid malignancies to highlight the utility of single gene testing and/or larger panels.
© 2017 by The American Society of Hematology.

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Year:  2017        PMID: 28600338      PMCID: PMC5813726          DOI: 10.1182/blood-2017-03-734533

Source DB:  PubMed          Journal:  Blood        ISSN: 0006-4971            Impact factor:   22.113


  85 in total

1.  Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia.

Authors:  Davide Rossi; Silvia Rasi; Giulia Fabbri; Valeria Spina; Marco Fangazio; Francesco Forconi; Roberto Marasca; Luca Laurenti; Alessio Bruscaggin; Michaela Cerri; Sara Monti; Stefania Cresta; Rosella Famà; Lorenzo De Paoli; Pietro Bulian; Valter Gattei; Anna Guarini; Silvia Deaglio; Daniela Capello; Raul Rabadan; Laura Pasqualucci; Riccardo Dalla-Favera; Robin Foà; Gianluca Gaidano
Journal:  Blood       Date:  2011-11-10       Impact factor: 22.113

2.  Inhibition of mutant IDH1 in acute myeloid leukaemia.

Authors:  Farhat Yaqub
Journal:  Lancet Oncol       Date:  2014-11-28       Impact factor: 41.316

3.  IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL.

Authors:  R P Kuiper; E Waanders; V H J van der Velden; S V van Reijmersdal; R Venkatachalam; B Scheijen; E Sonneveld; J J M van Dongen; A J P Veerman; F N van Leeuwen; A Geurts van Kessel; P M Hoogerbrugge
Journal:  Leukemia       Date:  2010-05-06       Impact factor: 11.528

4.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

Authors:  Xose S Puente; Magda Pinyol; Víctor Quesada; Laura Conde; Gonzalo R Ordóñez; Neus Villamor; Georgia Escaramis; Pedro Jares; Sílvia Beà; Marcos González-Díaz; Laia Bassaganyas; Tycho Baumann; Manel Juan; Mónica López-Guerra; Dolors Colomer; José M C Tubío; Cristina López; Alba Navarro; Cristian Tornador; Marta Aymerich; María Rozman; Jesús M Hernández; Diana A Puente; José M P Freije; Gloria Velasco; Ana Gutiérrez-Fernández; Dolors Costa; Anna Carrió; Sara Guijarro; Anna Enjuanes; Lluís Hernández; Jordi Yagüe; Pilar Nicolás; Carlos M Romeo-Casabona; Heinz Himmelbauer; Ester Castillo; Juliane C Dohm; Silvia de Sanjosé; Miguel A Piris; Enrique de Alava; Jesús San Miguel; Romina Royo; Josep L Gelpí; David Torrents; Modesto Orozco; David G Pisano; Alfonso Valencia; Roderic Guigó; Mónica Bayés; Simon Heath; Marta Gut; Peter Klatt; John Marshall; Keiran Raine; Lucy A Stebbings; P Andrew Futreal; Michael R Stratton; Peter J Campbell; Ivo Gut; Armando López-Guillermo; Xavier Estivill; Emili Montserrat; Carlos López-Otín; Elías Campo
Journal:  Nature       Date:  2011-06-05       Impact factor: 49.962

5.  Contribution of ABL kinase domain mutations to imatinib resistance in different subsets of Philadelphia-positive patients: by the GIMEMA Working Party on Chronic Myeloid Leukemia.

Authors:  Simona Soverini; Sabrina Colarossi; Alessandra Gnani; Gianantonio Rosti; Fausto Castagnetti; Angela Poerio; Ilaria Iacobucci; Marilina Amabile; Elisabetta Abruzzese; Ester Orlandi; Franca Radaelli; Fabrizio Ciccone; Mario Tiribelli; Roberto di Lorenzo; Clementina Caracciolo; Barbara Izzo; Fabrizio Pane; Giuseppe Saglio; Michele Baccarani; Giovanni Martinelli
Journal:  Clin Cancer Res       Date:  2006-12-15       Impact factor: 12.531

Review 6.  Prognostic factors for acute myeloid leukaemia in adults--biological significance and clinical use.

Authors:  Ruediger Liersch; Carsten Müller-Tidow; Wolfgang E Berdel; Utz Krug
Journal:  Br J Haematol       Date:  2014-02-01       Impact factor: 6.998

7.  Acute myeloid leukemia ontogeny is defined by distinct somatic mutations.

Authors:  R Coleman Lindsley; Brenton G Mar; Emanuele Mazzola; Peter V Grauman; Sarah Shareef; Steven L Allen; Arnaud Pigneux; Meir Wetzler; Robert K Stuart; Harry P Erba; Lloyd E Damon; Bayard L Powell; Neal Lindeman; David P Steensma; Martha Wadleigh; Daniel J DeAngelo; Donna Neuberg; Richard M Stone; Benjamin L Ebert
Journal:  Blood       Date:  2014-12-30       Impact factor: 22.113

8.  Somatic mutations of calreticulin in myeloproliferative neoplasms.

Authors:  Thorsten Klampfl; Heinz Gisslinger; Ashot S Harutyunyan; Harini Nivarthi; Elisa Rumi; Jelena D Milosevic; Nicole C C Them; Tiina Berg; Bettina Gisslinger; Daniela Pietra; Doris Chen; Gregory I Vladimer; Klaudia Bagienski; Chiara Milanesi; Ilaria Carola Casetti; Emanuela Sant'Antonio; Virginia Ferretti; Chiara Elena; Fiorella Schischlik; Ciara Cleary; Melanie Six; Martin Schalling; Andreas Schönegger; Christoph Bock; Luca Malcovati; Cristiana Pascutto; Giulio Superti-Furga; Mario Cazzola; Robert Kralovics
Journal:  N Engl J Med       Date:  2013-12-10       Impact factor: 91.245

9.  Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders.

Authors:  M Ladetto; M Brüggemann; L Monitillo; S Ferrero; F Pepin; D Drandi; D Barbero; A Palumbo; R Passera; M Boccadoro; M Ritgen; N Gökbuget; J Zheng; V Carlton; H Trautmann; M Faham; C Pott
Journal:  Leukemia       Date:  2013-12-17       Impact factor: 11.528

10.  Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2.

Authors:  Satoshi Inoue; Wanda Y Li; Alan Tseng; Isabel Beerman; Andrew J Elia; Sean C Bendall; François Lemonnier; Ken J Kron; David W Cescon; Zhenyue Hao; Evan F Lind; Naoya Takayama; Aline C Planello; Shu Yi Shen; Alan H Shih; Dana M Larsen; Qinxi Li; Bryan E Snow; Andrew Wakeham; Jillian Haight; Chiara Gorrini; Christian Bassi; Kelsie L Thu; Kiichi Murakami; Alisha R Elford; Takeshi Ueda; Kimberly Straley; Katharine E Yen; Gerry Melino; Luisa Cimmino; Iannis Aifantis; Ross L Levine; Daniel D De Carvalho; Mathieu Lupien; Derrick J Rossi; Garry P Nolan; Rob A Cairns; Tak W Mak
Journal:  Cancer Cell       Date:  2016-07-14       Impact factor: 31.743

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  16 in total

1.  Clinical Utility of Next-Generation Sequencing in Acute Myeloid Leukemia.

Authors:  Fei Yang; Tauangtham Anekpuritanang; Richard D Press
Journal:  Mol Diagn Ther       Date:  2020-02       Impact factor: 4.074

Review 2.  Measurement of Residual Disease in Acute Myeloid Leukemia.

Authors:  Rahul S Vedula; R Coleman Lindsley
Journal:  Curr Hematol Malig Rep       Date:  2017-12       Impact factor: 3.952

3.  Exosomes in the Healthy and Malignant Bone Marrow Microenvironment.

Authors:  Caitlyn A Moore; Alejandra I Ferrer; Sara Alonso; Sri Harika Pamarthi; Oleta A Sandiford; Pranela Rameshwar
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

4.  Patient-Specific Assays Based on Whole-Genome Sequencing Data to Measure Residual Disease in Children With Acute Lymphoblastic Leukemia: A Proof of Concept Study.

Authors:  Cecilia Arthur; Fatemah Rezayee; Nina Mogensen; Leonie Saft; Richard Rosenquist; Magnus Nordenskjöld; Arja Harila-Saari; Emma Tham; Gisela Barbany
Journal:  Front Oncol       Date:  2022-07-05       Impact factor: 5.738

5.  Detection of the KITD816V mutation in myelodysplastic and/or myeloproliferative neoplasms and acute myeloid leukemia with myelodysplasia-related changes predicts concurrent systemic mastocytosis.

Authors:  Jeffrey W Craig; Robert P Hasserjian; Annette S Kim; Jon C Aster; Geraldine S Pinkus; Jason L Hornick; David P Steensma; R Coleman Lindsley; Daniel J DeAngelo; Elizabeth A Morgan
Journal:  Mod Pathol       Date:  2020-01-02       Impact factor: 7.842

6.  Targeted massively parallel sequencing of mature lymphoid neoplasms: assessment of empirical application and diagnostic utility in routine clinical practice.

Authors:  Adam R Davis; Sara L Stone; Amanda R Oran; Robyn T Sussman; Siddharth Bhattacharyya; Jennifer J D Morrissette; Adam Bagg
Journal:  Mod Pathol       Date:  2020-12-12       Impact factor: 7.842

Review 7.  Genetic Markers in Lung Cancer Diagnosis: A Review.

Authors:  Katarzyna Wadowska; Iwona Bil-Lula; Łukasz Trembecki; Mariola Śliwińska-Mossoń
Journal:  Int J Mol Sci       Date:  2020-06-27       Impact factor: 5.923

Review 8.  Nanopore Sequencing in Blood Diseases: A Wide Range of Opportunities.

Authors:  Crescenzio Francesco Minervini; Cosimo Cumbo; Paola Orsini; Luisa Anelli; Antonella Zagaria; Giorgina Specchia; Francesco Albano
Journal:  Front Genet       Date:  2020-02-19       Impact factor: 4.599

9.  Prognostic roles of metabolic reprogramming-associated genes in patients with hepatocellular carcinoma.

Authors:  Lijuan Cui; Huan Xue; Zhitong Wen; Zhihong Lu; Yunfeng Liu; Yi Zhang
Journal:  Aging (Albany NY)       Date:  2020-11-12       Impact factor: 5.682

10.  Independent Validation of Early-Stage Non-Small Cell Lung Cancer Prognostic Scores Incorporating Epigenetic and Transcriptional Biomarkers With Gene-Gene Interactions and Main Effects.

Authors:  Ruyang Zhang; Chao Chen; Xuesi Dong; Sipeng Shen; Linjing Lai; Jieyu He; Dongfang You; Lijuan Lin; Ying Zhu; Hui Huang; Jiajin Chen; Liangmin Wei; Xin Chen; Yi Li; Yichen Guo; Weiwei Duan; Liya Liu; Li Su; Andrea Shafer; Thomas Fleischer; Maria Moksnes Bjaanæs; Anna Karlsson; Maria Planck; Rui Wang; Johan Staaf; Åslaug Helland; Manel Esteller; Yongyue Wei; Feng Chen; David C Christiani
Journal:  Chest       Date:  2020-02-28       Impact factor: 9.410

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