Rapid Capture Next-Generation Sequencing in Clinical Diagnostics of Kinase Pathway Aberrations in B-Cell Precursor ALL

Pediatric Blood and Cancer

Volumn 63, Issue 7, 2016, Pages 1283-1286

  Stadt, Udo zur ^a   Escherich, Gabriele ^a   Indenbirken, Daniela ^b   Alawi, Malik ^a,b   Adao, Manuela ^a   Horstmann, Martin A ^a,c  

^a UNIVERSITY MEDICAL CENTER HAMBURG EPPENDORF   (Germany)

^b LEIBNIZ INSTITUTE FOR EXPERIMENTAL VIROLOGY   (Germany)

^c Research Institute Children's Cancer Center   (Germany)

Author keywords

Acute lymphoblastic leukemia; Genomic breakpoints; NGS; Ph like ALL

Indexed keywords

CYTOKINE RECEPTOR; PHOSPHOTRANSFERASE; IKAROS TRANSCRIPTION FACTOR; IKZF1 PROTEIN, HUMAN;

ACUTE LYMPHOBLASTIC LEUKEMIA; ADOLESCENT; ARTICLE; CANCER PATIENT; CHILD; GENE DELETION; GENE FUSION; GENE MAPPING; GENE MUTATION; GENE REARRANGEMENT; GENETIC VARIATION; GENOMICS; HIGH RISK PATIENT; HUMAN; IKZF1 GENE; MINIMAL RESIDUAL DISEASE; NEXT GENERATION SEQUENCING; ONCOGENE; POLYMERASE CHAIN REACTION; PRESCHOOL CHILD; PRIORITY JOURNAL; SCHOOL CHILD; ENZYMOLOGY; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; MALE; MUTATION; PRECURSOR B-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA; PROCEDURES;

ADOLESCENT; CHILD; CHILD, PRESCHOOL; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IKAROS TRANSCRIPTION FACTOR; MALE; MUTATION; PRECURSOR B-CELL LYMPHOBLASTIC LEUKEMIA-LYMPHOMA;

EID: 84961794786     PISSN: 15455009     EISSN: 15455017     Source Type: Journal    
DOI: 10.1002/pbc.25975     Document Type: Article

References (15)

1. Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, Harvey RC, Chen IM, Clifford RJ, Carroll WL, Reaman G, Bowman WP, Devidas M, Gerhard DS, Yang W, Relling MV et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 2009;360:470-480.
2. Den Boer ML, van Slegtenhorst M, De Menezes RX, Cheok MH, Buijs-Gladdines JG, Peters ST, Van Zutven LJ, Beverloo HB, Van der Spek PJ, Escherich G, Horstmann MA, Janka-Schaub GE, Kamps WA, Evans WE, Pieters R. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: A genome-wide classification study. Lancet Oncol 2009;10:125-134.
3. Roberts KG, Li Y, Payne-Turner D, Harvey RC, Yang YL, Pei D, McCastlain K, Ding L, Lu C, Song G, Ma J, Becksfort J, Rusch M, Chen SC, Easton J, Cheng J, Boggs K, Santiago-Morales N, Iacobucci I, Fulton RS et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med 2014;371:1005-1015.
4. Roberts KG, Morin RD, Zhang J, Hirst M, Zhao Y, Su X, Chen SC, Payne-Turner D, Churchman ML, Harvey RC, Chen X, Kasap C, Yan C, Becksfort J, Finney RP, Teachey DT, Maude SL, Tse K, Moore R, Jones S et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell 2012;22:153-166.
5. Biondi A, Schrappe M, De Lorenzo P, Castor A, Lucchini G, Gandemer V, Pieters R, Stary J, Escherich G, Campbell M, Li CK, Vora A, Arico M, Rottgers S, Saha V, Valsecchi MG. Imatinib after induction for treatment of children and adolescents with Philadelphia-chromosome-positive acute lymphoblastic leukaemia (EsPhALL): A randomised, open-label, intergroup study. Lancet Oncol 2012;13:936-945.
6. Weston BW, Hayden MA, Roberts KG, Bowyer S, Hsu J, Fedoriw G, Rao KW, Mullighan CG. Tyrosine kinase inhibitor therapy induces remission in a patient with refractory EBF1-PDGFRB-positive acute lymphoblastic leukemia. J Clin Oncol 2013;31:e413-e416.
7. Loh ML, Zhang J, Harvey RC, Roberts K, Payne-Turner D, Kang H, Wu G, Chen X, Becksfort J, Edmonson M, Buetow KH, Carroll WL, Chen IM, Wood B, Borowitz MJ, Devidas M, Gerhard DS, Bowman P, Larsen E, Winick N et al. Tyrosine kinome sequencing of pediatric acute lymphoblastic leukemia: A report from the Children's Oncology Group TARGET Project. Blood 2013;121:485-488.
8. Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, Pritchard CC, Grossmann AH, Wallander ML, Pfeifer JD, Lockwood CM, Duncavage EJ. Detection of gene rearrangements in targeted clinical next-generation sequencing. J Mol Diagn 2014;16:405-417.
9. Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 2014;30:2114-2120.
10. Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermuller J, Stadler PF. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol 2014;15:R34.
11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078-2079.
12. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297-1303.
13. van der Velden VH, Cazzaniga G, Schrauder A, Hancock J, Bader P, Panzer-Grumayer ER, Flohr T, Sutton R, Cave H, Madsen HO, Cayuela JM, Trka J, Eckert C, Foroni L, Zur Stadt U, Beldjord K, Raff T, van der Schoot CE, van Dongen JJ. European Study Group on MRD in ALL. Analysis of minimal residual disease by Ig/TCR gene rearrangements: Guidelines for interpretation of real-time quantitative PCR data. Leukemia 2007;21:604-611.
14. van der Veer A, Waanders E, Pieters R, Willemse ME, Van Reijmersdal SV, Russell LJ, Harrison CJ, Evans WE, van der Velden VH, Hoogerbrugge PM, Van Leeuwen F, Escherich G, Horstmann MA, Mohammadi Khankahdani L, Rizopoulos D, De Groot-Kruseman HA, Sonneveld E, Kuiper RP, Den Boer ML. Independent prognostic value of BCR-ABL1-like signature and IKZF1 deletion, but not high CRLF2 expression, in children with B-cell precursor ALL. Blood 2013;122:2622-2629.
15. Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: Insights and treatment implications. Nat Rev Clin Oncol 2015;12:344-357.