TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

Diagnostic Pathology

Volumn 11, Issue 1, 2016, Pages

  Minervini, Crescenzio Francesco ^a   Cumbo, Cosimo ^a   Orsini, Paola ^a   Brunetti, Claudia ^a   Anelli, Luisa ^a   Zagaria, Antonella ^a   Minervini, Angela ^a   Casieri, Paola ^a   Coccaro, Nicoletta ^a   Tota, Giuseppina ^a   Impera, Luciana ^a   Giordano, Annamaria ^a   Specchia, Giorgina ^a   Albano, Francesco ^a  

^a UNIVERSITY OF BARI   (Italy)

Author keywords

Chronic Lymphocytic Leukemia; MinION; Nanopore; Sequencing; TP53

Indexed keywords

PROTEIN P53; TP53 PROTEIN, HUMAN; TUMOR MARKER;

ADULT; AGED; CHRONIC LYMPHATIC LEUKEMIA; COMPARATIVE STUDY; COST BENEFIT ANALYSIS; DNA MUTATIONAL ANALYSIS; ECONOMICS; FEMALE; GENETICS; HEALTH CARE COST; HIGH THROUGHPUT SEQUENCING; HUMAN; MALE; MIDDLE AGED; MUTATION; PATHOLOGY; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE; PROCEDURES; REPRODUCIBILITY;

ADULT; AGED; BIOMARKERS, TUMOR; COST-BENEFIT ANALYSIS; DNA MUTATIONAL ANALYSIS; FEMALE; HEALTH CARE COSTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; MALE; MIDDLE AGED; MUTATION; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE OF TESTS; REPRODUCIBILITY OF RESULTS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84990862184     PISSN: None     EISSN: 17461596     Source Type: Journal    
DOI: 10.1186/s13000-016-0550-y     Document Type: Article

References (33)

1. Lu W-J, Amatruda JF, Abrams JM. p53 ancestry: gazing through an evolutionary lens. Nat Rev Cancer. 2009;9:758-62.
2. Junttila MR, Evan GI. p53--a Jack of all trades but master of none. Nat Rev Cancer. 2009;9:821-9.
3. Dreger P, Corradini P, Kimby E, Michallet M, Milligan D, Schetelig J, et al. Indications for allogeneic stem cell transplantation in chronic lymphocytic leukemia: the EBMT transplant consensus. Leukemia. 2007;21:12-7.
4. Döhner H, Stilgenbauer S, Benner A, Leupolt E, Kröber A, Bullinger L, et al. Genomic Aberrations and Survival in Chronic Lymphocytic Leukemia. N Engl J Med. 2000;343:1910-6.
5. Mauro FR, Molica S, Laurenti L, Cortelezzi A, Carella AM, Zaja F, et al. Fludarabine plus alemtuzumab (FA) front-line treatment in young patients with chronic lymphocytic leukemia (CLL) and an adverse biologic profile. Leuk Res. 2014;38:198-203.
6. Zenz T, Krober A, Scherer K, Habe S, Buhler A, Benner A, et al. Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: results from a detailed genetic characterization with long-term follow-up. Blood. 2008;112:3322-9.
7. Tam CS, Shanafelt TD, Wierda WG, Abruzzo LV, Van Dyke DL, O'Brien S, et al. De novo deletion 17p13.1 chronic lymphocytic leukemia shows significant clinical heterogeneity: the M. D. Anderson and Mayo Clinic experience. Blood. 2009;114:957-64.
8. Tam CS, O'Brien S, Lerner S, Khouri I, Ferrajoli A, Faderl S, et al. The natural history of fludarabine-refractory chronic lymphocytic leukemia patients who fail alemtuzumab or have bulky lymphadenopathy. Leuk Lymphoma. 2007;48:1931-9.
9. Zenz T, Häbe S, Denzel T, Mohr J, Winkler D, Bühler A, et al. Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial. Blood. 2009;114:2589-97.
10. Gonzalez D, Martinez P, Wade R, Hockley S, Oscier D, Matutes E, et al. 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. J Clin Oncol. 2011;29:2223-9.
11. Rossi D, Cerri M, Deambrogi C, Sozzi E, Cresta S, Rasi S, et al. The prognostic value of TP53 mutations in chronic lymphocytic leukemia is independent of Del17p13: implications for overall survival and chemorefractoriness. Clin Cancer Res. 2009;15:995-1004.
12. Malcikova J, Pavlova S, Kozubik KS, Pospisilova S. TP53 mutation analysis in clinical practice: lessons from chronic lymphocytic leukemia. Hum Mutat. 2014;35:663-71.
13. Pospisilova S, Gonzalez D, Malcikova J, Trbusek M, Rossi D, Kater AP, et al. ERIC recommendations on TP53 mutation analysis in chronic lymphocytic leukemia. Leukemia. 2012;26:1458-61.
14. Loman NJ, Quinlan AR. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics. 2014;30:3399-401.
15. Storlazzi CT, Albano F, Locunsolo C, Lonoce A, Funes S, Guastadisegni MC, et al. t(3;12)(q26;q14) in polycythemia vera is associated with upregulation of the HMGA2 gene. Leukemia. 2006;20:2190-2.
16. Albano F, Anelli L, Zagaria A, Coccaro N, Minervini A, Rossi AR, et al. Decreased TET2 gene expression during chronic myeloid leukemia progression. Leuk Res. 2011;35:e220-2.
17. Carr IM, Camm N, Taylor GR, Charlton R, Ellard S, Sheridan EG, et al. GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms. J Med Genet. 2011;48:123-30.
18. Watson M, Thomson M, Risse J, Talbot R, Santoyo-Lopez J, Gharbi K, et al. poRe: an R package for the visualization and analysis of nanopore sequencing data. Bioinformatics. 2014;31:114-5.
19. Leggett RM, Heavens D, Caccamo M, Clark MD, Davey RP. NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. Bioinformatics. 2015;32:142-4.
20. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010;Chapter 19:Unit 19.10.1-21.
21. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5.
22. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11:R86.
23. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589-95.
24. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14:178-92.
25. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24-6.
26. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-76.
27. Norris AL, Workman RE, Fan Y, Eshleman JR, Timp W. Nanopore sequencing detects structural variants in cancer. Cancer Biol Ther. 2016;17:246-53.
28. Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015;12:733-5.
29. Qiao W, Yang Y, Sebra R, Mendiratta G, Gaedigk A, Desnick RJ, et al. Long-Read Single Molecule Real-Time Full Gene Sequencing of Cytochrome P450-2D6. Hum Mutat. 2016;37:315-23.
30. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002;18:452-64.
31. Quick J, Quinlan AR, Loman NJ. A reference bacterial genome dataset generated on the MinION(TM) portable single-molecule nanopore sequencer. Gigascience. 2014;3:22.
32. Rusk N. Genomics: MinION takes center stage. Nat Methods. 2014;12:12-3.
33. Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M. Improved data analysis for the MinION nanopore sequencer. Nat Methods. 2015;12:351-6.