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A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides. PLoS One 2016; 11:e0166911. [PMID: 27861573 PMCID: PMC5115841 DOI: 10.1371/journal.pone.0166911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes.
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Jang W, Yoon JH, Park J, Lee GD, Kim J, Kwon A, Choi H, Han K, Nahm CH, Kim HJ, Min WS, Kim M, Kim Y. Significance of KIT exon 17 mutation depends on mutant level rather than positivity in core-binding factor acute myeloid leukemia. Blood Cancer J 2016; 6:e387. [PMID: 26771813 PMCID: PMC4742633 DOI: 10.1038/bcj.2015.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 10/19/2015] [Indexed: 01/22/2023] Open
Abstract
KIT exon 17 mutation is a poor prognostic factor in core-binding factor acute myeloid leukemia. However, the mutation detection method used for risk assessment is not assigned. It is necessary to verify the analytical and clinical performance before applying new methods. Herein, we firstly applied a highly sensitive allele-specific, real-time quantitative PCR (AS-qPCR) assay to analyze KIT mutations, which demonstrated excellent sensitivity and specificity. Much higher incidence of KIT mutations (62.2%, 69/111) and prevalence of multiple mutations (43.5%, 30/69) were observed using AS-qPCR, which meant the existence of multiple KIT mutant subclones. The relative KIT mutant level was variable (median, 0.3 per control allele 100 copies, 0.002–532.7) and was divided into two groups: high (⩾10, n=26) and low (<10) mutant level. Interestingly, rather than mutation positivity, mutant level was found to be associated with clinical outcome. High mutant level showed significantly inferior overall survival (P=0.005) and event-free survival (P=0.03), whereas low level did not influence the prognosis. The follow-up data showed that the mutant level were along with fusion transcripts in the majority (n=29), but moved separately in some cases, including the loss of mutations (n=5) and selective proliferation of minor clones (n=2) at relapse. This study highlighted that the KIT mutation should be analyzed using sensitive and quantitative techniques and set a cutoff level for identifying the risk group.
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Affiliation(s)
- W Jang
- Department of Laboratory Medicine, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - J-H Yoon
- Department of Hematology, Catholic Blood and Marrow Transplantation Center, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - J Park
- Department of Laboratory Medicine, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - G D Lee
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - J Kim
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - A Kwon
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - H Choi
- Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - K Han
- Department of Laboratory Medicine, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - C H Nahm
- Department of Laboratory Medicine, College of Medicine, Inha University, Incheon, Korea
| | - H-J Kim
- Department of Hematology, Catholic Blood and Marrow Transplantation Center, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - W-S Min
- Department of Hematology, Catholic Blood and Marrow Transplantation Center, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - M Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Y Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
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