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Bergeron J, Capo-Chichi JM, Tsui H, Mahe E, Berardi P, Minden MD, Brandwein JM, Schuh AC. The Clinical Utility of FLT3 Mutation Testing in Acute Leukemia: A Canadian Consensus. Curr Oncol 2023; 30:10410-10436. [PMID: 38132393 PMCID: PMC10742150 DOI: 10.3390/curroncol30120759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) mutations are detected in approximately 20-30% of patients with acute myeloid leukemia (AML), with the presence of a FLT3 internal tandem duplication (FLT3-ITD) mutation being associated with an inferior outcome. Assessment of FLT3 mutational status is now essential to define optimal upfront treatment in both newly diagnosed and relapsed AML, to support post-induction allogeneic hematopoietic stem cell transplantation (alloSCT) decision-making, and to evaluate treatment response via measurable (minimal) residual disease (MRD) evaluation. In view of its importance in AML diagnosis and management, the Canadian Leukemia Study Group/Groupe canadien d'étude sur la leucémie (CLSG/GCEL) undertook the development of a consensus statement on the clinical utility of FLT3 mutation testing, as members reported considerable inter-center variability across Canada with respect to testing availability and timing of use, methodology, and interpretation. The CLSG/GCEL panel identified key clinical and hematopathological questions, including: (1) which patients should be tested for FLT3 mutations, and when?; (2) which is the preferred method for FLT3 mutation testing?; (3) what is the clinical relevance of FLT3-ITD size, insertion site, and number of distinct FLT3-ITDs?; (4) is there a role for FLT3 analysis in MRD assessment?; (5) what is the clinical relevance of the FLT3-ITD allelic burden?; and (6) how should results of FLT3 mutation testing be reported? The panel followed an evidence-based approach, taken together with Canadian clinical and laboratory experience and expertise, to create a consensus document to facilitate a more uniform approach to AML diagnosis and treatment across Canada.
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Affiliation(s)
- Julie Bergeron
- CEMTL Installation Maisonneuve-Rosemont, Institut Universitaire d’Hématologie-Oncologie et de Thérapie Cellulaire, Université de Montréal, Montréal, QC H1T 2M4, Canada
| | - Jose-Mario Capo-Chichi
- Division of Clinical Laboratory Genetics, Department of Laboratory Medicine and Pathobiology, Laboratory Medicine Program, University Health Network, University of Toronto, Toronto, ON M5G 2C4, Canada;
| | - Hubert Tsui
- Division of Hematological Pathology, Department of Laboratory Medicine and Molecular Diagnostics, Precision Diagnostics and Therapeutics Program, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada;
- Department of Laboratory Medicine and Pathobiology, Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Etienne Mahe
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Division of Hematology and Hematological Malignancies, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Philip Berardi
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital/Eastern Ontario Regional Laboratory Association, Ottawa, ON K1H 8M2, Canada;
- Department of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mark D. Minden
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
| | - Joseph M. Brandwein
- Division of Hematology, Department of Medicine, University of Alberta, Edmonton, AB T6G 2G3, Canada;
| | - Andre C. Schuh
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; (M.D.M.); (A.C.S.)
- Department of Medicine, University of Toronto, Toronto, ON M5S 3H2, Canada
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Goto M, Sawanobori E, Inukai T, Hirata S, Mabuchi T. Quantitative Analysis of Mitochondrial DNA Heteroplasmy in Urinary Podocytes of Myoclonus Epilepsy With Ragged-Red Fibers Syndrome. Kidney Int Rep 2023; 8:2830-2832. [PMID: 38106588 PMCID: PMC10719592 DOI: 10.1016/j.ekir.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 12/19/2023] Open
Affiliation(s)
- Miwa Goto
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
- National Hospital Organization, Kofu National Hospital, Tenjin, Kofu, Yamanashi, Japan
| | - Emi Sawanobori
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
| | - Takeshi Inukai
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
| | - Shuji Hirata
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
| | - Tadashi Mabuchi
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Yamanashi, Shimokato, Chuo, Yamanashi, Japan
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Čmejlová J, Paprštein F, Suran P, Zelený L, Čmejla R. A New One-Tube Reaction Assay for the Universal Determination of Sweet Cherry ( Prunus avium L.) Self-(In)Compatible MGST- and S-Alleles Using Capillary Fragment Analysis. Int J Mol Sci 2023; 24:ijms24086931. [PMID: 37108095 PMCID: PMC10139232 DOI: 10.3390/ijms24086931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The sweet cherry plant (Prunus avium L.) is primarily self-incompatible, with so-called S-alleles responsible for the inability of flowers to be pollinated not only by their own pollen grains but also by pollen from other cherries having the same S-alleles. This characteristic has wide-ranging impacts on commercial growing, harvesting, and breeding. However, mutations in S-alleles as well as changes in the expression of M locus-encoded glutathione-S-transferase (MGST) can lead to complete or partial self-compatibility, simplifying orchard management and reducing possible crop losses. Knowledge of S-alleles is important for growers and breeders, but current determination methods are challenging, requiring several PCR runs. Here we present a system for the identification of multiple S-alleles and MGST promoter variants in one-tube PCR, with subsequent fragment analysis on a capillary genetic analyzer. The assay was shown to unequivocally determine three MGST alleles, 14 self-incompatible S-alleles, and all three known self-compatible S-alleles (S3', S4', S5') in 55 combinations tested, and thus it is especially suitable for routine S-allele diagnostics and molecular marker-assisted breeding for self-compatible sweet cherries. In addition, we identified a previously unknown S-allele in the 'Techlovicka´ genotype (S54) and a new variant of the MGST promoter with an 8-bp deletion in the ´Kronio´ cultivar.
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Affiliation(s)
- Jana Čmejlová
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic
| | - František Paprštein
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic
| | - Pavol Suran
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic
| | - Lubor Zelený
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic
| | - Radek Čmejla
- Research and Breeding Institute of Pomology Holovousy Ltd., Holovousy 129, 508 01 Hořice, Czech Republic
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Lee S, Sun CH, Jang H, Kim D, Yoon SS, Koh Y, Na SC, Cho SI, Kim MJ, Seong MW, Byun JM, Yun H. ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application. BMC Bioinformatics 2023; 24:62. [PMID: 36823555 PMCID: PMC9951415 DOI: 10.1186/s12859-023-05173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository.
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Affiliation(s)
- Sungyoung Lee
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XCenter for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Choong-Hyun Sun
- GenomeOpinion Inc., 117-3 Hoegiro, Dongdaemoon-gu, Seoul, Republic of Korea
| | - Heejun Jang
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daeyoon Kim
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Chan Na
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Center for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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Sfakianaki M, Tzardi M, Tsantaki K, Koutoulaki C, Messaritakis I, Datseri G, Moustou E, Mavroudis D, Souglakos J. Evaluation of Microsatellite Instability Molecular Analysis versus Immuno-Histochemical Interpretation in Malignant Neoplasms with Different Localizations. Cancers (Basel) 2023; 15:cancers15020353. [PMID: 36672302 PMCID: PMC9856558 DOI: 10.3390/cancers15020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/09/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
MMR gene germline mutations are considered a major genetic disorder in patients with hereditary nonpolyposis colon cancer (HNPCC) or Lynch syndrome; A total of 15% of sporadic colon carcinomas are MSI-High. MSI has also been observed in other cancers, such as endometrial, gastric, and ovarian cancer. The aim of the current study was to correlate and outline the optimal method between the molecular testing of the instability of microsatellite DNA regions (MSI status) and the loss of protein expression by immunehistochemistry (MMR). A total of 242 paraffin-embedded tissues from gastrointestinal, gynecological, genitourinary, lung, breast, and unknown primary cancer patients were analyzed for the expression of MLH1/MSH2/MSH6/PMS2 by immunohistochemistry, as well as for the molecular analysis of MSI status using PCR-based molecular fragment analysis. A total of 29 MSI-High patients were detected molecularly, while 23 patients were detected by immunohistochemistry, with rates that are comparable according to the literature. Based on the agreement coefficient of the two methods, a substantial agreement emerged (Kappa = 0.675 with standard error = 0.081, p < 0.001). Despite the substantial agreement, both methods ought to be established to determine MSI-H/dMMR status in all cancer types as a first-line screening test.
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Affiliation(s)
- Maria Sfakianaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Correspondence: (M.S.); (I.M.); Tel.: +30-281-039-4926 (I.M.)
| | - Maria Tzardi
- Department of Pathology, University General Hospital of Heraklion, 71110 Heraklion, Greece
| | - Konstantina Tsantaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Chara Koutoulaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Ippokratis Messaritakis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Correspondence: (M.S.); (I.M.); Tel.: +30-281-039-4926 (I.M.)
| | - Galateia Datseri
- Department of Pathology, University General Hospital of Heraklion, 71110 Heraklion, Greece
| | - Eleni Moustou
- Department of Pathology, University General Hospital of Heraklion, 71110 Heraklion, Greece
| | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, 71500 Iraklio, Greece
| | - John Souglakos
- Laboratory of Translational Oncology, School of Medicine, University of Crete, 71003 Heraklion, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, 71500 Iraklio, Greece
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Buono V, Burgio S, Macrì N, Catania G, Hauffe HC, Mucci N, Davoli F. Microsatellite Characterization and Panel Selection for Brown Bear ( Ursus arctos) Population Assessment. Genes (Basel) 2022; 13:2164. [PMID: 36421838 PMCID: PMC9690282 DOI: 10.3390/genes13112164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 10/28/2023] Open
Abstract
An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.
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Affiliation(s)
- Vincenzo Buono
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Salvatore Burgio
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, 40100 Bologna, Italy
| | - Nicole Macrì
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Giovanni Catania
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, 40100 Bologna, Italy
| | - Heidi C. Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione E. Mach, San Michele all’Adige, 38098 Trento, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
| | - Francesca Davoli
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell’Emilia, 40064 Bologna, Italy
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Friedrich C, Zalmaï L, Gay J, Coude MM, Bravetti C, Vazquez R, Temple M, Duroyon E, Darnige L, Decroocq J, Alary AS, Kosmider O. PCR-Fluo-ASXL1-FA: A fast, sensitive and inexpensive complementary method to detect ASXL1 mutations in haematological malignancies. Int J Lab Hematol 2022; 44:928-933. [PMID: 35793805 DOI: 10.1111/ijlh.13931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/27/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The additional sex combs like 1 (ASXL1) gene is frequently mutated in a number of haematological neoplasms. The c.1934dupG, known to be the most common alteration in ASXL1, is associated with poor clinical outcome. A systematic determination of ASXL1 mutational status in myeloid malignancies is therefore necessary for prognostic stratification. METHODS Because direct sequencing is not sensitive and next-generation sequencing (NGS) is time-consuming, expensive and sometimes does not allow the detection of the c.1934dupG, we have developed a fragment analysis assay, complementary to NGS, that allows the detection of c.1934dupG mutation in addition to other nearby insertions/deletions of ASXL1 located close to it. We called this assay the "PCR-Fluo-ASXL1-FA." RESULTS First, we evaluated the efficiency of our approach compared to NGS and Sanger. We showed that "PCR-Fluo-ASXL1-FA" could detect all insertional mutations of ASXL1 located on its area, with a high sensitivity (1.5%). Then, we have illustrated the interest of this technique by three concrete cases. DISCUSSION In summary, we have established a fragment analysis approach, which can detect most ASXL1 mutations, in particular the c.1934dupG, in a sensitive, fast and inexpensive manner. We therefore recommend the synchronous use of this method with NGS, to ensure complete detection of all clinically relevant ASXL1 mutations in patients suffering with myeloid neoplasms.
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Affiliation(s)
- Chloé Friedrich
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Loria Zalmaï
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Juliette Gay
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | | | - Clotilde Bravetti
- Hematology Department, Hôpital de la Pitié Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Romain Vazquez
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Marie Temple
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Eugénie Duroyon
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Luc Darnige
- Hematology Department, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | - Justine Decroocq
- Clinical Hematology department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
| | | | - Olivier Kosmider
- Hematology Department, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris (APHP-CUP), Paris, France
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Cho H, Shin S, Chung H, Jang JE, Kim YR, Cheong JW, Min YH, Lee ST, Choi JR, Kim JS. Real-world data on prognostic value of measurable residual disease assessment by fragment analysis or next-generation sequencing in multiple myeloma. Br J Haematol 2022; 198:503-514. [PMID: 35505579 DOI: 10.1111/bjh.18211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 01/12/2023]
Abstract
Measurable residual disease (MRD) negativity is a strong prognostic indicator in multiple myeloma (MM). However, the optimal use of MRD in daily clinical practice has been hampered by the limited feasibility of MRD testing. Therefore, we examined the clinical relevance of commercially available MRD modalities based on clonality assays by fragment analysis with IdentiClone® (n = 73 patients) and next-generation sequencing (NGS) with LymphoTrack® (n = 116 patients) in newly diagnosed patients with MM who received autologous stem cell transplantation (ASCT). MRD was assessed at the end of induction (pre-ASCT) and/or at 100 days after ASCT (post-ASCT). MRD could not predict survival when assessed by fragment analysis. However, NGS-based MRD negativity at pre- or post-ASCT was beneficial in terms of progression-free and overall survival. Moreover, NGS-based MRD negativity was independently associated with improved progression-free and overall survival, and MRD-positive patients both pre- and post-ASCT had worst outcome. Indeed, initial adverse prognostic features by high-risk cytogenetics could be mitigated upon achieving MRD negativity by NGS. We demonstrate the feasibility and clinical benefit of achieving MRD negativity by commercially available clonality-based MRD assays in MM and support incorporating NGS, but not fragment analysis, to tailor therapeutic strategies in real-world practice.
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Affiliation(s)
- Hyunsoo Cho
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Haerim Chung
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yu Ri Kim
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yoo Hong Min
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Seok Kim
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Mizuta S, Yamane N, Mononobe S, Watanabe A, Kitamura R, Takahara T, Matsushima C, Yoshida A, Okamoto S, Tanaka K, Iwai A, Ikegawa A, Wada T, Usami I, Maihara T, Komai T, Heike T, Nishida Y, Kobayashi K. Sensitive detection of GATA1 mutations using complementary DNA-based analysis for transient abnormal myelopoiesis associated with the Down syndrome. Int J Lab Hematol 2021; 44:349-355. [PMID: 34761527 DOI: 10.1111/ijlh.13756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/26/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION GATA1 mutation plays an important role in initiating transient abnormal myelopoiesis (TAM) and in the clonal evolution towards acute megakaryoblastic leukaemia (AMKL) associated with Down syndrome (DS). This study aimed to develop and validate the clinical utility of a complementary DNA (cDNA) analysis in parallel with the conventional genomic DNA (gDNA) Sanger sequencing (Ss), as an initial screening test for GATA1 mutations. METHODS GATA1 mutations were evaluated using both gDNA and cDNA in 14 DS patients using Ss and fragment analysis (FA), respectively. RESULTS The detection sensitivity of conventional gDNA sequencing was limited in low blast percentage TAM (LBP-TAM); however, cDNA-based Ss readily detected all the pathognomonic GATA1 mutations. The cDNA-based FA readily detected GATA1 frameshift mutation with a reliable sensitivity ranging from 0.005% to 0.01% of clonal cells. CONCLUSIONS GATA1 mutations are heterogeneous; therefore, we would like to propose a dual cDNA and gDNA analysis as a standard diagnostic approach, especially for LBP-TAM. cDNA-based FA promises an excellent sensitivity for detecting frameshift GATA1 mutations in the longitudinal clonal evolution towards AMKL without using a patient specific primer.
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Affiliation(s)
- Shumpei Mizuta
- Department of Clinical Laboratory, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Laboratory of Hematology, Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Noriko Yamane
- Department of Clinical Laboratory, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Saya Mononobe
- Department of Clinical Laboratory, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Asami Watanabe
- Department of Clinical Laboratory, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Ritsuko Kitamura
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Tadamori Takahara
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Chieko Matsushima
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Atushi Yoshida
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Seiji Okamoto
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Kuniaki Tanaka
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Pediatric Hematology and Oncology, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan
| | - Atsushi Iwai
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Pediatric Hematology and Oncology, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan
| | - Atsuko Ikegawa
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Takahito Wada
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ikuya Usami
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Toshiro Maihara
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Takao Komai
- Department of Clinical Laboratory, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Toshio Heike
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Yoshinobu Nishida
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Neonatology, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Kenichiro Kobayashi
- Department of Pediatrics, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan.,Department of Pediatric Hematology and Oncology, Hyogo Prefectural Amagasaki General Medical Center, Hyogo, Japan.,Department of Pediatric Hematology and Oncology Research, Research Institute, National Center for Child Health and Development, Tokyo, Japan
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Hindley A, Catherwood MA, McMullin MF, Mills KI. Significance of NPM1 Gene Mutations in AML. Int J Mol Sci 2021; 22:ijms221810040. [PMID: 34576201 PMCID: PMC8467861 DOI: 10.3390/ijms221810040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
The aim of this literature review is to examine the significance of the nucleophosmin 1 (NPM1) gene in acute myeloid leukaemia (AML). This will include analysis of the structure and normal cellular function of NPM1, the type of mutations commonly witnessed in NPM1, and the mechanism by which this influences the development and progression of AML. The importance of NPM1 mutation on prognosis and the treatment options available to patients will also be reviewed along with current guidelines recommending the rapid return of NPM1 mutational screening results and the importance of employing a suitable laboratory assay to achieve this. Finally, future developments in the field including research into new therapies targeting NPM1 mutated AML are considered.
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Affiliation(s)
- Andrew Hindley
- Clinical Haematology, Belfast City Hospital, Belfast BT9 7AB, UK;
- Correspondence:
| | | | - Mary Frances McMullin
- Centre for Medical Education, Queen’s University Belfast, Belfast BT7 1NN, UK;
- Northern Ireland and Belfast Health and Social Care Trust, Belfast BT9 7AB, UK
| | - Ken I. Mills
- Patrick G Johnston Center for Cancer Research, Queens University Belfast, Belfast BT9 7AE, UK;
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11
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Abstract
Introduction There is a great deal of heterogeneity, both phenotypically and genotypically among the autosomal dominant cerebellar ataxias (ADCA). Their prevalence also varies in different populations. Trinucleotide repeat expansions (CTG/CAG) have been shown predominantly to cause a number of ADCAs. Aim The present study describes the frequency of spinocerebellar ataxias (SCA) and the CAG repeat sizes among the different regions of India. Settings and Design Molecular data from our central reference laboratory were retrospectively analyzed for SCAs 1, 2, 3, 6, 7, 10, 12, 17 and DRPLA. Correlation between age at diagnosis and the CAG repeats of the expanded and the normal alleles were tested with the Spearman correlation test. Results The presence of SCAs vary according to geographical regions and ethnicities; SCA 12 was detected with the highest frequency (229/901), but was restricted to a specific ethnic population, followed by SCA 2 with a positivity of 12% (101/845). SCA 3 previously known as Machado-Joseph Disease had a prevalence of 4.05% (32/789), whereas SCA 1 was diagnosed in 30/773 (3.88%). No positivity was seen for SCA 10 from the 103 samples tested and for SCA 17 from the 131 samples tested either as a part of an extended panel or stand-alone. Conclusion In this report, we are able to expand the portrait of SCAs in India by presenting the largest ever molecular data from a central reference laboratory.
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Affiliation(s)
| | | | - Bibhu R Das
- Research and Development, Mumbai, Maharashtra, India
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12
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Shetty O, Pai T, Gurav M, Rekhi B. Comparison between Fluorescence in-situ Hybridization (FISH), Reverse Transcriptase PCR (RT-PCR) and fragment analysis, for detection of t (X; 18) (p11; q11) translocation in synovial sarcomas. INDIAN J PATHOL MICR 2020; 63:64-72. [PMID: 32031125 DOI: 10.4103/ijpm.ijpm_851_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Synovial sarcoma (SS) is an aggressive, but a relatively chemosensitive soft tissue sarcoma, characterized by a specific, t (X;18)(p11;q11) translocation, leading to formation of SS18-SSX chimeric transcript. This translocation can be detected by various techniques, such as fluorescence in-situ hybridization (FISH), reverse transcriptase PCR (RT-PCR) and fragment analysis. Objectives To compare the results of detection of t (X;18)(p11;q11) translocation, across three different platforms, in order to determine the most optimal and sensitive technique. Methods Formalin-fixed paraffin embedded (FFPE) tissue sections of 45 soft tissue sarcomas were analyzed, including 16 cases of SS confirmed by histopathology, immunohistochemistry and molecular technique (s)(Group 1); 13 cases, wherein SS was one of the differential diagnosis, preceding molecular testing (Group 2) and 16 cases of various other sarcomas (Group 3). Various immunohistochemical (IHC) markers studied, including INI1/SMARCB1. All cases were tested for t (X;18) translocation, by fragment Analysis, FISH and RT-PCR. Results There were 23 cases of SS, including 16 of group 1 and 7 of group 2. By fragment analysis, t (X;18)(p11;q11) translocation was detected in 22/23 cases (95.6%). By FISH, SS18 gene rearrangement was detected in 18/22 cases (78.2%), whereas by RT-PCR, SS18-SSX transcripts were detected in 15/23 cases (65.2%). Immunohistochemically, a unique "weak to absent"/reduced INI1 immunostaining pattern was exclusively observed in 12/13 cases of SS (92.3%). Fragment analysis and FISH were relatively more sensitive techniques. Unique "weak to absent"INI1 immunoexpression significantly correlated with positive t (X;18) translocation results (P = 0.0001). Conclusion The present study constitutes first such study from our subcontinent. Fragment analysis is a promising technique for detection of t (X;18)(p11;q11) translocation. FISH and INI1 immunostaining pattern were also relatively more sensitive, over RT-PCR.
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Affiliation(s)
- Omshree Shetty
- Division of Molecular Pathology and Translational Medicine, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Trupti Pai
- Division of Molecular Pathology and Translational Medicine; Department of Surgical Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Mamta Gurav
- Division of Molecular Pathology and Translational Medicine, Tata Memorial Centre, Mumbai, Maharashtra, India
| | - Bharat Rekhi
- Division of Molecular Pathology and Translational Medicine; Department of Surgical Pathology, Tata Memorial Centre, Mumbai, Maharashtra, India
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13
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Di Ciaccio P, Kearney A, Ling S. Comparing the area under the curve and peak height methods in the calculation of FLT3-ITD allelic ratio. Int J Lab Hematol 2020; 42:e234-e236. [PMID: 32533751 DOI: 10.1111/ijlh.13263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/23/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Pietro Di Ciaccio
- Department of Haematology, Liverpool Hospital, Sydney, NSW, Australia
| | - Anabel Kearney
- Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
| | - Silvia Ling
- Department of Haematology, Liverpool Hospital, Sydney, NSW, Australia.,Ingham Institute for Applied Medical Research, Sydney, NSW, Australia
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14
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Halder AK, Giri AK, Cordeiro MNDS. Multi-Target Chemometric Modelling, Fragment Analysis and Virtual Screening with ERK Inhibitors as Potential Anticancer Agents. Molecules 2019; 24:molecules24213909. [PMID: 31671605 PMCID: PMC6864583 DOI: 10.3390/molecules24213909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/21/2019] [Accepted: 10/25/2019] [Indexed: 02/07/2023] Open
Abstract
Two isoforms of extracellular regulated kinase (ERK), namely ERK-1 and ERK-2, are associated with several cellular processes, the aberration of which leads to cancer. The ERK-1/2 inhibitors are thus considered as potential agents for cancer therapy. Multitarget quantitative structure–activity relationship (mt-QSAR) models based on the Box–Jenkins approach were developed with a dataset containing 6400 ERK inhibitors assayed under different experimental conditions. The first mt-QSAR linear model was built with linear discriminant analysis (LDA) and provided information regarding the structural requirements for better activity. This linear model was also utilised for a fragment analysis to estimate the contributions of ring fragments towards ERK inhibition. Then, the random forest (RF) technique was employed to produce highly predictive non-linear mt-QSAR models, which were used for screening the Asinex kinase library and identify the most potential virtual hits. The fragment analysis results justified the selection of the hits retrieved through such virtual screening. The latter were subsequently subjected to molecular docking and molecular dynamics simulations to understand their possible interactions with ERK enzymes. The present work, which utilises in-silico techniques such as multitarget chemometric modelling, fragment analysis, virtual screening, molecular docking and dynamics, may provide important guidelines to facilitate the discovery of novel ERK inhibitors.
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Affiliation(s)
- Amit Kumar Halder
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
| | - Amal Kanta Giri
- Department of Chemistry and Biochemistry, University of Porto, 4169-007 Porto, Portugal.
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15
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Kroupin P, Chernook A, Karlov G, Soloviev A, Divashuk M. Effect of Dwarfing Gene Ddw1 on Height and Agronomic Traits in Spring Triticale in Greenhouse and Field Experiments in a Non-Black Earth Region of Russia. Plants (Basel) 2019; 8:plants8050131. [PMID: 31100890 PMCID: PMC6571949 DOI: 10.3390/plants8050131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/09/2019] [Accepted: 05/14/2019] [Indexed: 01/17/2023]
Abstract
Triticale is a relatively new crop which still possesses serious drawbacks that can be significantly improved by breeding. The dwarfing genes proved to be very useful in the development of new lodging resistant and productive cultivars of winter triticale. The aim of our research was to assess the effect of the Ddw1 dwarfing gene from rye on the agronomic valuable traits in spring triticale. The Ddw1 effect was studied in the greenhouse experiment in segregating the F2:3 population and in the field of F3:4 and F4:5 families derived from crossing winter triticale ‘Hongor’ (Ddw1Ddw1) and spring triticale ‘Dublet’ (ddw1ddw1). As a result, in all three generations, a strong decrease in plant height was demonstrated that was accompanied by a decrease in grain weight per spike and 1000-grain weight. In field experiments, a decrease in spike length and increase in spike density and delay in flowering and heading were observed. As a result of decrease in culm vegetative weight due to Ddw1, the harvest index measured in F4:5 increased. The spike fertility and number of grains were not affected by Ddw1. The comparison of Ddw1 in rye, winter, and spring triticale, and the possible role of Ddw1 in improving spring triticale are discussed.
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Affiliation(s)
- Pavel Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Anastasiya Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Gennady Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
| | - Alexander Soloviev
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Department of Distant Hybridization, N.V. Tsitsin Main Botanical Garden of Russian Academy of Sciences, Botanicheskaya str., 4, Moscow 127276, Russia.
| | - Mikhail Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University ⁻ Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow 127550, Russia.
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16
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Patel TN, Chakraborty M, Bhattacharya P. Microsatellite Instability in Chronic Myeloid Leukemia using D17S261 and D3S643 markers: A Pilot Study in Gujarat Population. Indian J Cancer 2018; 54:426-429. [PMID: 29469071 DOI: 10.4103/ijc.ijc_275_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CONTEXT Tumor progresses through a series of genetic alterations that involve proto-oncogenes and tumor suppressor genes - the gatekeeper, caretakers, and landscaper genes. Microsatellites are short tandem repeat sequences, present over the span of human genome and are known to be variable at multiple loci due to errors in DNA Mismatch Repair machinery. AIM The present study was aimed to evaluate the association between Microsatellite Instability (MSI) and evolution of Chronic Myeloid Leukemia (CML) - genetically a rare event but profound in this pilot study. SETTINGS AND DESIGNS We explore the possibility of MSI in primary CML patients confirmed by t(9;22) using capillary electrophoresis. Fifteen CML patients and healthy individual samples, respectively, were used to study the markers D17S261 and D3S643. MATERIALS AND METHODS The DNA was amplified using tagged and nontagged primers and further subjected to bioanalysis and fragment analysis. RESULTS While the results from bioanalyzer fluctuated, fragment analysis indicated the presence of microsatellite variability in 80% of the patients' samples as compared to no MSI in normal individuals for both the markers. CONCLUSION These findings suggest that MSI is a genetic event that may have a role in CML progression or evolution. Further studies are warranted to understand the plausible underlying causes.
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Affiliation(s)
- T N Patel
- Departments of Integrative Biology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Chakraborty
- Departments of Biomedical Genetics, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - P Bhattacharya
- Departments of Integrative Biology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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17
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Schranz K, Hubmann M, Harin E, Vosberg S, Herold T, Metzeler KH, Rothenberg-Thurley M, Janke H, Bräundl K, Ksienzyk B, Batcha AMN, Schaaf S, Schneider S, Bohlander SK, Görlich D, Berdel WE, Wörmann BJ, Braess J, Krebs S, Hiddemann W, Mansmann U, Spiekermann K, Greif PA. Clonal heterogeneity of FLT3-ITD detected by high-throughput amplicon sequencing correlates with adverse prognosis in acute myeloid leukemia. Oncotarget 2018; 9:30128-45. [PMID: 30046393 DOI: 10.18632/oncotarget.25729] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/19/2018] [Indexed: 12/14/2022] Open
Abstract
In acute myeloid leukemia (AML), internal tandem duplications (ITDs) of FLT3 are frequent mutations associated with unfavorable prognosis. At diagnosis, the FLT3-ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3-ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. FLT3-ITD status determined by routine diagnostics was confirmed by HTAS in 242 out of 250 patients (97%). The total number of ITDs detected by HTAS was higher than in routine diagnostics (n = 312 vs. n = 274). In particular, HTAS detected a higher number of ITDs per patient compared to fragment analysis, indicating higher sensitivity for subclonal ITDs. Patients with more than one ITD according to HTAS had a significantly shorter overall and relapse free survival. There was a close correlation between FLT3-ITD mRNA levels in fragment analysis and variant allele frequency in HTAS. However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. In summary, this study demonstrates that HTAS is a feasible approach for FLT3-ITD detection in AML patients, delivering length, position, sequence and mutational burden of this alteration in a single assay with high sensitivity. Our findings provide insights into the clonal architecture of FLT3-ITD positive AML and have clinical implications.
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18
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Shoombuatong W, Prachayasittikul V, Anuwongcharoen N, Songtawee N, Monnor T, Prachayasittikul S, Prachayasittikul V, Nantasenamat C. Navigating the chemical space of dipeptidyl peptidase-4 inhibitors. Drug Des Devel Ther 2015; 9:4515-49. [PMID: 26309399 PMCID: PMC4539085 DOI: 10.2147/dddt.s86529] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study represents the first large-scale study on the chemical space of inhibitors of dipeptidyl peptidase-4 (DPP4), which is a potential therapeutic protein target for the treatment of diabetes mellitus. Herein, a large set of 2,937 compounds evaluated for their ability to inhibit DPP4 was compiled from the literature. Molecular descriptors were generated from the geometrically optimized low-energy conformers of these compounds at the semiempirical AM1 level. The origins of DPP4 inhibitory activity were elucidated from computed molecular descriptors that accounted for the unique physicochemical properties inherently present in the active and inactive sets of compounds as defined by their respective half maximal inhibitory concentration values of less than 1 μM and greater than 10 μM, respectively. Decision tree analysis revealed the importance of molecular weight, total energy of a molecule, topological polar surface area, lowest unoccupied molecular orbital, and number of hydrogen-bond donors, which correspond to molecular size, energy, surface polarity, electron acceptors, and hydrogen bond donors, respectively. The prediction model was subjected to rigorous independent testing via three external sets. Scaffold and chemical fragment analysis was also performed on these active and inactive sets of compounds to shed light on the distinguishing features of the functional moieties. Docking of representative active DPP4 inhibitors was also performed to unravel key interacting residues. The results of this study are anticipated to be useful in guiding the rational design of novel and robust DPP4 inhibitors for the treatment of diabetes.
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Affiliation(s)
- Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Veda Prachayasittikul
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand ; Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Nuttapat Anuwongcharoen
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Napat Songtawee
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Teerawat Monnor
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Supaluk Prachayasittikul
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand ; Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
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19
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MANSOR F, ZAMRI L, HAMZAH SS. Electrophoretic Techniques for the Detection of Human Microsatellite D19S884. Malays J Med Sci 2015; 22:18-24. [PMID: 26023291 PMCID: PMC4438088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 01/24/2015] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND The detection and analysis of microsatellites is very important for the mapping of genetic diseases because they are commonly used as genetic markers. Microsatellite marker D19S884 has been associated with polycystic ovary syndrome (PCOS), the most common reproductive endocrine disease of women in their childbearing years. It is responsible for an estimated 70% of cases of anovulatory infertility. In this work, we detected microsatellites in DNA extracted from the blood of PCOS patients. METHODS DNA microsatellites were amplified by polymerase chain reaction (PCR) using a pair of specific primers tagged with fluorescence to yield products of 160-200 base pairs in length. Alleles were separated on 4% low-melting agarose gels; stained with a safe gel staining, GelRed™, which is an alternative to ethidium bromide; and visualised by ultraviolet illumination. RESULTS Bands were observed, but their base-pairs differences were difficult to distinguish. To identify each allele clearly, the PCR products were also analysed using capillary gel electrophoresis for fragment analysis where it was possible to discriminate even in case of difference between two pairs of bases between the alleles. CONCLUSION In this article, we present a protocol that combines the use of gel electrophoresis and fragment analysis in the identification of genetic biomarkers for PCOS.
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Affiliation(s)
- Fazliana MANSOR
- Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Liyana ZAMRI
- Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Siti Sarah HAMZAH
- Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
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20
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Shewale JG, Qi L, Calandro LM. Principles, Practice, and Evolution of Capillary Electrophoresis as a Tool for Forensic DNA Analysis. Forensic Sci Rev 2012; 24:79-100. [PMID: 26244266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Capillary electrophoresis (CE) is a versatile and widely used analysis platform with application in diverse areas such as analytical chemistry, chiral separations, clinical, forensics, molecular biology, natural products, organic chemistry, and the pharmaceutical industry. Forensic applications of CE include fragment analysis, DNA sequencing, SNP typing, and analysis of gunshot residues, explosive residues, and drugs. Fragment analysis is a widely used method for short tandem repeat (STR) profiling for human identification (HID) due to the single-base resolution capability of CE. This approach circumvents the tedious and expensive approach of DNA sequencing for STR typing. The high sizing precision, ability to detect fluorescence emitted from multiple dyes, automated electrophoretic runs, and data collection software are key factors in the worldwide adoption of CE as the preferred platform for forensic DNA analysis. The most common CE systems used in forensic DNA analysis include the ABI PRISM® 310, 3100, 3100 Avant, 3130, 3130xl, 3500, and 3500xL Genetic Analyzers (GAs). The 3500 series GAs are developed with features useful for forensic scientists, including a normalization feature for analysis of the data designed to reduce the variation in peak height from instrument to instrument and injection to injection. Other hardware and software features include improved temperature control, radio frequency identification (RFID) tags for monitoring instrument consumables, HID-focused software features, and security and maintenance.
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Affiliation(s)
- J G Shewale
- Life Technologies Corporation, Foster City, CA, USA
| | - L Qi
- Life Technologies Corporation, Foster City, CA, USA
| | - L M Calandro
- Life Technologies Corporation, Foster City, CA, USA.
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Avula R, Rand A, Black JL, O'Kane DJ. Simultaneous genotyping of multiple polymorphisms in human serotonin transporter gene and detection of novel allelic variants. Transl Psychiatry 2011; 1:e32. [PMID: 22832606 PMCID: PMC3309506 DOI: 10.1038/tp.2011.34] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The serotonin transporter, called SLC6A4, SERT or 5-HTT, modulates neurotransmission by removal of serotonin from the synapse of serotonergic neurons, facilitating serotonin reuptake into the presynaptic terminus. Selective serotonin reuptake inhibitors block the action of the serotonin transporter and are used to treat depression and other neuropsychiatric disorders. Three polymorphisms in the 5-HTT gene have been implicated in treatment response and neuropsychiatric disorders. A 44-bp promoter ins/del polymorphism (5-HTTLPR) produces primarily long and/or short alleles due to either 14 (short) or 16 (long) repeats of variably conserved 20-23 bp units. Also implicated, a 17-18 bp variable number tandem repeat found in intron2 (StIn2) is expressed as triallelic content with 9, 10, or 12 repeats (StIn2.9, StIn2.10 or StIn2.12). Finally, a single nucleotide polymorphism rs25531 located within the promoter polymorphic-linked region alters the function of the long promoter allele. We developed a PCR-based fragment analysis assay, which is analyzed on an ABI sequencer, whereby we are able to detect all three genotypes simultaneously. Using this technique, we identified novel sequences, which demonstrate promoter repeat regions containing (1) a 17 repeat with rs25531 A/G polymorphism, (2) two with 18-repeat units, (3) one with 20-repeat units and (4) a 24-repeat sequence. The novel repeats were confirmed by direct sequencing of gel-purified amplicons.
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Affiliation(s)
- R Avula
- Department of Laboratory Medicine and Pathology, Nucleotide Polymorphism Lab, Mayo Clinic, Rochester, MN 55905, USA.
| | - A Rand
- Department of Laboratory Medicine and Pathology, Nucleotide Polymorphism Lab, Mayo Clinic, Rochester, MN, USA
| | - J L Black
- Department of Laboratory Medicine and Pathology, Nucleotide Polymorphism Lab, Mayo Clinic, Rochester, MN, USA
| | - D J O'Kane
- Department of Laboratory Medicine and Pathology, Nucleotide Polymorphism Lab, Mayo Clinic, Rochester, MN, USA
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Angelopoulou K, Diamandis EP. Identification of deletions and insertions in the p53 gene using multiplex PCR and high-resolution fragment analysis: application to breast and ovarian tumors. J Clin Lab Anal 1998; 12:250-6. [PMID: 9671178 PMCID: PMC6807817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
We have developed a simple and highly efficient method to detect deletions and insertions in the p53 gene. All 11 exons of the p53 gene were amplified along with a control sequence in four multiplex PCR reactions in the presence of fluorescein-labeled primers. The PCR products were resolved on an automated sequencing gel and the DNA fragments were detected by fluorescence. Using this method, we screened 7 DNA specimens from ovarian tumors, 19 from breast tumors, and 26 from normal breast tissues. No abnormality was found in any of the DNA samples extracted from the normal tissues. A 19 base pair deletion in exon 5 of the p53 gene was detected in one ovarian tumor. Insertions were identified in two breast and two ovarian tumors. The insertions were identical in 3 of these tumors and consisted of a 16 bp repeat within intron 3 of the p53 gene. It appears that the insertion within intron 3 may represent a hot spot for duplication of the normal sequence at that site.
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Affiliation(s)
- Katerina Angelopoulou
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University of Toronto, Ontario, Canada
| | - Eleftherios P. Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Clinical Biochemistry, University of Toronto, Ontario, Canada
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