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Ampatzidou M, Papadhimitriou SI, Paisiou A, Paterakis G, Tzanoudaki M, Papadakis V, Florentin L, Polychronopoulou S. The Prognostic Effect of CDKN2A/2B Gene Deletions in Pediatric Acute Lymphoblastic Leukemia (ALL): Independent Prognostic Significance in BFM-Based Protocols. Diagnostics (Basel) 2023; 13:diagnostics13091589. [PMID: 37174980 PMCID: PMC10178600 DOI: 10.3390/diagnostics13091589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
One of the most frequent genes affected in pediatric ALL is the CDKN2A/2B gene, acting as a secondary cooperating event and playing an important role in cell-cycle regulation and chemosensitivity. Despite its inclusion in combined CNA (copy-number alterations) classifiers, like the IKZF1plus entity and the UKALL CNA profile, the prognostic impact of the individual gene deletions outside the context of a combined CNA evaluation remains controversial. Addressing the CDKN2A/2B deletions' additive prognostic effect in current risk-stratification algorithms, we present a retrospective study of a Greek pediatric ALL cohort comprising 247 patients studied over a 24-year period (2000-2023). Herein, we provide insight regarding the correlation with disease features, MRD clearance, and independent prognostic significance for this ALL cohort treated with contemporary BFM-based treatment protocols. Within an extended follow-up time of 135 months, the presence of the CDKN2A/2B deletions (biallelic or monoallelic) was associated with inferior EFS rates (65.1% compared to 91.8% for the gene non-deleted subgroup, p < 0.001), with the relapse rate accounting for 22.2% and 5.9%, respectively (p < 0.001). The presence of the biallelic deletion was associated with the worst outcomes (EFS 57.2% vs. 89.6% in the case of any other status, monoallelic or non-deleted, p < 0.001). Survival differences were demonstrated for B-ALL cases (EFS 65.3% vs. 93.6% for the non-deleted B-ALL subgroup, p < 0.001), but the prognostic effect was not statistically significant within the T-ALL cohort (EFS 64.3 vs. 69.2, p = 0.947). The presence of the CDKN2A/2B deletions clearly correlated with inferior outcomes within all protocol-defined risk groups (standard risk (SR): EFS 66.7% vs. 100%, p < 0.001, intermediate risk (IR): EFS 77.1% vs. 97.9%, p < 0.001, high risk (HR): EFS 42.1% vs. 70.5% p < 0.001 for deleted vs non-deleted cases in each patient risk group); additionally, in this study, the presence of the deletion differentiated prognosis within both MRD-positive and -negative subgroups on days 15 and 33 of induction. In multivariate analysis, the presence of the CDKN2A/2B deletions was the most important prognostic factor for relapse and overall survival, yielding a hazard ratio of 5.2 (95% confidence interval: 2.59-10.41, p < 0.001) and 5.96 (95% confidence interval: 2.97-11.95, p < 0.001), respectively, designating the alteration's independent prognostic significance in the context of modern risk stratification. The results of our study demonstrate that the presence of the CDKN2A/2B deletions can further stratify all existing risk groups, identifying patient subgroups with different outcomes. The above biallelic deletions could be incorporated into future risk-stratification algorithms, refining MRD-based stratification. In the era of targeted therapies, future prospective controlled clinical trials will further explore the possible use of cyclin-dependent kinase inhibitors (CDKIs) in CDKN2A/2B-affected ALL pediatric subgroups.
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Affiliation(s)
- Mirella Ampatzidou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Stefanos I Papadhimitriou
- Laboratory of Hematology, Unit of Molecular Cytogenetics, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Anna Paisiou
- Bone Marrow Transplantation Unit, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Georgios Paterakis
- Laboratory of Flow Cytometry, Department of Immunology, "G. Gennimatas" General Hospital, 11527 Athens, Greece
| | - Marianna Tzanoudaki
- Department of Immunology, "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Vassilios Papadakis
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
| | - Lina Florentin
- Alfa Laboratory Diagnostic Center, YGEIA Hospital, 11524 Athens, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology (TAO), "Aghia Sophia" Children's Hospital, 11527 Athens, Greece
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Xie V, Tong D, Wallington-Beddoe CT, Bradstock KF, Bendall LJ. Sphingosine kinase 2 supports the development of BCR/ABL-independent acute lymphoblastic leukemia in mice. Biomark Res 2018; 6:6. [PMID: 29441205 PMCID: PMC5800079 DOI: 10.1186/s40364-018-0120-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023] Open
Abstract
Background Sphingosine kinase (SphK) 2 has been implicated in the development of a range of cancers and inhibitors of this enzyme are currently in clinical trial. We have previously demonstrated a role for SphK2 in the development of acute lymphoblastic leukemia (ALL). Methods In this and our previous study we use mouse models: in the previous study the disease was driven by the proto-oncogene BCR/ABL1, while in this study cancer risk was elevated by deletion of the tumor suppressor ARF. Results Mice lacking ARF and SphK2 had a significantly reduced incidence of ALL compared mice with wild type SphK2. Conclusions These results show that the role of SphK2 in ALL development is not limited to BCR/ABL1 driven disease extending the potential use of inhibitors of this enzyme to ALL patients whose disease have driver mutations other than BCR/ABL1.
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Affiliation(s)
- Vicki Xie
- 1Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Daochen Tong
- 1Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Craig T Wallington-Beddoe
- 1Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,3Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia.,4College of Medicine and Public Health, Flinders University, Adelaide, Australia.,5School of Medicine, University of Adelaide, Adelaide, Australia
| | - Ken F Bradstock
- 2Haematology Department, Westmead Hospital, Westmead, NSW Australia
| | - Linda J Bendall
- 1Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
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Vázquez-Reyes A, Bobadilla-Morales L, Barba-Barba C, Macías-Salcedo G, Serafín-Saucedo G, Velázquez-Rivera ME, Almodóvar-Cuevas MC, Márquez-Mora A, Pimentel-Gutiérrez HJ, Ortega-de-la-Torre C, Cruz-Osorio RM, Nava-Gervasio S, Rivera-Vargas J, Sánchez-Zubieta F, Corona-Rivera JR, Corona-Rivera A. Aneuploidy identification in pre-B acute lymphoblastic leukemia patients at diagnosis by Multiplex Ligation-dependent Probe Amplification (MLPA). Leuk Res 2017. [PMID: 28624713 DOI: 10.1016/j.leukres.2017.05.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Three-quarters of the patients with acute lymphoblastic leukemia (ALL), show numerical or structural chromosomal alterations, which are important factors in leukemogenesis. The use of Multiplex Ligation-dependent Probes Amplification (MLPA) has been mainly limited for searching copy number alterations of genes, suggesting that MLPA could detect numerical alterations in cancer. However, the use of MLPA in pediatrics to analyze subtelomeric sequences for aneuploidy detection has not been considered in previous studies. The aim of this study was to identify aneuploidy for the first time using MLPA and correlate the results with karyotype and DNA-index (DI), from preB ALL patients. Forty-two bone marrow samples were analyzed by cytogenetics and flow cytometry to determine the DI. The chromosomal gains and/or losses were detected by the SALSA MLPA P036 Subtelomere Mix 1 probemix®. The chromosomal number matched in 36 out of 42 samples between MLPA and karyotype (R2=0.7829, p=3.7×10-10), 18/42 between MLPA and DI (R2=0.1556, p=0.023), and 20/42 between karyotype and DI (R2=0.1509, p=0.015). MLPA results correlated with karyotype and DI. The use of MLPA led us to identify a gained marker chromosome. Our results indicate that MLPA could be a useful and fast alternative tool for aneuploidy identification in pediatric leukemia.
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Affiliation(s)
- A Vázquez-Reyes
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Doctorado en Ciencias en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - L Bobadilla-Morales
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - C Barba-Barba
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - G Macías-Salcedo
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - G Serafín-Saucedo
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - M E Velázquez-Rivera
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - M C Almodóvar-Cuevas
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - A Márquez-Mora
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - H J Pimentel-Gutiérrez
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - C Ortega-de-la-Torre
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - R M Cruz-Osorio
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - S Nava-Gervasio
- Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - J Rivera-Vargas
- Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - F Sánchez-Zubieta
- Servicio de Hematología y Oncología Pediátrica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - J R Corona-Rivera
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | - A Corona-Rivera
- Laboratorio de Citogenética, Genotoxicidad y Biomonitoreo, Instituto de Genética Humana "Dr. Enrique Corona", Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico; Unidad de Citogenética, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico; Servicio de Genética Médica, División de Pediatría, Nuevo Hospital Civil "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico.
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Braun M, Pastorczak A, Fendler W, Madzio J, Tomasik B, Taha J, Bielska M, Sedek L, Szczepanski T, Matysiak M, Derwich K, Lejman M, Kowalczyk J, Kazanowska B, Badowska W, Styczynski J, Irga-Jaworska N, Trelinska J, Zalewska-Szewczyk B, Pierlejewski F, Wlodarska I, Młynarski W. Biallelic loss of CDKN2A is associated with poor response to treatment in pediatric acute lymphoblastic leukemia. Leuk Lymphoma 2016; 58:1162-1171. [PMID: 27756164 DOI: 10.1080/10428194.2016.1228925] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The inactivation of tumor suppressor genes located within 9p21 locus (CDKN2A, CDKN2B) occurs in up to 30% of children with B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but its independent prognostic significance remains controversial. In order to investigate the prognostic impact of deletions and promoter methylation within 9p21, 641 children with newly diagnosed BCP-ALL using methylation specific multiplex ligation-dependent probe amplification (MS-MLPA) were investigated. A total of 169 (26.4%) microdeletions in 9p21 were detected, of which 71 were homozygous. Patients with CDKN2A homozygous deletions were older at diagnosis (p < .001), more frequently steroid resistant (p = .049), had higher WBC count (p < .001), higher MRD at Day 15 (p = .013) and lower relapse-free survival [p = .028, hazard ratio: 2.28 (95% confidence interval: 1.09-4.76)] than patients without these alterations. CDKN2A homozygous deletions coexisted with IKZF1 and PAX5 deletions (p < .001). In conclusion, CDKN2A homozygous deletions, but not promoter methylation, are associated with poor response to treatment and increased relapse risk of pediatric BCP-ALL.
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Affiliation(s)
- Marcin Braun
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland.,b Department of Pathology , Medical University of Lodz , Lodz , Poland.,c Postgraduate School of Molecular Medicine , Medical University of Warsaw , Warsaw , Poland
| | - Agata Pastorczak
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Wojciech Fendler
- d Department of Biostatistics and Translational Medicine , Medical University of Lodz , Lodz , Poland
| | - Joanna Madzio
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland.,c Postgraduate School of Molecular Medicine , Medical University of Warsaw , Warsaw , Poland
| | - Bartlomiej Tomasik
- d Department of Biostatistics and Translational Medicine , Medical University of Lodz , Lodz , Poland
| | - Joanna Taha
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Marta Bielska
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Lukasz Sedek
- e Department of Pediatric Hematology and Oncology , Medical University of Silesia , Zabrze , Poland
| | - Tomasz Szczepanski
- e Department of Pediatric Hematology and Oncology , Medical University of Silesia , Zabrze , Poland
| | - Michal Matysiak
- f Department of Pediatric Hematology and Oncology , Medical University of Warsaw , Warsaw , Poland
| | - Katarzyna Derwich
- g Department of Pediatric Hematology , Oncology and Transplantology, University of Medical Sciences , Poznan , Poland
| | - Monika Lejman
- h Department of Pediatric Hematology and Oncology , Medical University of Lublin , Lublin , Poland
| | - Jerzy Kowalczyk
- h Department of Pediatric Hematology and Oncology , Medical University of Lublin , Lublin , Poland
| | - Bernarda Kazanowska
- i Department of Pediatric Hematology , Oncology and Transplantology, Medical University of Wroclaw , Wroclaw , Poland
| | - Wanda Badowska
- j Department of Pediatric Hematology and Oncology , Olsztyn , Poland
| | - Jan Styczynski
- k Department of Pediatric Hematology and Oncology, Collegium Medicum , Nicolaus Copernicus University , Bydgoszcz , Poland
| | - Nina Irga-Jaworska
- l Department of Pediatric Hematology , Gdansk Medical University , Gdansk , Poland
| | - Joanna Trelinska
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Beata Zalewska-Szewczyk
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | - Filip Pierlejewski
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
| | | | - Wojciech Młynarski
- a Department of Pediatrics, Oncology, Hematology and Diabetology , Medical University of Lodz , Lodz , Poland
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Mai H, Liu X, Chen Y, Li C, Cao L, Chen X, Chen S, Liu G, Wen F. Hypermethylation of p15 gene associated with an inferior poor long-term outcome in childhood acute lymphoblastic leukemia. J Cancer Res Clin Oncol 2016; 142:497-504. [PMID: 26501552 DOI: 10.1007/s00432-015-2063-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022]
Abstract
PURPOSE To quantitate methylation of the CpG island of the promoter region of the p15 gene in childhood acute lymphoblastic leukemia (ALL) and explore its effect on prognosis. METHODS We assessed methylation of the CpG island on the p15 gene in bone marrow mononuclear cells in 93 ALL cases and in a control group of 20 children with idiopathic thrombocytopenia (ITP) by restriction enzyme Eco52I digestion combined with polymerase chain reaction techniques. We explored the effect of varying levels of methylation on event-free survival (EFS). RESULTS The mean methylation level was 25 % in de novo ALL and significantly higher than the control group 2 %, P < 0.01). Forty-two percent of cases (39/93) had hypermethylation (level over 10 %). Fifty-seven percent (12/21) and 38 % (27/72) T- and precursor-B ALL patients had hypermethylation (not significant). For all patients, the 8-year EFS was (83 ± 4) %, standard risk (91 ± 4) %, intermediate risk (IR) (82 ± 5) %, and high risk (HR) (43 ± 19) % (χ(2) = 11.58, P < 0.01). Hypermethylation was associated with a lower 8-year EFS (71 ± 7 vs. 91 ± 4 %, P = 0.02) in univariate analyses. CONCLUSIONS Children with ALL have higher levels of p15 CpG island methylation than a control group of children with ITP. Among children with ALL, hypermethylation was associated with inferior EFS. Higher levels of p15 CpG island methylation may be a poor prognostic marker in childhood ALL.
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Konialis C, Savola S, Karapanou S, Markaki A, Karabela M, Polychronopoulou S, Ampatzidou M, Voulgarelis M, Viniou NA, Variami E, Koumarianou A, Zoi K, Hagnefelt B, Schouten JP, Pangalos C. Routine application of a novel MLPA-based first-line screening test uncovers clinically relevant copy number aberrations in haematological malignancies undetectable by conventional cytogenetics. Hematology 2013; 19:217-24. [DOI: 10.1179/1607845413y.0000000112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | | | | | | | | | - Sophia Polychronopoulou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Maria Ampatzidou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Michael Voulgarelis
- Pathophysiology DepartmentSchool of Medicine, University of Athens, Athens, Greece
| | - Nora-Athina Viniou
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | - Eleni Variami
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | | | - Katerina Zoi
- Haematology Research LaboratoryBiomedical Research Foundation, Academy of Athens, Athens, Greece
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7
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Lukackova R, Gerykova Bujalkova M, Majerova L, Mladosievicova B. Molecular genetic methods in the diagnosis of myelodysplastic syndromes. A review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2013; 158:339-45. [PMID: 24263214 DOI: 10.5507/bp.2013.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/06/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Myelodysplastic syndromes (MDS) represent a heterogeneous group of premalignant hematologic disorders characterized by ineffective hematopoiesis, peripheral blood cytopenias and increased risk of progression to acute leukemia. Cytogenetic analysis still plays a central role in the diagnosis of MDS, as clonal chromosomal abnormalities are observed in 30-50% of MDS patients. Despite their technical limitations, standard karyotyping and fluorescence in situ hybridization (FISH) are routinely used for identifying recurrent chromosomal rearrangements. However, using this approach means that submicroscopic and not targeted chromosomal aberrations, as well as somatic mutations and epigenetic changes remain largely undetected. METHODS AND RESULTS Introduction of methods for the analysis of copy-number variations (CNV), including array-based technologies and Multiplex ligation-dependent probe amplification (MLPA) has provided novel insights into the molecular pathogenesis of MDS and considerably extended possibilities for genetic laboratory testing. Several novel molecular markers have been discovered and used for diagnosis and prognostic evaluation of patients with MDS. At present, mutational analysis is not routinely performed, as the clinical significance of somatic mutations in MDS has only begun to emerge. However, recently introduced Next-generation sequencing (NGS) technologies could help to elucidate the relationship between chromosomal and molecular aberrations in MDS and lead to further improvement in its diagnosis. CONCLUSION This review focuses on the advantages, limitations, clinical applications and future perspectives of three molecular methods (array-based analysis, MLPA and NGS) currently used in genetic testing and/ or translational research of MDS. In conclusion, a brief summary for clinicians from the routine diagnostic point of view is given.
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Affiliation(s)
- Renata Lukackova
- Department of Clinical Genetics, Medirex a.s., Bratislava, Slovak Republic
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8
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Alpar D, de Jong D, Holczer-Nagy Z, Kajtar B, Savola S, Jakso P, David M, Kosztolanyi S, Kereskai L, Pajor L, Szuhai K. Multiplex ligation-dependent probe amplification and fluorescence in situ hybridization are complementary techniques to detect cytogenetic abnormalities in multiple myeloma. Genes Chromosomes Cancer 2013; 52:785-93. [PMID: 23720363 DOI: 10.1002/gcc.22074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 04/22/2013] [Indexed: 11/06/2022] Open
Abstract
Multiple myeloma (MM) is a genetically heterogeneous disease with diverse clinical outcomes. Interphase fluorescence in situ hybridization (i-FISH) is the most commonly used approach to detect recurrent cytogenetic abnormalities in this malignancy. We aimed to assess the performance of multiplex ligation-dependent probe amplification (MLPA) to reveal copy number abnormalities (CNAs) in MM. Diagnostic bone marrow samples from 81 patients were analyzed using 42 MLPA probes for the following regions: 1p32-31, 1p21, 1q21.3, 1q23.3, 5q31.3, 12p13.31, 13q14, 16q12, 16q23, and 17p13. All samples were also screened by i-FISH for the presence of hyperdiploidy, deletion/monosomy of chromosome 13, deletion of TP53, disruption of the immunoglobulin heavy-chain gene, t(4;14), t(11;14), t(14;16), t(8;14), gain of 5q and abnormalities of chromosome 1. A total of 245 alterations were detected in 79 cases (98%). Investigating the same aberrations, the two methods showed a congruency of higher than 90%. A low proportion of cells with the relevant abnormality, focal CNAs and unmatched probes were responsible for the discrepancies. MLPA revealed 95 CNAs not detected by i-FISH providing additional information in 53 cases (65%). Scrutiny of CNAs on chromosome 1, using more than 20 probes, revealed significant heterogeneity in size and location, and variable intra-chromosomal and intra-clonal rates of loss or gain. Our results suggest that MLPA is a reliable high-throughput technique to detect CNAs in MM. Since balanced aberrations are key to prognostic classification of this disease, MLPA and i-FISH should be applied as complementary techniques in diagnostic pathology.
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Affiliation(s)
- Donat Alpar
- Department of Pathology, Medical School, University of Pecs, Pecs, Hungary
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9
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Multiplex ligation-dependent probe amplification (MLPA) in tumor diagnostics and prognostics. ACTA ACUST UNITED AC 2013; 21:189-206. [PMID: 23111197 DOI: 10.1097/pdm.0b013e3182595516] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The increasing knowledge about genetic alterations and molecular biomarkers in cancer initiation and progression opens new possibilities for the treatment of various types of cancer. This requires the inclusion of sensitive, and preferably multiplex, methods for the detection of molecular genetic alterations in the toolbox of classic pathology. Multiplex ligation-dependent probe amplification (MLPA) is a multiplex polymerase chain reaction-based method that can detect changes in the gene copy number status, DNA methylation, and point mutations simultaneously. MLPA probes recognize target sequences of only 50 to 100 nucleotides in length. This makes it possible to use MLPA even on highly fragmented DNA, and allows the detection of small deletions encompassing only a single exon. MLPA is a reliable, cost-effective, and robust method that can be performed using a standard thermocycler and capillary electrophoresis equipment, generating results within 24 hours with a short hands-on working time. Up to 50 different genomic locations can be tested in a single reaction, which can be sufficient to detect those genetic alterations that are of diagnostic and prognostic significance in a certain tumor entity. In the last years, MLPA has been used successfully in tumor diagnostics and in cancer research. This review gives an overview on the collected experience of MLPA applications on tumor DNA, about the advantages but also potential pitfalls and limitations of this technique.
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