1
|
Behrens YL, Pietzsch S, Antić Ž, Zhang Y, Bergmann AK. The landscape of cytogenetic and molecular genetic methods in diagnostics for hematologic neoplasia. Best Pract Res Clin Haematol 2024; 37:101539. [PMID: 38490767 DOI: 10.1016/j.beha.2024.101539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 03/17/2024]
Abstract
Improvements made during the last decades in the management of patients with hematologic neoplasia have resulted in increase of overall survival. These advancements have become possible through progress in our understanding of genetic basis of different hematologic malignancies and their role in the current risk-adapted treatment protocols. In this review, we provide an overview of current cytogenetic and molecular genetic methods, commonly used in the genetic characterization of hematologic malignancies, describe the current developments in the cytogenetic and molecular diagnostics, and give an outlook into their future development. Furthermore, we give a brief overview of the most important public databases and guidelines for sequence variant interpretation.
Collapse
Affiliation(s)
- Yvonne Lisa Behrens
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Stefan Pietzsch
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany
| | - Yanming Zhang
- Cytogenetics Laboratory, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anke K Bergmann
- Department of Human Genetics, Hannover Medical School, 30625, Hannover, Germany.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Skhoun H, Khattab M, Belkhayat A, Takki Chebihi Z, Dakka N, El Baghdadi J. A prognostic approach on a case of pediatric Philadelphia chromosome-positive acute lymphoblastic leukemia with monosomy-7. Clin Case Rep 2021; 9:e05207. [PMID: 34963805 PMCID: PMC8710846 DOI: 10.1002/ccr3.5207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/04/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022] Open
Abstract
In this work, we present the first case of a Ph-positive ALL Moroccan girl with t(9;22)(q34;q11) and monosomy-7. She was diagnosed with Ph-positive ALL based on bone marrow examination, immunophenotyping, and cytogenetic analysis. She relapsed after treatment with the persistence of the Ph chromosome and the appearance of a monosomy-7.
Collapse
Affiliation(s)
- Hanaa Skhoun
- Genetics UnitMilitary Hospital Mohammed VRabatMorocco
- Laboratory of Human Pathologies BiologyGenomic Center of Human PathologiesFaculty of SciencesMohammed V University in RabatRabatMorocco
| | - Mohammed Khattab
- Department of Pediatric Hemato‐OncologyChildren's Hospital of RabatRabatMorocco
| | | | | | - Nadia Dakka
- Laboratory of Human Pathologies BiologyGenomic Center of Human PathologiesFaculty of SciencesMohammed V University in RabatRabatMorocco
| | | |
Collapse
|
4
|
Zito Marino F, Brunelli M, Rossi G, Calabrese G, Caliò A, Nardiello P, Martignoni G, Squire JA, Cheng L, Massi D, Franco R. Multitarget fluorescence in situ hybridization diagnostic applications in solid and hematological tumors. Expert Rev Mol Diagn 2021; 21:161-173. [PMID: 33593207 DOI: 10.1080/14737159.2021.1887733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Multitarget FISH (mFISH) is a technique allowing for simultaneous detection of multiple targets sequences on the same slide through the choice of spectrally distinct fluorophore labels. The mFISH could represent a useful tool in the field of precision oncology.Areas covered: This review discusses the potential applications of mFISH technology in the molecular diagnosis of different solid and hematological tumors, including non-small cell lung cancers, melanomas, renal cell carcinomas, bladder carcinomas, germ cell tumors, and multiple myeloma, as commonly required in the clinical practice.Expert Opinion: In this emerging era of the tailored therapies and newer histo-molecular classifications, there are increasing numbers of predictive and diagnostic biomarkers required for effective clinical care. The mFISH approach may have several applications in the common clinical practice, improving the molecular diagnosis in terms of time, cost and preservation of biomaterial for tumors with a limited amount of tumor available. The mFISH provides several advantages compared to other high-throughput technologies; however, it requires high level of expertise required to interpret complex results.
Collapse
Affiliation(s)
- Federica Zito Marino
- Department of Mental and Physic Health and Preventive Medicine, Pathology Unit, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Matteo Brunelli
- Department of Pathology, University of Verona, Verona, Italy
| | - Giulio Rossi
- Pathology Unit, Ospedale Santa Maria Delle Croci, Ravenna, Italy
| | | | - Anna Caliò
- Department of Pathology, University of Verona, Verona, Italy
| | - Pamela Nardiello
- Section of Pathology, Department of Health Sciences, University of Florence Florence, Italy
| | - Guido Martignoni
- Pathology Unit, Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona, Italy
| | - Jeremy A Squire
- Departments of Genetics, University of Sao Paulo, Ribeirão Preto, Brazil
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Daniela Massi
- Section of Pathology, Department of Health Sciences, University of Florence Florence, Italy
| | - Renato Franco
- Department of Mental and Physic Health and Preventive Medicine, Pathology Unit, University of Campania Luigi Vanvitelli, Napoli, Italy
| |
Collapse
|
5
|
Bhandari P, Ahmad F, Das BR. Molecular profiling of gene copy number abnormalities in key regulatory genes in high-risk B-lineage acute lymphoblastic leukemia: frequency and their association with clinicopathological findings in Indian patients. Med Oncol 2017; 34:92. [PMID: 28401483 DOI: 10.1007/s12032-017-0940-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/31/2017] [Indexed: 02/06/2023]
Abstract
Genes related to key cellular pathways are frequently altered in B cell ALL and are associated with poor survival especially in high-risk (HR) subgroups. We examined gene copy number abnormalities (CNA) in 101 Indian HR B cell ALL patients and their correlation with clinicopathological features by multiplex ligation-dependent probe amplification. Overall, CNA were detected in 59 (59%) cases, with 26, 10 and 23% of cases harboring 1, 2 or +3 CNA. CNA were more prevalent in BCR-ABL1 (60%), pediatric (64%) and high WCC (WBC count) (63%) patients. Frequent genes deletions included CDNK2A/B (26%), IKZF1 (25%), PAX5 (14%), JAK2 (7%), BTG1 (6%), RB1 (5%), EBF1 (4%), ETV6 (4%), while PAR1 region genes were predominantly duplicated (20%). EBF1 deletions selectively associated with adults, IKZF1 deletions occurred frequently in high WCC and BCR-ABL1 cases, while PAR1 region gains significantly associated with MLL-AF4 cases. IKZF1 haploinsufficiency group was predominant, especially in adults (65%), high WCC (60%) patients and BCR-ABL1-negative (78%) patients. Most cases harbored multiple concurrent CNA, with IKZF1 concomitantly occurring with CDNK2A/B, PAX5 and BTG1, while JAK2 occurred with CDNK2A/B and PAX5. Mutually exclusive CNA included ETV6 and IKZF1/RB1, and EBF1 and JAK2. Our results corroborate with global reports, aggregating molecular markers in Indian HR B-ALL cases. Integration of CNA data from rapid methods like MLPA, onto background of existing gold-standard methods detecting significant chromosomal abnormalities, provides a comprehensive genetic profile in B-ALL.
Collapse
Affiliation(s)
- Prerana Bhandari
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India
| | - Firoz Ahmad
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India
| | - Bibhu Ranjan Das
- Research and Development Division, Molecular Pathology, Clinical Research Services, SRL Limited, Plot No.1, Prime Square Building, S.V. Road, Goregaon (W), Mumbai, 400062, India.
| |
Collapse
|
6
|
Sand M, Bechara FG, Gambichler T, Sand D, Bromba M, Hahn SA, Stockfleth E, Hessam S. Circular RNA expression in cutaneous squamous cell carcinoma. J Dermatol Sci 2016; 83:210-8. [PMID: 27298156 DOI: 10.1016/j.jdermsci.2016.05.012] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/12/2016] [Accepted: 05/23/2016] [Indexed: 12/24/2022]
Abstract
BACKGROUND CircularRNAs (circRNAs) are a reinvented class of abundant, stable, and evolutionary conserved non-coding RNAs with pivotal impacts on the cellular regulatory network and epigenetics by sequestering microRNAs (miRNAs) like a sponge. OBJECTIVE Purpose of the present study was to investigate circRNA expression in cutaneous squamous cell carcinoma (cSCC). METHODS A total of six cSCC and six non-lesional skin (control) biopsies were harvested. Microarray based circRNA expression was determined in the cSCC (n=3) and compared with the non-lesional skin (n=3) from a group of 13,617 distinct human circRNAs found in the Arraystar circRNA Array V2.0 (Arraystar, Rockville, USA). Microarray data were validated by quantitative real-time reverse transcription polymerase chain reaction in a separate group (cSCC, n=3 and non-lesional skin, n=3). miRNA binding to miRNA response elements (MREs) sequence data were acquired bioinformatically. Further data mining was performed to identify circRNAs containing MRE sequences that interacted with previously described miRNAs playing a role in cSCC formation. RESULTS A total of 322 circRNAs (143 up- and 179 down-regulated; fold change ≥2 and p<0.05) were identified as differentially expressed in cSCC. Furthermore, we identified a total of 1603 MREs that were part of the differentially expressed circRNAs. Among those circRNAs, a complementary MRE sequence was identified in 23 miRNAs previously known to be cSCC relevant. CONCLUSION This study showed that circRNAs are differentially expressed in cSCC and play an important role in tumor formation by interfering with cSCC relevant miRNAs through miRNA sequence complementary MREs participating in epigenetic control.
Collapse
Affiliation(s)
- Michael Sand
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum 44791 Bochum, Germany; Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany.
| | - Falk G Bechara
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum 44791 Bochum, Germany
| | - Thilo Gambichler
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum 44791 Bochum, Germany
| | - Daniel Sand
- University of Michigan Kellogg Eye Center, Ann Arbor, MI 48105, USA
| | - Michael Bromba
- Department of Plastic Surgery, St. Josef Hospital, Catholic Clinics of the Ruhr Peninsula, 45257 Essen, Germany
| | - Stephan A Hahn
- Department of Internal Medicine, Knappschaftskrankenhaus University of Bochum, Zentrum für Klinische Forschung, Labor für Molekulare Gastroenterologische Onkologie, 44780 Bochum, Germany, Germany
| | - Eggert Stockfleth
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum 44791 Bochum, Germany
| | - Schapoor Hessam
- Dermatologic Surgery Unit, Department of Dermatology, Venereology and Allergology, Ruhr-University Bochum 44791 Bochum, Germany
| |
Collapse
|
7
|
Fuka G, Farias-Vieira TM, Hummel L, Blunck CB, Santoro JC, Terra-Granado E, Barbosa TC, Emerenciano M, Pombo-de-Oliveira MS. Evaluation of multiplex ligation dependent probe amplification (MLPA) for identification of acute lymphoblastic leukemia with an intrachromosomal amplification of chromosome 21 (iAMP21) in a Brazilian population. Mol Cytogenet 2015; 8:35. [PMID: 26060508 PMCID: PMC4460763 DOI: 10.1186/s13039-015-0147-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/20/2015] [Indexed: 12/02/2022] Open
Abstract
Background An intrachromosomal amplification of chromosome 21 (iAMP21) defines a unique subgroup of B-cell precursor acute lymphoblastic leukemia (BCP-ALL). The finding of three or more extra copies of the RUNX1 gene by fluorescence in situ hybridization (FISH) is internationally used to define an iAMP21. Genomic profiling of chromosome 21 has been suggested for assisting diagnostic case identification. Due to limitations of comparative genomic hybridization, in terms of a routine application as first line-screening tests we evaluated the multiplex ligation-dependent probe amplification (MLPA) SALSA P327_A1 and P327_B1 probe sets for detecting chromosome 21 copy number alterations in Brazilian childhood BCP-ALL. Results In 74 out of 368 patients gain of genetic material was detected. For data confirmation RUNX1 directed FISH was performed. Cells with ≥5 RUNX1 signals (n = 9) were considered as “true iAMP21” while <5 RUNX1 signals (n = 41) were counted as evidence for additional copies of intact chromosomes 21. All patients with an iAMP21 had high MLPA peak ratios (≥1.8), while the majority of patients with <5 RUNX1 presented low MLPA peak ratios (<1.8). Observed differences gained statistical strength by comparing probes located within the common region of amplification. Next, a principal component analysis was performed in order to illustrate distribution of cases according to their MLPA peak profile in two dimensions. Cases with an iAMP21 mostly clustered together, however additional cases with <5 RUNX1 signals or no available FISH data located in proximity. Conclusions MLPA qualified as a high throughput technique that could be employed in future studies for a critical comparison with data obtained by FISH, especially in cases where metaphase nuclei are not available. Taking submicroscopic aberrations into account examined by MLPA, cases exhibiting an “iAMP21 like” peak ratio profile but <5 RUNX1 signals should be considered as candidates for this chromosomal abnormality. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0147-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gerhard Fuka
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Tállita M Farias-Vieira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Leticia Hummel
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Caroline B Blunck
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Júlio C Santoro
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Eugênia Terra-Granado
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Thayana Conceição Barbosa
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Mariana Emerenciano
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| | - Maria S Pombo-de-Oliveira
- Pediatric Hematology-Oncology Program, Research Center, Instituto Nacional de Câncer (INCA), Rua André Cavalcanti, 37, Rio de Janeiro, RJ 20231-050 Brazil
| |
Collapse
|
8
|
Sengstake S, Bablishvili N, Schuitema A, Bzekalava N, Abadia E, de Beer J, Tadumadze N, Akhalaia M, Tuin K, Tukvadze N, Aspindzelashvili R, Bachiyska E, Panaiotov S, Sola C, van Soolingen D, Klatser P, Anthony R, Bergval I. Optimizing multiplex SNP-based data analysis for genotyping of Mycobacterium tuberculosis isolates. BMC Genomics 2014; 15:572. [PMID: 25001491 PMCID: PMC4117977 DOI: 10.1186/1471-2164-15-572] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background Multiplex ligation-dependent probe amplification (MLPA) is a powerful tool to identify genomic polymorphisms. We have previously developed a single nucleotide polymorphism (SNP) and large sequence polymorphisms (LSP)-based MLPA assay using a read out on a liquid bead array to screen for 47 genetic markers in the Mycobacterium tuberculosis genome. In our assay we obtain information regarding the Mycobacterium tuberculosis lineage and drug resistance simultaneously. Previously we called the presence or absence of a genotypic marker based on a threshold signal level. Here we present a more elaborate data analysis method to standardize and streamline the interpretation of data generated by MLPA. The new data analysis method also identifies intermediate signals in addition to classification of signals as positive and negative. Intermediate calls can be informative with respect to identifying the simultaneous presence of sensitive and resistant alleles or infection with multiple different Mycobacterium tuberculosis strains. Results To validate our analysis method 100 DNA isolates of Mycobacterium tuberculosis extracted from cultured patient material collected at the National TB Reference Laboratory of the National Center for Tuberculosis and Lung Diseases in Tbilisi, Republic of Georgia were tested by MLPA. The data generated were interpreted blindly and then compared to results obtained by reference methods. MLPA profiles containing intermediate calls are flagged for expert review whereas the majority of profiles, not containing intermediate calls, were called automatically. No intermediate signals were identified in 74/100 isolates and in the remaining 26 isolates at least one genetic marker produced an intermediate signal. Conclusion Based on excellent agreement with the reference methods we conclude that the new data analysis method performed well. The streamlined data processing and standardized data interpretation allows the comparison of the Mycobacterium tuberculosis MLPA results between different experiments. All together this will facilitate the implementation of the MLPA assay in different settings. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-572) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sarah Sengstake
- KIT Biomedical Research, Royal Tropical Institute, Meibergdreef 39, 1105 AZ Amsterdam, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|