Molecular Genetic Detection Research Articles

Comparison of molecular genetic methods of detection of mutations in the CALR gene in myeloproliferative disorders

Molecular genetic detection of CALR gene somatic mutations is required for myeloproliferative neoplasms diagnosis and treatment according to the novel WHO clinical recommendations. CALR mutations are found in approximately 25–35 % cases of essential thrombocythemia and primary myelofibrosis and they are associated with benign clinical outcome. In this study we have compared sensitivity and selectivity of seve ral different options of CALR mutation molecular genetic detection in blood samples of 379 CMD patients and 17 healthy donors. Among methods compared in our study there have been conventional polymerase chain reaction with electrophoretic detection, real-time quantitative polymerase chain reaction, direct Sanger sequencing of polymerase chain reaction fragments and polymerase chain reaction high resolution melting curve analysis. By means of melting curve analysis CALR mutations have been found in 97 (25.5 %) patients, whereas in the cases of Sanger sequencing and polymerase chain reaction there have been 87 (23.0 %) and 84 (22.1 %) CALR mutation positive patients respectively.

Scientists Find Link Between Cancer and Highly Processed Foods.

This news section offers Cancer readers timely information on events, public policy analysis, topical issues, and personalities. In this issue, we profile David Sidransky, MD, and his pioneering research on molecular genetic detection of cancer. We also report on rates of untreated depression in caregiving spouses of patients with cancer and new research on the link between cancer and highly processed foods.

First Person: David Sidransky, MD

This news section offers Cancer readers timely information on events, public policy analysis, topical issues, and personalities. In this issue, we profile David Sidransky, MD, and his pioneering research on molecular genetic detection of cancer. We also report on rates of untreated depression in caregiving spouses of patients with cancer and new research on the link between cancer and highly processed foods.

Untreated depression common in caregiving spouses of patients with cancer

This news section offers Cancer readers timely information on events, public policy analysis, topical issues, and personalities. In this issue, we profile David Sidransky, MD, and his pioneering research on molecular genetic detection of cancer. We also report on rates of untreated depression in caregiving spouses of patients with cancer and new research on the link between cancer and highly processed foods.

Toxin production ability of Bacillus cereus strains from food product of Ukraine

Potential pathogens of foodborne toxic infections – bacterial contaminants Bacillus cereus isolated from plant raw materials and food products from the Ukrainian region were investigated. When determining of the proportion of isolated bacilli from the plant samples, it was established that the epidemiologically significant microorganisms of Bacillus cereus as agents of food poisoning are the second largest. The average value of contaminated samples of Ukrainian plant raw materials and processed products with Bacillus cereus is 36,2 %. The ability of Bacillus cereus strains identified by a complex of morphological, tinctorial, cultural and biochemical properties, to produce specific emetic and enterotoxins was studied. Molecular genetic diagnosis and detection of the toxin-producing ability of isolated 42 Bacillus cereus strains showed both the possibility of their rapid identification and the presence of specific toxicity genes. Multiplex polymerase chain reaction (PCR) was carried out with specific primers to detect toxicity determined of various bacilli genes: nheA, hblD, cytK, cesВ. The distribution of toxigenic genes is significantly different among the Bacillus cereus isolates from various sources. The nheA, hblD and cytK enterotoxin genes were detected in 100, 83,3 and 61,9 % of the investigated strains of Bacillus cereus, respectively. The cesB gene encoding emetic toxin was detected in 4,8 % of strains. Molecular-genetic PCR-method confirmed that all the isolated strains belong to the Bacillus cereus group, and the ability to produce toxins can be attributed to five groups. The main toxins that produce the investigated Bacillus cereus strains were nhe and hbl enterotoxins encoded by the corresponding genes of nheA and hblD. The enterotoxic type of Bacillus cereus was predominant in Ukrainian region. Studies of domestic plant food raw materials and products have confirmed the need to improve microbiological control of product safety by introducing accelerated specific diagnostics of contaminants by molecular genetics methods.

PCR diagnostika infekcí

The practices based on microbe cultivation are the corner stone of laboratory diagnostics of infectious diseases etiology. However, cultivation-independent molecular methods for microorganism detection are increasingly being used in a routine clinical setting as an important complement to the conventional procedures and, in some cases, they have already become the golden diagnostic standard. The PCR-based methods are used the most frequently.Key words: molecular genetic detection of microorganisms - polymerase chain reaction (PCR).

Strong Evidence for Molecular Genetic Risk Assessment in Patients with Aneurysms of the Ascending Aorta

Objectives: The genetic origin of thoracic aortic aneurysm (TAA) is well known since 20% of all TAA-patients show a positive family history with co-segregation of causative mutations with disease. Currently, molecular screening of established disease genes discovers the causative mutation only in 20% of familial TAA-patients. Therefore testing is initiated only in a small proportion of patients. A large proportion of TAA-patients will die due to complications of aortic aneurysms. For these patients premature aortic repair is a powerful strategy to prevent acute dissection. To date, the diameter of the dilated aorta is used to decide on surgical intervention. In a German TAA-family we want to demonstrate the usefulness of molecular genetic analysis and mutation detection as an additional and more powerful tool in the assessment of the need for preventive aortic repair.

A PULMONARY INFECTION CAUSED BY MYCOBACTERIUM PEREGRINUM– A CASE REPORT

Mycobacterium peregrinum is a member of the group of rapidly growing Nontuberculous Mycobacteria (NTM). It can be found in high frequency in natural and laboratory environments and is considered to be uncommonrare pathogen for both immunocompetent and immunosuppressed individuals. Currently, pulmonary infections caused by Mycobacterium peregrinum are unusual and diagnosed only in limited number of cases. Here, we present a clinical case of elderly man (72 years) with 1 month history of non-specific respiratory symptomatic. The patient was without underlying immunosuppressive condition or lung disease. Chest X-ray demonstrated persistent pleural effusion, opacities and cavitations in the right lobe. One of the sputum culturesgrewa rapidly growing mycobacterium and the isolated strain was found to be Mycobacterium peregrinumas identified by molecular genetic detection (PCR and DNA strip technology). To our knowledge, this is the third case in the world to report Mycobacterium peregrinumas a possible causative agent of pulmonary infection.

High prevalence of spotted fever group rickettsiae in Amblyomma variegatum from Uganda and their identification using sizes of intergenic spacers

The spotted fever group (SFG) rickettsiae are obligate intracellular bacteria transmitted by ticks that cause several tick-borne rickettsioses in humans worldwide. This study was intended to determine the prevalence of SFG rickettsiae in Amblyomma variegatum from 7 districts across Uganda. In addition to sequencing of gltA and ompA genes, identification of Rickettsia species based on the sizes of highly variable intergenic spacers, namely, dksA-xerC, mppA-purC, and rpmE-tRNAfMet was carried out. Application of multiplex PCR for simultaneous amplification of 3 spacers combined with capillary electrophoresis separation allowed simple, accurate, and high-throughput fragment sizing with considerable time and cost savings. Rickettsia genus-specific real-time PCR detected 136 positives out of 140 samples, giving an overall prevalence of 97.1%. Most samples (n=113) had a size combination of 225, 195, and 341bp for dksA-xerC, mppA-purC, and rpmE-tRNAfMet, respectively, which was identical to that of R. africae, a causative agent of African tick bite fever. In addition, several samples had size variants in either dksA-xerC or rpmE-tRNAfMet. Nonetheless, the partial sequences of gltA and ompA genes of samples of all size combinations showed the greatest similarity to R. africae (99.3–100% for gltA and 98.1–100% for ompA). Given these results, it is highly possible that the tested ticks were infected with R. africae or closely related species. This is a first report on molecular genetic detection of R. africae and its high endemicity in Uganda. Clinicians in this country should be aware of this pathogen as a cause of non-malarial febrile illness. This study provided a starting point for the development of Rickettsia species identification based on the sizes of intergenic spacers. The procedure is simple, rapid, and cost-effective to perform; hence it might be particularly well suited for preliminary species identification in epidemiological investigations. The results may be more detailed and reliable when simultaneous sequencing analysis is performed.

Fieber, Husten und Dyspnoe bei einer nierentransplantierten 38-jährigen Patientin

This article reports on a 38-year-old kidney transplant patient who presented with fever, coughing and dypnea. The patient was immunosuppressed with mycophenolate and prednisone. Due to the suspicion of community acquired pneumonia antibiotic treatment was initiated and the patient was admitted to the intensive care unit. Despite antibiotic treatment the condition did not improve and in the subsequently performed bronchioalveolar lavage parainfluenza virus was diagnosed.Infections with respiratory viruses can be fatal in immunosuppressed patients. Human parainfluenza virus is the third most common pathogen of viral pneumonia. Molecular genetic detection methods allow fast and sensitive diagnosis of respiratory materials. As the treatment options are limited for these infections prophylactic measurements are important.

Optic Atrophy Differentially Diagnosed as Spinocerebellar Ataxia from Leber Hereditary Optic Neuropathy by Gene Mutation Analysis

Optic atrophy describes a group of diseases of retinal ganglion cells and axons that eventually lead to loss of vision. Optic atrophy has both congenital and acquired causes, and its diagnosis (or differential diagnosis) is complicated. This case report describes a 20-year-old man who presented with a 1-year history of progressive vision loss in both eyes and no obvious systemic symptoms. Fundus examination revealed bilateral optic atrophy. Based on clinical characteristics, visual field analysis and pattern visual evoked potential examination, the presumptive diagnosis was Leber hereditary optic neuropathy (LHON). Analysis of mitochondrial DNA indicated the absence of all of three common mutations associated with LHON (m.3460G>A, m.11778G>A, m.14484T>C). Detailed questioning of the patient revealed a history of prolonged language development and poor balance. Neurological examination indicated abnormal co-ordination, suggesting the presence of inherited spinocerebellar ataxia (SCA). Analysis of the SCA7 gene revealed a high number of trinucleotide repeats [(CAG)(n), n > 64], confirming the diagnosis of SCA. The aetiology of optic atrophies is complicated and the molecular genetic detection approach provides the best information for diagnosing these diseases.

A Comparative Analysis of Molecular Genetic and Conventional Cytogenetic Detection of Diagnostically Important Translocations in More Than 400 Cases of Acute Leukemia, Highlighting the Frequency of False-Negative Conventional Cytogenetics

A Comparative Analysis of Molecular Genetic and Conventional Cytogenetic Detection of Diagnostically Important Translocations in More Than 400 Cases of Acute Leukemia, Highlighting the Frequency of False-Negative Conventional Cytogenetics

A Comparative Analysis of Molecular Genetic and Conventional Cytogenetic Detection of Diagnostically Important Translocations in More Than 400 Cases of Acute Leukemia, Highlighting the Frequency of False-Negative Conventional Cytogenetics

In this study, we correlated the results of concurrent molecular and cytogenetic detection of entity-defining translocations in adults with acute leukemia to determine the frequency of cryptic translocations missed by conventional cytogenetics (CC) and of recurrent, prognostically relevant translocations not detectable by multiplex reverse transcriptase-polymerase chain reaction (MRP). During a 5.5-year period, 442 diagnostic acute leukemia specimens were submitted for MRP-based detection of 7 common recurrent translocations: t(8;21), t(15;17), inv(16), t(9;22), t(12;21), t(4;11), and t(1;19), with a detection rate of 15.2% (67/442). CC was performed in 330 (74.7%) of 442 cases. In 7 of these 330 cases, CC missed the translocation detected by MRP. In 50 additional cases, CC revealed 1 of the MRP-detectable translocations (all were also MRP positive), yielding a false-negative rate of 12% (7/57) for the CC assay. The remaining 140 of 190 cases with clonal cytogenetic changes harbored abnormalities that were not targeted by the MRP assay, including 8 that define specific acute myeloid leukemia entities. This study revealed the frequent occurrence of false-negative, entity-defining CC analysis and highlighted the complementary nature of MRP and CC approaches in detecting genetic abnormalities in acute leukemia.

Genetic bases of the repertoire of immunoglobulins in application to diagnostics of clonality of B-cell lymphoid populations

Molecular mechanisms underlying the formation of B-cell lymphomas in connection with processes associated with the maturation of B lymphocytes are reviewed. The currently used diagnostic methods do not always distinguish lymphomas from reactive changes of the lymphoid tissue. The principle of the molecular genetic method ofclonality detection in lymphocyte populations, technical problems, and the strategy of its application in clinical diagnostics of lymphomas are described in detail.

Prevalence of virulence genes among bulgarian nosocomial and cystic fibrosis isolates of Pseudomonas aeruginosa

The aim of this study was to evaluate the prevalence of some virulence genes among 202 Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients (n=42) and non-CF in-patients (n=160) and to analyze the values according to the patient groups, infection localization and antimicrobial resistance. The following frequencies in all studied strains were established: algD (encoding GDP-mannose 6-dehydrogenase AlgD) – 91.1%, pilB (type IV fimbrial biogenesis protein PilB) – 23.8%, nan1 (neuraminidase) – 21.3%, lasB (elastase LasB) – 100%, plcH (haemolytic phospholipase C precursor) – 91.6%, exoS (exoenzyme S) – 62.4%, and exoU (exoenzyme U) – 30.2%. The prevalence of nan1 was significantly higher (P<0.01) in CF isolates (38.1%) than that in non-CF isolates (16.9%). The nan1–positive CF strains were cultured from 16 patients with recurrent lung exacerbations. This study revealed a statistically significant difference (P<0.01) between the portion of multidrug-resistant (MDR) nosocomial P. aeruginosa strains containing a large number (≥5) of virulence genes (38.1%) and the respective part of non-MDR isolates (17.6%). Moreover, pilB, exoU and nan1 manifested a higher spread (P<0.001) among MDR than in non-MDR strains (respectively, 39.1% vs. 13.2%; 40.2% vs. 17.7% and 26.1% vs. 4.4%). In conclusion, the dissemination of nan1 in CF isolates was moderate and correlated with the lower proportion of patients with lung exacerbations. The molecular-genetic detection of this gene may be used as an indirect measure of CF pulmonary disease evolution. Simultaneous determination of virulence factors and antimicrobial resistance is the contemporary approach for examination of the microbiological aspects of infections caused by P. aeruginosa.

Suitability of Rapid Aneuploidy Detection for Prenatal Diagnosis

ObjectiveTo determine the suitability of replacing full karyotype analysis with molecular genetic rapid aneuploidy detection (RAD) methods, in particular quantitative fluorescence polymerase chain reaction (QF-PCR), for prenatal diagnosis in amniotic fluid samples obtained by amniocentesis. MethodsWe reviewed all fetal karyotypes done at our centre between August 29, 2000, and February 28, 2006. Outcome measures included (1) the proportion of prenatal samples with abnormal karyotypes that would not have been detected by RAD, as a whole and for each indication, and (2) pregnancy outcome for each chromosome abnormality that was predicted to be clinically significant or of uncertain significance and would not have been detected by RAD. ResultsOf the 6411 karyotypes reported in the study period, 70 (1.09%) were abnormal karyotypes which would not have been detected by RAD alone. These included 32 cases (0.50%) predicted to confer no increased risk to the fetus, 17 (0.27%) predicted to have a low risk of fetal abnormality, and 21 (0.33%) with an uncertain or high risk of fetal abnormality. If full karyotype was added for nuchal translucency greater than 3.5 mm, structural fetal abnormality on ultrasound, or parental balanced chromosome rearrangement, only five uncertain or high risk cases (0.08%) would not have been detected by RAD alone. ConclusionThese results suggest that if the policy of offering full karyotype analysis to all women were to be changed to a policy of offering RAD alone to women without other risk factors such as fetal abnormalities on ultrasound, increased nuchal translucency, or history of chromosome abnormality, this would mean that a chromosome abnormality with a substantial risk of clinically significant fetal abnormality would be missed in fewer than 1/1000 amniocenteses. Our results are similar to others previously reported.

Molecular genetic analysis of haematological malignancies II: mature lymphoid neoplasms

Molecular genetic techniques have become an integral part of the diagnostic assessment for many lymphomas and other chronic lymphoid neoplasms. The demonstration of a clonal immunoglobulin or T cell receptor gene rearrangement offers a useful diagnostic tool in cases where the diagnosis is equivocal. Molecular genetic detection of other genomic rearrangements may not only assist with the diagnosis but can also provide important prognostic information. Many of these rearrangements can act as molecular markers for the detection of low levels of residual disease. In this review, we discuss the applications of molecular genetic analysis to the chronic lymphoid malignancies. The review concentrates on those disorders for which molecular genetic analysis can offer diagnostic and/or prognostic information.

Analysis of the TP53 gene in laser-microdissected glioblastoma vasculature

Malignant transformation of human gliomas is accompanied by extensive proliferation of stromal blood vessels. Recent data suggest mesenchymal transdifferentiation of neoplastic cells in various human cancers, including colon and breast cancer as well as gliosarcoma. In this study, we have analyzed proliferating stromal blood vessels in glioblastoma multiforme for the presence of mutations in the tumor suppressor gene TP53. Using tissue arrays derived from glioblastoma specimens, cases with significant immunohistochemical p53 accumulation were selected for molecular genetic detection of TP53 mutations in exons 5 to 8. None of the tumors included in this series displayed properties of gliosarcoma. Proliferating glomeruloid stromal vessels were isolated by laser microdissection from paraffin sections. In six cases, single-strand conformation polymorphism analysis for mutations of the TP53 gene in stromal blood vessels compared with adjacent tumor cells and subsequent DNA sequencing of the resulting DNA fragments were carried out. Glioblastoma cells of these cases exhibited TP53 mutations in exons 5, 7 and 8. None of these tumors showed TP53 mutations in microdissected samples from glomeruloid vessels. The absence of TP53 mutations in vascular stromal components of glioblastoma multiforme supports the hypothesis that microvascular proliferations originate from the tumor stroma and are not derived from transdifferentiated glioblastoma cells.

Post-transplant lymphoproliferative disorders in kidney transplantation: histological and molecular genetic assessment.

We performed histopathological and immunohistochemical studies, in situ hybridization (ISH) for Epstein-Barr virus (EBV) and molecular genetic analysis using the PCR method for the immunoglobulin heavy chain gene in six patients with post-transplant lymphoproliferative disorders (PTLD) to clarify these problems. In two patients, PTLD developed in the graft, and in the remaining four it developed in systemic lymphoid tissues or organs. In terms of morphological classification, lesions in the graft of two patients were polymorphic with features of rejection in the background. In the other four patients, three of them presented monomorphic lesions and the remaining one presented features of reactive lymphoid hyperplasia. All the patients were positive for EBV as determined by ISH. The molecular genetic study could be performed for four patients, the cells in lesions of two patients were found to be monoclonal and those of the remaining two were polyclonal in IgH as determined by PCR. We conclude that PTLD are of two types, namely, intragraft PTLD and extra-graft PTLD. In the cases of intragraft PTLD their diagnosis is relatively difficult, because lesions are mixed with features of rejection. Molecular genetic analysis and detection of EBV by ISH are useful for diagnosis. In contrast, the diagnosis of extra-graft PTLD is easier than that of intragraft PTLD, by basing of the latest classification of malignant lymphoma. Grading of severity of PTLD should be carried out according to the newest system and protocols for treatment based on the grade of the lesion should be established as soon as possible.

Mutation screening in the ryanodine receptor 1 gene (RYR1) in patients susceptible to malignant hyperthermia who show definite IVCT results: identification of three novel mutations.

The ryanodine receptor of the skeletal muscle (RYR1) seems to be of outstanding importance in the pathogenesis of malignant hyperthermia (MH). It has been shown that point mutations in the RYR1 gene are strongly associated with the MH phenotype. A correctly determined phenotype is the basic prerequisite for adequate genetic MH screening. In this study we examined only those MH susceptible patients for the presence of potential RYR1 mutations who showed strong pathological muscle responses in the in vitro contracture test (IVCT). A total of 56 MHS index patients who complied with the following IVCT criteria were included in the molecular genetic investigation: Contracture forces > or =4 mN at a caffeine concentration of 2.0 mmol/l and > or =8 mN at a halothane concentration of 0.44 mmol/l. DNA sequences of exons 2, 6, 9, 11, 12, 14, 15, 17, 39, 40, 45, 46, 102 of the RYR1 gene were analysed by the direct sequencing technique. Furthermore, if an MH mutation was identified in an index patient, all relatives were screened for their family specific RYR1 defect. In 39 index patients an RYR1 mutation was detected: Arg163Cys (n = 2), Asp166Asn (n = 1), Gly341Arg (n = 2), Arg401His (n = 2), Arg614Cys (n = 12), Asp2129Glu (n = 1),Vol2168Met (n = 1), Thr2206Met (n = 9), Ala2428Thr (n = 1), Gly2434Arg (n = 2), Arg2435His (n = 1), Arg2452Trp (n = 1), Arg2454His (n = 4). Three new RYR1 mutations were identified. We found a potential MH mutation in a further 130 relatives of the 39 index patients. Thirty-seven individuals were classified as MHS exclusively by molecular genetic techniques and did not have to undergo the IVCT. The ascertained high rate of successful MH mutation screening (69.64%) is obviously associated with the more clearly defined MHS diagnosis in the IVCT. According to the EMHG guidelines for the molecular genetic detection of MH susceptibility, a positive MH disposition could be determined in numerous persons by a less invasive technique.