scholarly journals Molecular Diagnostics of Adult Gliomas in Neuropathological Practice

2021 ◽  
Vol 50 (1) ◽  
pp. 29
Author(s):  
Sebastian Brandner
Keyword(s):  
Dna Methylation ◽  
Brain Tumours ◽  
Molecular Techniques ◽  
Small Samples ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Low Grade ◽  
High Grade ◽  
Braf Mutations ◽  
Methylation Profiling

<p>This review focuses on adult gliomas, highlighting the most relevant biomarkers in the diagnosis of these tumours and the use of DNA methylation arrays to complement conventional molecular diagnostic techniques. The discovery and characterisation of diagnostic and prognostic biomarkers in brain tumours has significantly changed the neuropathological landscape over the last decade. These include mutations in the IDH1 and IDH2 genes in astrocytomas and oligodendrogliomas, histone H3 K27M mutations in midline gliomas, or BRAF mutations in a range of low-grade and high-grade glial and glioneuronal tumours. Other biomarkers of relevance are mutations in the TERT promoter, the ATRX gene, and genomic alterations such as 1p/19q codeletion, EGFR amplification, and chromosome 7 gain and 10 loss. The development of DNA methylation profiling and algorithmic classification of brain tumours has further enhanced the diagnostic abilities of neuropathologists. Methylation profiling is particularly useful for the diagnostic workup of biopsies with an inconclusive molecular test results, small samples, or samples with indistinctive low-grade or high-grade histology. This technology has become indispensable for the risk stratification of ependymal tumours, medulloblastomas and meningiomas.</p><p><strong>Conclusion</strong>. This review highlights the importance of an integrated approach to brain tumour diagnostics and gives a balanced view of the relevance and choice of conventional and molecular techniques in the workup of adult gliomas in diagnostic neuropathology practice.</p><div> </div>

EPCO-17. METHYLATION ANALYSIS OF MATCHED PRIMARY AND RECURRENT IDHmt ASTROCYTOMA; AN UPDATE FROM THE GLIOMA LONGITUDINAL ANALYSIS NL (GLASS-NL) CONSORTIUM

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi5-vi5
Author(s):  
Wies Vallentgoed ◽  
Anneke Niers ◽  
Karin van Garderen ◽  
Martin van den Bent ◽  
Kaspar Draaisma ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Surgical Resection ◽  
Molecular Mechanisms ◽  
Relative Proportion ◽  
Low Grade ◽  
High Grade ◽  
Primary Tumors ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Abstract The GLASS-NL consortium, was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Here, we present the first results of genome-wide DNA-methylation profiling of GLASS-NL samples. 110 adult patients were identified with an IDH-mutant astrocytoma at first diagnosis. All patients underwent a surgical resection of the tumor at least twice, separated by at least 6 months (median 40.9 months (IQR: 24.0, 64.7). In 37% and 18% of the cases, patients were treated with radiotherapy or chemotherapy respectively, before surgical resection of the recurrent tumor. DNA-methylation profiling was done on 235 samples from 103 patients (102 1st, 101 2nd, 29 3rd, and 3 4th resection). Copy number variations were also extracted from these data. Methylation classes were determined according to Capper et al. Overall survival (OS) was measured from date of first surgery. Of all primary tumors, the methylation-classifier assigned 85 (87%) to the low grade subclass and 10 (10%) to the high grade subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). Methylation classes were prognostic, both in primary and recurrent tumors. The overall DNA-methylation levels of recurrent samples was lower than that of primary samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. In an unsupervised analysis, DNA-methylation data derived from primary and first recurrence samples of individual patients mostly (79%) cluster together. Recurrent samples that do not cluster with their primary tumor, form a separate group with relatively low genome-wide DNA-methylation. Our data demonstrate that methylation profiling identifies a shift towards a higher grade at tumor progression coinciding with reduced genome-wide DNA-methylation levels.

OS05.5.A Methylation analysis of matched primary and recurrent IDHmt astrocytoma; an update from the Glioma Longitudinal Analysis NL (GLASS-NL) consortium

2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii7-ii8
Author(s):  
W R Vallentgoed ◽  
J M Niers ◽  
M J van den Bent ◽  
M C M Kouwenhoven ◽  
J M Kros ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Surgical Resection ◽  
Molecular Mechanisms ◽  
Clinical Decision Making ◽  
Relative Proportion ◽  
Low Grade ◽  
High Grade ◽  
Primary Tumors ◽  
Genome Wide ◽  
Methylation Profiling

Abstract BACKGROUND The evolutionary processes that drive progression in patients with IDH-mutant astrocytoma remain unclear. The GLASS-NL consortium, as part of the larger worldwide GLASS consortium, was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Such markers can ultimately assist clinical decision making. Here, we present the first results of genome wide methylation profiling of samples included in the GLASS-NL study. MATERIAL AND METHODS 110 adult patients were identified with an IDH-mutant astrocytoma at first diagnosis. All patients underwent a surgical resection of the tumor at least twice, separated by at least 6 months with a median of 40.9 months (IQR: 24.0, 64.7), in 37% and 18% of the cases, patients were treated with radiotherapy or chemotherapy respectively, before surgical resection of the recurrent tumor. Methylation profiling was done on (macro dissected) DNA isolated of 235 samples from 103 patients (102 1st, 101 2nd, 29 3rd, and 3 4th resection), using the Infinium MethylationEPIC BeadChip array. Copy number variations were also derived from these data. Methylation classes were determined according to Capper et al. (2018). Overall survival (OS) was measured from date of first surgery. RESULTS Of all primary tumors, the methylation-classifier assigned 85 (87%) to the A_IDH (‘low grade’) subclass and 10 (10%) to the A_IDH_HG (‘high grade’) subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). The overall DNA-methylation levels of recurrent samples was lower than that of primary samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. In an unsupervised analysis, methylation data derived from first and second resections of individual patients mostly (79%) cluster together. This indicates that variability between tumors is larger than temporal heterogeneity within tumors. Recurrent samples that do not cluster with their primary tumor, form a separate cluster and have relatively low genome-wide DNA-methylation. CONCLUSION Our data demonstrate that methylation profiling identifies a shift towards a higher grade at tumor progression coinciding with reduced genome-wide DNA-methylation levels.

Diagnosis of melioidosis: the role of molecular techniques

2021 ◽  
Vol 16 (4) ◽  
pp. 271-288
Author(s):  
Ian Gassiep ◽  
Delaney Burnard ◽  
Michelle J Bauer ◽  
Robert E Norton ◽  
Patrick N Harris
Keyword(s):  
Laboratory Diagnosis ◽  
Diagnostic Techniques ◽  
Molecular Techniques ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Molecular Diagnostic Techniques ◽  
Detection And Identification ◽  
Life Years ◽  
Culture Independent ◽  
Future Utility

Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.

scholarly journals DNA Methylation Profiling for Diagnosing Undifferentiated Sarcoma with Capicua Transcriptional Receptor (CIC) Alterations

2020 ◽  
Vol 21 (5) ◽  
pp. 1818 ◽  
Author(s):  
Evelina Miele ◽  
Rita De Vito ◽  
Andrea Ciolfi ◽  
Lucia Pedace ◽  
Ida Russo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Soft Tissue ◽  
Abdominal Wall ◽  
Current Knowledge ◽  
Soft Tissue Sarcomas ◽  
Molecular Techniques ◽  
Round Cell ◽  
Undifferentiated Sarcoma ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

Undifferentiated soft tissue sarcomas are a group of diagnostically challenging tumors in the pediatric population. Molecular techniques are instrumental for the categorization and differential diagnosis of these tumors. A subgroup of recently identified soft tissue sarcomas with undifferentiated round cell morphology was characterized by Capicua transcriptional receptor (CIC) rearrangements. Recently, an array-based DNA methylation analysis of undifferentiated tumors with small blue round cell histology was shown to provide a highly robust and reproducible approach for precisely classifying this diagnostically challenging group of tumors. We describe the case of an undifferentiated sarcoma of the abdominal wall in a 12-year-old girl. The patient presented with a voluminous mass of the abdominal wall, and multiple micro-nodules in the right lung. The tumor was unclassifiable with current immunohistochemical and molecular approaches. However, DNA methylation profiling allowed us to classify this neoplasia as small blue round cell tumor with CIC alterations. The patient was treated with neoadjuvant chemotherapy followed by complete surgical resection and adjuvant chemotherapy. After 22 months, the patient is disease-free and in good clinical condition. To put our experience in context, we conducted a literature review, analyzing current knowledge and state-of-the-art diagnosis, prognosis, and clinical management of CIC rearranged sarcomas. Our findings further support the use of DNA methylation profiling as an important tool to improve diagnosis of non-Ewing small round cell tumors.

scholarly journals Multicentre study of perfusion magnetic resonance imaging in paediatric brain tumours

2019 ◽  
Vol 21 (Supplement_4) ◽  
pp. iv10-iv10 ◽  
Author(s):  
Stephanie Withey ◽  
Lesley MacPherson ◽  
Adam Oates ◽  
Stephen Powell ◽  
Jan Novak ◽  
...  
Keyword(s):  
Contrast Agent ◽  
Brain Tumours ◽  
Cerebral Blood Volume ◽  
Perfusion Magnetic Resonance Imaging ◽  
Low Grade ◽  
Dynamic Susceptibility ◽  
High Grade ◽  
Dynamic Susceptibility Contrast ◽  
Perfusion Studies ◽  
Paediatric Brain Tumours

Abstract Studies in adults have shown that brain tumour perfusion correlates with grade. These studies are dominated by gliomas grade II to IV which are rare in children. The standard method, Dynamic Susceptibility Contrast MRI, provides estimates of relative cerebral blood volume (rCBV) but contrast agent leakage affects rCBV accuracy. The majority of perfusion studies have been conducted at single centres and variation in acquisition protocols makes the generalizability of results questionable. The aim of this study was to compare leakage-corrected rCBV with grade in paediatric brain tumours at multiple centres. Scans were analysed from 85 patients at 4 centres on 6 scanners prior to treatment. MRI protocols varied between centres. Histological diagnoses including grade were obtained. Whole-tumour median rCBV was significantly higher in the 45 high grade than the 40 low grade tumours (2.54 ± 1.63 ml/100ml vs 1.68 ± 1.36 ml/100ml, p=0.010). Low grade tumours, particularly pilocytic astrocytomas (grade I), displayed more contrast agent leakage consistent with their appearance on contrast enhanced images and required more leakage correction than high grade tumours. This finding differs from that in adults where contrast agent uptake is usually associated with higher grade. A cut-off of 1.70 ml/100ml for rCBV gave sensitivity and specificity of 76% and 65% respectively for discriminating grade. In summary, perfusion MRI can be used to help distinguish between low and high grade paediatric brain tumours. This finding is robust across multiple centres and acquisition protocols but correction should be made for leakage of contrast agent from the vessels.

scholarly journals Male infertility: biomolecular aspects

2014 ◽  
Vol 5 (6) ◽  
pp. 449-456 ◽  
Author(s):  
Damiano Pizzol ◽  
Alessandro Bertoldo ◽  
Carlo Foresta
Keyword(s):  
Male Infertility ◽  
Semen Analysis ◽  
Diagnostic Techniques ◽  
Molecular Techniques ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Assisted Reproductive Technique ◽  
Sperm Analysis ◽  
Precise Diagnosis ◽  
Near Future

AbstractMale infertility is a problem that faces increasing interest, and the continuous development of assisted reproduction techniques solicits attempts to identify a precise diagnosis, in particular for idiopathic infertile couples and those undergoing assisted reproductive technique cycles. To date, diagnosis of male infertility is commonly based on standard semen analysis, but in many cases, this is not enough to detect any sperm abnormality. A better understanding of biomolecular issues and mechanism of damaged spermatogenesis and the refinement of the molecular techniques for sperm evaluation and selection are important advances that can lead to the optimization of diagnostic and therapeutic management of male and couple infertility. Faced with a growing number of new proposed techniques and diagnostic tests, it is fundamental to know which tests are already routinely used in the clinical practice and those that are likely to be used in the near future. This review focuses on the main molecular diagnostic techniques for male infertility and on newly developed methods that will probably be part of routine sperm analysis in the near future.

High Throughput Methylation Arrays Allow for Identification of Complex Methylation Patterns in MDS.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2437-2437
Author(s):  
Ying Jiang ◽  
Christine L. OKeefe ◽  
Andrew Dunbar ◽  
Anjali Advani ◽  
Mikkael A. Sekeres ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Tumor Suppressor ◽  
High Throughput ◽  
Tumor Suppressor Genes ◽  
Methylation Status ◽  
Epigenetic Silencing ◽  
Low Grade ◽  
High Grade ◽  
Methylation Patterns ◽  
Hypermethylated Genes

Abstract Genomic imprinting and epigenetic silencing determine tissue-specific methylation patterns. Altered methylation of CpG islands within gene promoters has been hypothesized as one pathogenetic mechanism operative in myelodysplastic syndrome (MDS). Promoter hypermethylation of various empirically selected tumor suppressor genes has been found in MDS prompting application of hypomethylating drugs in this disease. Identification of hypermethylated genes predicting response to these drugs would have a major impact on clinical practice. However, to date methylation-based prognostic algorithms have not been established. Global analysis of DNA methylation patterns may help to identify hypermethylated genes/promoters associated with the pathogenesis of MDS. Recently, microarray-based DNA methylation analysis platforms enabled a powerful, high-throughput analysis of the methylation status of hundreds of genes. The GoldenGate Methylation Cancer Panel I, spanning 1,536 independent CpG sites selected from 807 selected genes was applied to determine the methylation status in MDS patients (N=51; 21 low grade (RA, MDS-U, RARS or RCMD), 26 high grade (AML or RAEB) and 4 CMML). The methylation status was determined based on an internal reference and compared to healthy controls (N=22). Methylation values were averaged among the patients or analyzed separately for each patient in comparison to average values obtained in controls. Overall, controls showed a lesser degree of methylation than advanced MDS patients (average intensity 0.326 vs. 0.339, p&lt;0.05). Subsequently, we concentrated on hypermethylated genes. There were no genes uniformly hypermethylated in all patients. For 70%, 50%, and 30% of patients with advanced MDS, 1, 26, and 85 loci were concordantly hypermethylated, while in 70%, 50% and 30% of low risk patients 5, 23 and 31 were hypermethylated, respectively. The most consistently hypermethylated genes (&gt;50% of patients), included tumor suppressor genes (DCC, SLC22A18, FAT, TUSC3), genes involved in DNA repair (OGG1, DDB2, BCR, PARP1), cell cycle control (DBC1, SMARCB1), differentiation (MYOD1, TDGF1, FGF2, NOTCH4) and apoptosis (HDAC1, ALOX12, AXIN1). Despite the variability, the aberrant methylation spectrum in CMML, low grade MDS and high grade MDS showed significant overlap (for example FZD9, IL16, EVI2A, MBD2 and BCR), which suggests that these genes may relate to the common tumorigenesis in MDS. Certain genes show specific methylation correlating to the morphologic diagnosis and may serve as diagnostic markers. For example, the promoter of HDAC1 is hypomethylated in 81% of sAML/RAEB1/2 patients but hypermethylated in 81% of low risk cases. To assess the link between epigenetic changes and chromosomal abnormalities, we also investigated methylation pattern of MDS with del5q for selected genes at the 5q locus. Some genes that are involved in apoptosis (WNT1, TNF receptor) and proliferation (MAP3K8, CSF3) were found to be hypermethylated in comparison to controls, suggesting that epigenetic silencing may enhance the effect of haploinsuffciency for some of the genes. In sum, our study, the first application of a high-throughput microarray methylation assay in MDS, demonstrates that complex methylation patterns exist in MDS and may allow for identification for clinically relevant methylation markers.

Parasitological versus molecular diagnosis of strongyloidiasis in serial stool samples: how many?

2017 ◽  
Vol 92 (1) ◽  
pp. 12-16 ◽  
Author(s):  
E. Dacal ◽  
J.M. Saugar ◽  
T. Soler ◽  
J.M. Azcárate ◽  
M.S. Jiménez ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Correct Diagnosis ◽  
Molecular Techniques ◽  
Maximum Sensitivity ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Molecular Technique ◽  
Asymptomatic Patients ◽  
Stool Samples

AbstractStrongyloidiasis is usually an asymptomatic disease in immunocompetent patients, caused by Strongyloides stercoralis. However, in immunocompromised patients it can produce a severe clinical profile. Therefore, a correct diagnosis is necessary in these cases and in those chronic asymptomatic patients. The low sensitivity of classical parasitological techniques requires the analysis of multiple serial stool samples. Molecular diagnostic techniques represent an improvement in the detection of the parasite. The objective of this study was to evaluate the minimum number of samples necessary to achieve maximum sensitivity by real-time polymerase chain reaction (PCR). A total of 116 stool samples from 39 patients were analysed by direct microscopic observation, agar culture, Harada–Mori and real-time PCR, in one, two, three and four or more consecutive samples. After two serial samples, 6 out of 39 patients were positive by parasitological and molecular techniques, while 16 of them were real-time PCR positive, and all the patients detected by parasitology were also detected by the molecular technique, reaching 100.00% sensitivity versus 83.00% when analysing a single sample. These data also reflect apparently low specificity (51.52%) and positive predictive value (PPV) (27.27 %) values, due to the high number of cases detected by real-time PCR and not by parasitological techniques. These cases were confirmed as true positives when analysing three, four or more samples from the same patient. In conclusion, the application of molecular techniques decreases the number of serial stool samples necessary to give a diagnosis with the maximum sensitivity.

scholarly journals Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain

2016 ◽  
Author(s):  
S. Ambrós ◽  
F. Martínez ◽  
P. Ivars ◽  
C. Hernández ◽  
F. de la Iglesia ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Plant Species ◽  
Rna Virus ◽  
Diagnostic Techniques ◽  
Plant Viruses ◽  
Reservoir Host ◽  
Molecular Techniques ◽  
Tomato Mosaic Virus ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques

AbstractTomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Koch’s postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

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