Avoiding New Biopsies by Identification of IDH1 and TERT Promoter Mutation in Nondiagnostic Biopsies From Glioma Patients

Neurosurgery ◽  
2020 ◽  
Vol 87 (4) ◽  
pp. E513-E519 ◽  
Author(s):  
Marc Barritault ◽  
Thiébaud Picart ◽  
Delphine Poncet ◽  
Tanguy Fenouil ◽  
Anne d’Hombres ◽  
...  
Keyword(s):  
Idh1 Mutation ◽  
Endoscopic Biopsy ◽  
Molecular Testing ◽  
Chain Reaction ◽  
Biopsy Needle ◽  
Mutation Status ◽  
Tert Promoter ◽  
Imaging Characteristics ◽  
Polymerase Chain ◽  
High Level

Abstract BACKGROUND Biopsies in patients with a suspected glioma are occasionally nondiagnostic. OBJECTIVE To explore the utility of molecular testing in this setting by determining whether IDH1 and TERT promoter (pTERT) mutations could be detected in nondiagnostic biopsies from glioma patients. METHODS Using SNaPshot polymerase chain reaction, we retrospectively assessed IDH1 and pTERT mutation status in nondiagnostic biopsies from 28 glioma patients. RESULTS The nondiagnostic biopsy (needle biopsy n = 25, open or endoscopic biopsy n = 3) consisted of slight glial cell hypercellularity, hemorrhage, and/or necrosis. After another biopsy (n = 23) or a subsequent surgical resection (n = 5) the diagnosis was an IDH1-wildtype (WT) pTERT-mutant glioma (glioblastoma n = 16, astrocytoma n = 4), an IDH1-mutant pTERT-mutant oligodendroglioma (n = 1), an IDH1-mutant pTERT-WT astrocytoma (n = 1), and an IDH1-WT pTERT-WT glioblastoma (n = 6). An IDH1 mutation was identified in the nondiagnostic biopsies of the 2 IDH-mutant gliomas, and a pTERT mutation in the nondiagnostic biopsies of 16 out of the 21 of pTERT mutant-gliomas (76%). Overall, an IDH1 and/or a pTERT mutation were detected in 17 out of 28 (61%) of nondiagnostic biopsies. Retrospective analysis of the nondiagnostic biopsies based on these results and on imaging characteristics suggested that a new biopsy could have been avoided in 6 patients in whom a diagnosis of “molecular glioblastoma” could have been done with a high level of confidence. CONCLUSION In the present series, IDH1 and pTERT mutations could be detected in a high proportion of nondiagnostic biopsies from glioma patients. Molecular testing may facilitate the interpretation of nondiagnostic biopsies in patients with a suspected glioma.

scholarly journals Primary neural leprosy: systematic review

2013 ◽  
Vol 71 (6) ◽  
pp. 397-404 ◽  
Author(s):  
Jose Antonio Garbino ◽  
Wilson Marques Jr ◽  
Jaison Antonio Barreto ◽  
Carlos Otto Heise ◽  
Marcia Maria Jardim Rodrigues ◽  
...  
Keyword(s):  
Systematic Review ◽  
Scientific Evidence ◽  
Specific Treatment ◽  
Nerve Biopsy ◽  
Molecular Testing ◽  
Chain Reaction ◽  
Online Databases ◽  
Polymerase Chain ◽  
Definition Of ◽  
Based Medicine

The authors proposed a systematic review on the current concepts of primary neural leprosy by consulting the following online databases: MEDLINE, Lilacs/SciELO, and Embase. Selected studies were classified based on the degree of recommendation and levels of scientific evidence according to the “Oxford Centre for Evidence-based Medicine”. The following aspects were reviewed: cutaneous clinical and laboratorial investigations, i.e. skin clinical exam, smears, and biopsy, and Mitsuda's reaction; neurological investigation (anamnesis, electromyography and nerve biopsy); serological investigation and molecular testing, i.e. serological testing for the detection of the phenolic glycolipid 1 (PGL-I) and the polymerase chain reaction (PCR); and treatment (classification criteria for the definition of specific treatment, steroid treatment, and cure criteria).

scholarly journals Molecular Confirmation of Salmonella typhimuriumin Poultry from Kathmandu Valley

2018 ◽  
Vol 4 ◽  
pp. 86-89 ◽  
Author(s):  
Sanjeev Kumar Adhikari ◽  
Arrogya Gyawali ◽  
Sajan Shrestha ◽  
Swoyam Prakash Shrestha ◽  
Meera Prajapati ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Molecular Level ◽  
Kathmandu Valley ◽  
Agarose Gel ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Selective Media ◽  
Poultry Products ◽  
Polymerase Chain ◽  
High Level

A prevalence study was carried to isolate Salmonella typhimurium from blood (n= 50) and gut samples (n=100) of poultry in Kathmandu valley during early 2016. Salmonella typhimurium bacteria isolated in the selective media were biochemically confirmed based on Bergey’s Manual. Two sets of oligonucleotide primers-the genus specific 16S rRNA and the organism specific invA were employed for molecular level confirmation by the Polymerase Chain Reaction (PCR) assay. The amplified fragments in 1% agarose gel observed at 406bp and 285bp, respectively confirmed the isolates to be Salmonella typhimurium. Of 150 samples tested, Salmonella typhimurium were isolated from 49 samples, among which nine were from blood (18%) and forty from the gut (40%). The present result indicated an alarmingly high level of Salmonella typhimurium, which can result inzoonotic infection in humans owing to increased contact with poultry and consumption of poultry products in the Kathmandu valley.

Subtyping of High-Level Plasmid-Mediated Tetracycline Resistant Neisseria Gonorrhoeae Isolated in Scotland between 1992 and 1998

1999 ◽  
Vol 10 (10) ◽  
pp. 646-651 ◽  
Author(s):  
T Beattie ◽  
A Moyes ◽  
C Patrizio ◽  
H Young
Keyword(s):  
Polymerase Chain Reaction ◽  
Neisseria Gonorrhoeae ◽  
Base Pair ◽  
Tetracycline Resistance ◽  
Cytoplasmic Protein ◽  
Gonococcal Infection ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Polymerase Chain ◽  
High Level

Tetracycline resistant Neisseria gonorrhoeae (TRNG) contain a 25.2 MDa TetM plasmid encoding a 68KDa cytoplasmic protein which confers high-level tetracycline resistance. The aim of this study was to subtype all TRNG isolated in Scotland between 1992 and 1998. Subtyping was performed by a polymerase chain reaction (PCR) assay which characterizes the TetM plasmid as either the Dutch variant (443 base pair product) or the American variant (777 base pair product). Of the 78 TRNG isolates, 35 were the American variant and 43 were the Dutch variant. TRNG were distributed amongst 30 serovar/auxotype classes, the most common being 1A6/NR (11.5%), 1A6/P (14.1%) and 1B4/NR (14.1%). The country where infection was acquired was known for 36 of the 46 TRNG strains isolated between 1996 and 1998. All infections acquired in Asia and South America were the Dutch variant whereas all infections acquired in Africa were the American variant. A penicillinase plasmid was present in 66% (23/35) of the American variant TRNG compared with 51% (22/43) of the Dutch variant: the 3.2 MDa penicillinase plasmid was found in 87% of the American variant TRNG whereas the 4.4 MDa penicillinase plasmid was found in 68% of the Dutch variant TRNG. We conclude that subtyping of TRNG by PCR is a useful tool in studying the epidemiology of gonococcal infection due to plasmid-mediated resistant isolates.

scholarly journals Ontogeny of erythropoietin gene expression in the sheep fetus: effect of dexamethasone at 60 days of gestation

Blood ◽  
1994 ◽  
Vol 84 (2) ◽  
pp. 460-466
Author(s):  
GB Lim ◽  
K Jeyaseelan ◽  
EM Wintour
Keyword(s):  
Gene Expression ◽  
Mrna Levels ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Fetal Plasma ◽  
Liver And Kidney ◽  
Polymerase Chain ◽  
High Level ◽  
A Site ◽  
Sheep Fetus

We have used competitive reverse transcription and polymerase chain reaction (RT/PCR) to compare the levels of erythropoietin (Epo) mRNA in the liver and kidneys of the sheep fetus at 60, 80, 100, 130, and 140 days of gestation (term = 145 to 150 days). The effect of dexamethasone infusion in the ewe on Epo gene expression in the 60-day fetus was also investigated. Epo mRNA levels were highest at 60 days of gestation, the earliest age studied, in both liver and kidney. In the liver, Epo mRNA expression declined as gestation proceeded. Kidney Epo mRNA was maintained at a high level until 100 days of gestation, declining significantly in the 130-day fetus (P < .01). Treatment of ewes carrying 60-day fetuses with 0.76 mg/h dexamethasone for 48 hours resulted in a significant decrease in fetal plasma Epo values and Epo mRNA levels in both the liver and kidney. In the dexamethasone-treated fetuses, Epo mRNA in the liver was 52% of control values (P < .05), and in the kidney, 33% of control (P < .001). The results suggest that the kidney may play a more important role as a site of Epo synthesis in the early gestation sheep fetus than previously thought. Glucocorticoids may have a role in the regulation of Epo gene expression.

scholarly journals GENETIC VARIATION AND RELATEDNESS AMONG HIGH YIELDING RICE VARIETIES (Oryza sativa L.) REVEALED BY RAPD MARKERS

2008 ◽  
Vol 21 (1) ◽  
pp. 07-14
Author(s):  
F. Easmin ◽  
M. S. Rahman ◽  
M. S. Islam ◽  
M. A. Samad ◽  
M. S. Alam
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Chain Reaction ◽  
Rice Varieties ◽  
Upgma Dendrogram ◽  
Polymerase Chain ◽  
High Level

Genetic variation is a principal concern for the plant breeders. Genetic variation and relationship among high yielding rice varieties viz. Binadhan 4, Binadhan 5, Binadhan 6, Binasail, BRRI dhan28 and BRRI dhan29 were analyzed using four decamer random primers. Polymerase Chain Reaction (PCR) amplified 22 RAPD markers, of which 18 (81.82%) were polymorphic. The proportion of polymorphic loci and the gene diversity values were 59.09% and 0.25 for the Binadhan 4; 59.09% and 0.21 for Binadhan 6; 54.55% and 0.23 for Binasail; 54.55% and 0.19 for BRRI dhan29; 50.00% and 0.19 for Binadhan 5 and 45.45% and 0.18 for BRRI dhan28, respectively. The coefficient of gene differentiation (Gst) across all loci was calculated as 0.35 reflecting the existence of high level of genetic variation among the six modern rice varieties. UPGMA dendrogram based on Nei’s genetic distance segregated the six high yielding rice varieties into two clusters: all four mutant varieties viz. Binadhan 4, Binadhan 5, Binadhan 6 and Binasail formed one cluster and two varieties of BRRI grown in boro season, BRRI dhan28 and BRRI dhan29 grouped together in another cluster. Among the mutants, two boro season varieties, developed from the same parent, Binadhan 5 and Binadhan 6 grouped together with genetic distance of 0.10. Therefore, RAPD offer a reliable method to evaluate genetic variation and relatedness among the high yielding rice varieties.DOI: http://dx.doi.org/10.3329/bjpbg.v21i1.17042

scholarly journals Cutaneous Leishmaniasis of Lip and Role of Polymerase Chain Reaction: A Case Report

2020 ◽  
Vol 58 (227) ◽  
Author(s):  
Niraj Parajuli ◽  
Srijan Shrestha ◽  
Krishna Das Manandhar ◽  
Anup Bastola
Keyword(s):  
Polymerase Chain Reaction ◽  
Cutaneous Leishmaniasis ◽  
Leishmania Donovani ◽  
Polymerase Chain Reaction Test ◽  
Molecular Testing ◽  
Chain Reaction ◽  
Chain Reactions ◽  
Reaction Test ◽  
Polymerase Chain ◽  
Chain Reaction Test

The diagnosis of cutaneous leishmaniasis is mostly confirmed by the identification of parasitein a skin smear or biopsy. However, this method may not always be sensitive enough to detectthe disease when parasitic load is low. Molecular test such as polymerase chain reactions canbe useful in such circumstances. Here, we report a case of cutaneous leishmaniasis diagnosedby a polymerase chain reaction test when both smear and biopsy failed to confirm the diagnosis.A 17-years-old female from mountainous district of Nepal, presented with a crusted plaqueover the upper lip for a duration of 6 months. Both skin smear and biopsy from the lesionfailed to demonstrate Leishmania parasite but a polymerase chain reaction test was positivefor Leishmania donovani. This case emphasizes on the importance of molecular testing suchas polymerase chain reaction when commonly performed diagnostics test fails to supportconfirmation of clinical diagnosis.

scholarly journals Qualitative and Quantitative Analysis of IDH1 Mutation in Progressive Gliomas by Allele-Specific qPCR and Western Blot Analysis

2019 ◽  
Vol 18 ◽  
pp. 153303381982839 ◽  
Author(s):  
Moritz Perrech ◽  
Lena Dreher ◽  
Gabriele Röhn ◽  
Pantelis Stavrinou ◽  
Boris Krischek ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Western Blot ◽  
Real Time ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Idh1 Mutation ◽  
World Health ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Health Organization

To date, diagnosis of IDH1 mutation is based on DNA sequencing and immunohistochemistry, methods limited in terms of sensitivity and ease of use. Recently, the diagnosis of IDH1 mutation by real-time polymerase chain reaction was introduced as an alternative method. In this study, real-time polymerase chain reaction was validated as a tool for detection of IDH1 mutation, and expression levels were analyzed for correlation with course of the disease. A total of 113 tumor samples were obtained intraoperatively from 84 patients with glioma having a diagnosis of diffuse glioma (World Health Organization II), anaplastic glioma (World Health Organization III), secondary glioblastoma ± chemotherapy, primary glioblastoma ± chemotherapy (World Health Organization IV). Tumor samples were snap frozen and processed for sectioning and RNA and protein isolation. Presence of IDH1 mutation was determined by DNA sequencing. Hereafter, quantitative expression of IDH1 messenger RNA was assessed using real-time polymerase chain reaction with specific primers for IDH1 mutation and –wt; protein expression was verified by Western Blot analysis and immunohistochemistry. Additionally, 19 samples of low-grade glioma and their consecutive high-grade glioma were analyzed at different time points of the disease. IDH1 mutation was identified in 63% of samples by DNA sequencing. In correlation with the real-time polymerase chain reaction results, a cutoff value was determined. Above this threshold, sensitivity and specificity of real-time polymerase chain reaction in detecting IDH1 mutation were 98% and 94%, respectively. Quantitative analysis revealed that IDH1 mutation expression is upregulated in secondary glioblastoma (mean ± standard error of mean: 3.52 ± 0.55) compared to lower grade glioma (II = 1.54 ± 0.22; III = 1.67 ± 0.23). In contrast, IDH1 wt expression is upregulated in all glioma grades (concentration >0.1) compared to control brain tissue (0.007 ± 0.0016). Western Blot analysis showed a high concordance to both sequencing and real-time polymerase chain reaction results in qualitative analysis of IDH1 mutation status (specificity 100% and sensitivity 100%). Moreover, semiquantitative protein expression analysis also showed higher expression levels of mutated IDH1 in secondary glioblastoma. In our study, real-time polymerase chain reaction and Western Blot analysis were found to be highly efficient methods in detecting IDH1 mutation in glioma samples. As cost-effective and time-saving methods, real-time polymerase chain reaction and Western Blot analysis may therefore play an important role in IDH1 mutation analysis in the future. IDH1 mutation expression level was found to correlate with the course of disease to a certain extent. Yet, clinical factors as recurrent disease or prior radiochemotherapy did not alter IDH1 mutation expression level.

scholarly journals A Polymerase Chain Reaction-Based Method to Specifically Detect Alternaria alternata Apple Pathotype (A. mali), the Causal Agent of Alternaria Blotch of Apple

2000 ◽  
Vol 90 (9) ◽  
pp. 973-976 ◽  
Author(s):  
R. D. Johnson ◽  
L. Johnson ◽  
K. Kohmoto ◽  
H. Otani ◽  
C. R. Lane ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Alternaria Alternata ◽  
Crucial Role ◽  
Chain Reaction ◽  
Alternaria Species ◽  
Apple Cultivars ◽  
Polymerase Chain ◽  
Alternaria Blotch ◽  
High Level ◽  
Host Specific Toxins

Alternaria alternata apple pathotype (previously A. mali) causes Alternaria blotch on susceptible apple cultivars through the production of a host-specific toxin, AM-toxin. Identification of some Alternaria species, especially those that produce host-specific toxins, has been extremely difficult due to a high level of variability which extends even to nonpathogenic isolates. We have recently cloned and characterized a gene (AMT) that plays a crucial role in AM-toxin biosynthesis and demonstrated that it is only present in isolates of A. alternata apple pathotype. Using primers designed for the AMT gene, we developed a polymerase chainreaction-based method to specifically detect AM-toxin producing isolates of A. alternata apple pathotype.

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