scholarly journals Nanopore sequencing for the screening of myeloid and lymphoid neoplasms with eosinophilia and rearrangement of PDGFRα, PDGFRβ, FGFR1 or PCM1-JAK2

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Simone Romagnoli ◽  
Niccolò Bartalucci ◽  
Francesca Gesullo ◽  
Manjola Balliu ◽  
Stefania Bonifacio ◽  
...  
Keyword(s):  
Diagnostic Accuracy ◽  
Whole Blood ◽  
Nanopore Sequencing ◽  
Gene Fusions ◽  
Clinical Phenotypes ◽  
Lymphoid Neoplasms ◽  
Heterogeneous Nature ◽  
Genomic Aberrations ◽  
Technical Challenges

AbstractEosinophilia represents a group of diseases with heterogeneous pathobiology and clinical phenotypes. Among the alterations found in primary Eosinophilia, gene fusions involving PDGFRα, PDGFRβ, FGFR1 or JAK2 represent the biomarkers of WHO-defined “myeloid and lymphoid neoplasms with eosinophilia”. The heterogeneous nature of genomic aberrations and the promiscuity of fusion partners, may limit the diagnostic accuracy of current cytogenetics approaches. To address such technical challenges, we exploited a nanopore-based sequencing assay to screen patients with primary Eosinophilia. The comprehensive sequencing approach described here enables the identification of genomic fusion in 60 h, starting from DNA purified from whole blood.

scholarly journals Diagnostic accuracy of a rapid whole-blood test for detection of Helicobacter pylori.

1997 ◽  
Vol 35 (10) ◽  
pp. 2695-2697 ◽  
Author(s):  
H Enroth ◽  
R Rigo ◽  
K Hultén ◽  
L Engstrand
Keyword(s):  
Helicobacter Pylori ◽  
Diagnostic Accuracy ◽  
Whole Blood ◽  
Blood Test

Common and variant gene fusions predict distinct clinical phenotypes in rhabdomyosarcoma.

1997 ◽  
Vol 15 (5) ◽  
pp. 1831-1836 ◽  
Author(s):  
K M Kelly ◽  
R B Womer ◽  
P H Sorensen ◽  
Q B Xiong ◽  
F G Barr
Keyword(s):  
Metastatic Disease ◽  
Fusion Gene ◽  
Gene Fusions ◽  
Event Free Survival ◽  
Free Survival ◽  
Clinical Phenotypes ◽  
Significant Difference ◽  
The Common ◽  
Polymerase Chain ◽  
Gene Status

PURPOSE We evaluated the clinical features of the common PAX3-FKHR and variant PAX7-FKHR gene fusions observed in rhabdomyosarcoma. PATIENTS AND METHODS Reverse-transcriptase polymerase chain reaction (RT-PCR) assays were used to detect the gene fusions in 34 cases of rhabdomyosarcoma. Clinical data were obtained retrospectively and compared with the molecular results. RESULTS The PAX3-FKHR and PAX7-FKHR gene fusions were present in tumors from 18 and 16 patients, respectively. The group with a PAX7-FKHR fusion was younger (P = .01) and presented more often with an extremity lesion (82% v 22%; P = .001). PAX7-FKHR tumors were more often localized than PAX3-FKHR tumors (P = .03). In patients with metastatic disease at diagnosis, the patterns were different: PAX7-FKHR patients had metastatic disease that involved only bone (n = 2) and distant nodes (n = 2), while the PAX3-FKHR group had multiple sites involved, including bone (n = 7), marrow (n = 7), lungs (n = 3), distant nodes (n = 2), skin (n = 1), and brain (n = 1). No significant difference in relapse rate was observed. A trend toward improved overall survival in the PAX7-FKHR group was noted (P = .09). Event-free survival for this PAX7-FKHR group was significantly longer (P = .04). CONCLUSION Our results suggest that the common PAX3-FKHR and the variant PAX7-FKHR fusions are associated with distinct clinical phenotypes. Identification of fusion gene status may be a useful diagnostic tool in rhabdomyosarcoma.

scholarly journals A Nanopore Sequencing–Based Assay for Rapid Detection of Gene Fusions

2019 ◽  
Vol 21 (1) ◽  
pp. 58-69 ◽  
Author(s):  
William R. Jeck ◽  
Jesse Lee ◽  
Hayley Robinson ◽  
Long P. Le ◽  
A. John Iafrate ◽  
...  
Keyword(s):  
Rapid Detection ◽  
Nanopore Sequencing ◽  
Gene Fusions

Common and Variant Gene Fusions Predict Distinct Clinical Phenotypes in Rhabdomyosarcoma

1998 ◽  
Vol 159 (3) ◽  
pp. 1098-1098
Author(s):  
K.M. Kelly ◽  
R.B. Womer ◽  
P.H.B. Sorensen ◽  
Q.-B. Xiong ◽  
F.G. Barr
Keyword(s):  
Gene Fusions ◽  
Clinical Phenotypes ◽  
Variant Gene

scholarly journals Comparison between B·R·A·H·M·S PCT direct, a new sensitive point-of-care testing device for rapid quantification of procalcitonin in emergency department patients and established reference methods – a prospective multinational trial

2016 ◽  
Vol 54 (4) ◽  
Author(s):  
Alexander Kutz ◽  
Pierre Hausfater ◽  
Michael Oppert ◽  
Murat Alan ◽  
Eva Grolimund ◽  
...  
Keyword(s):  
Emergency Department ◽  
Diagnostic Accuracy ◽  
Whole Blood ◽  
Point Of Care ◽  
Venous Blood ◽  
Reference Method ◽  
Point Of Care Test ◽  
Emergency Department Patients ◽  
Work Up

AbstractProcalcitonin (PCT) is increasingly being used for the diagnostic and prognostic work up of patients with suspected infections in the emergency department (ED). Recently, B·R·A·H·M·S PCT direct, the first high sensitive point-of-care test (POCT), has been developed for fast PCT measurement on capillary or venous blood samples.This is a prospective, international comparison study conducted in three European EDs. Consecutive patients with suspicion of bacterial infection were included. Duplicate determination of PCT was performed in capillary (fingertip) and venous whole blood (EDTA), and compared to the reference method. The diagnostic accuracy was evaluated by correlation and concordance analyses.Three hundred and three patients were included over a 6-month period (60.4% male, median age 65.2 years). The correlation between capillary or venous whole blood and the reference method was excellent: rThis study found a high diagnostic accuracy and a faster time to result of B·R·A·H·M·S PCT direct in the ED setting, allowing shortening time to therapy and a more wide-spread use of PCT.

Common and Variant Gene Fusions Predict Distinct Clinical Phenotypes in Rhabdomyosarcoma

1998 ◽  
pp. 1098
Author(s):  
K. M. Kelly ◽  
R. B. Womer ◽  
P. H. B. Sorensen ◽  
Q.-B. Xiong ◽  
F. G. Barr
Keyword(s):  
Gene Fusions ◽  
Clinical Phenotypes ◽  
Variant Gene

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

10.3791/59377 ◽  
2019 ◽  
Author(s):  
Andreas Mueller ◽  
Kerstin Fischer ◽  
Roland Suluku ◽  
Thomas Hoenen
Keyword(s):  
Whole Blood ◽  
Nanopore Sequencing

Evaluation of nanopore sequencing as a diagnostic tool for the rapid identification of Mycoplasma bovis from individual and pooled respiratory tract samples

2021 ◽  
Author(s):  
Jade Bokma ◽  
Nick Vereecke ◽  
Mathilde L. Pas ◽  
Laurens Chantillon ◽  
Marianne Vahl ◽  
...  
Keyword(s):  
Diagnostic Accuracy ◽  
Real Time ◽  
Diagnostic Tool ◽  
Real Time Pcr ◽  
Latent Class ◽  
Rapid Identification ◽  
Mycoplasma Bovis ◽  
Nanopore Sequencing ◽  
Convenience Sample ◽  
Pooled Samples

Rapid identification of Mycoplasma bovis infections in cattle is a key factor to guide antimicrobial therapy and biosecurity measures. Recently, nanopore sequencing became an affordable diagnostic tool for both clinically relevant viruses and bacteria, but the diagnostic accuracy for M. bovis identification is undocumented. Therefore, in this study nanopore sequencing was compared to rapid identification of M. bovis with MALDI-TOF MS (RIMM), and triplex real-time PCR in a Bayesian latent class model (BLCM) for M. bovis in bronchoalveolar lavage fluid (BALf) obtained from calves. In practice, pooling of samples is often used to save money, but the influence on diagnostic accuracy has not been described for M. bovis . Therefore, a convenience sample of 17 pooled samples containing 5 individual BALf samples per farm was analyzed as well. The results of the pooled samples were compared to the individual samples, to determine sensitivity (Se) and specificity (Sp). The BLCM showed a good Se (77.3%; 95% Credible Interval: 57.8%-92.8%) and high Sp (97.4%; 91.5%-99.7%) for nanopore sequencing compared to RIMM (Se: 93.0%; 76.8%-99.5%, Sp: 91.3; 82.5%-97.0%) and real-time PCR (Se: 94.6%; 89.7%-97.7%, Sp: 86.0%; 76.1-93.6%). Se and Sp of pooled analysis for M. bovis were 85.7% (95% confidence interval: 59.8-111.6%) and 90.0% (71.4-108.6%%) for nanopore sequencing and 100% (100%-100%) and 88.9% (68.4-109.4%) for RIMM, respectively. In conclusion, nanopore sequencing is a rapid, reliable tool for the identification of M. bovis . To reduce costs and increase the chance of M. bovis identification, pooling of 5 samples for nanopore sequencing and RIMM is possible.

scholarly journals USE OF 20 MINUTE WHOLE BLOOD CLOTTING TIME IN PATIENTS OF SNAKEBITE; AN EXPERIENCE FROM KOHAT, KHYBER PAKHTUNKHAH

2021 ◽  
Vol 71 (5) ◽  
pp. 1619-23
Author(s):  
Hammad Javed ◽  
Tariq Bashir ◽  
Atif Rauf ◽  
Syed Murtaza ◽  
Raja Jibran
Keyword(s):  
Diagnostic Accuracy ◽  
Snake Venom ◽  
Whole Blood ◽  
Blood Clotting ◽  
False Negative ◽  
False Negative Rate ◽  
Military Hospital ◽  
Clotting Time ◽  
Low Sensitivity ◽  
Blood Clotting Time

Objective: To study the diagnostic accuracy of 20-minute whole blood clotting time in hemotoxic snakebite. Study Design: Cross sectional validation study. Place and Duration of Study: Combined Military Hospital Kohat Pakistan, from Jul 2015 to Jun 2017. Methodology: Study included 52 patients who presented with the complaint of a snakebite. The data was recorded on predesigned proforma including clinical, laboratory features. All the patients were kept indoor for observation for a minimum of 72 hours from the time of presentation. Results: The study showed that males were more affected with age group between 20-50 years. Most common presenting features were local swelling 33 (71%) and pain and most common snakebite type was hemotoxic 33 (71%). The 20-minute whole blood clotting time was found to have low sensitivity (61%) and specificity (58%). A significant association was found between the dose of anti-snake venom and severity of coagulopathy (p<0.001), respiratory failure (p<0.001) and development of side effects due to anti snake venom (p<0.001). The mortality rate was 6.5% and was significantly related to age of the victims (p=0.003). The diagnostic accuracy of 20-minute whole blood clotting time was 60.25%. Conclusion: The use of 20-minute whole blood clotting time can not only be misleading but also a source of delay in administering anti snake venom given the low sensitivity and specificity and high false negative rate.

scholarly journals A comparison between two different in vitro basophil activation tests for gluten- and cow’s milk protein sensitivity in irritable bowel syndrome (IBS)-like patients

2013 ◽  
Vol 51 (6) ◽  
Author(s):  
Antonio Carroccio ◽  
Ignazio Brusca ◽  
Pasquale Mansueto ◽  
Alberto D’alcamo ◽  
Maria Barrale ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Diagnostic Accuracy ◽  
Whole Blood ◽  
Elimination Diet ◽  
Basophil Activation ◽  
The Other ◽  
Cow’S Milk ◽  
Cow's Milk ◽  
Irritable Bowel

AbstractThe diagnosis of food hypersensitivity (FH) in adult patients with gastrointestinal symptoms, beyond the immediate IgE-mediated clinical manifestations, is very often difficult. The aims of our study were to: 1) evaluate the frequency of FH in patients with irritable bowel syndrome (IBS)-like clinical presentation; and 2) compare the diagnostic accuracy of two different methods of in vitro basophil activation tests.Three hundred and five patients (235 females, age range 18–66 years) were included and underwent a diagnostic elimination diet and successive double-blind placebo-controlled (DBPC) challenges. Two different methods of in vitro basophil activation tests (BAT) (CD63 expression after in vitro wheat or cow’s milk proteins stimulation) were evaluated: one was performed on separated leukocytes, and the other on whole blood.Ninety patients of the 305 studied (29.5%) were positive to the challenges and were diagnosed as suffering from FH. BAT on separate leukocytes showed a sensitivity of 86% and a specificity of 91% in FH diagnosis. BAT on whole blood showed a sensitivity of 15%–20% and a specificity of 73% in FH diagnosis (p<0.0001 compared to the other method).About one third of the IBS patients included in the study were suffering from FH and were cured on the elimination diet. The BAT based on CD63 detection on whole blood samples did not work in FH diagnosis and showed a significantly lower sensitivity, specificity and diagnostic accuracy than the assay based on separated leukocytes.

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