Management and quality assurance in a molecular diagnostic laboratory (oncology): scope and challenges

2019 ◽  
Vol 07 ◽  
Author(s):  
Rekha Chaubey
Keyword(s):  
Quality Assurance ◽  
Molecular Diagnostic ◽  
Diagnostic Laboratory

Frequency of molecular detection of equine coronavirus in faeces and nasal secretions in 277 horses with acute onset of fever

2019 ◽  
Vol 184 (12) ◽  
pp. 385-385 ◽  
Author(s):  
Nicola Pusterla ◽  
Kaitlyn James ◽  
Samantha Mapes ◽  
Farifield Bain
Keyword(s):  
Clinical Signs ◽  
Acute Onset ◽  
Molecular Diagnostic ◽  
Nasal Discharge ◽  
Respiratory Pathogens ◽  
Sample Collection ◽  
Diagnostic Laboratory ◽  
Study Results ◽  
Streptococcus Equi ◽  
Nasal Secretions

ContextDue to the inconsistent development of enteric signs associated with ECoV infection in adult horses, many practitioners collect nasal secretions rather than feces for the molecular diagnostic work-up of such horses.Main conclusionECoV infection should be considered in horses presenting with acute onset of fever, especially when nasal discharge is absent as one of the cardinal clinical sign.ApproachA total of 277 adult horses with acute onset of fever were enrolled in this study. Feces were tested for ECoV and nasal secretions for common respiratory pathogens (equine herpesvirus (EHV)-1, EHV-4, equine influenza virus (EIV), equine rhinitis viruses (ERVs) and Streptococcus equi ss. equi) and ECoV by qPCR. Each submission was accompanied by a questionnaire requesting information pertaining to signalment, use, recent transportation, number of affected horses on the premise and presence of clinical signs at the time of sample collection.ResultsThe total number of horses testing qPCR-positive for ECoV in feces was 20 (7.2%), 4 of which also tested qPCR-positive for ECoV in nasal secretions. In the same population 9.0% of horses tested qPCR-positive for EHV-4, 6.1% for EIV, 4.3% for Streptococcus equi ss. equi, 3.2% for ERVs and 0.7% for EHV-1. Draft horses, pleasure use, multiple horses affected on a premise and lack of nasal discharge were significantly associated with ECoV qPCR-positive horses.InterpretationThe present study results showed that 7.2% of horses with acute onset of fever tested qPCR-positive for ECoV in feces, highlighting the importance of testing such horses for ECoV in feces. The various prevalence factors associated with ECoV qPCR-positive status likely relate to the high infectious nature of ECoV and breed-specific differences in management and husbandry practices.Significance of findingsECoV infection should be suspected and tested for in horses presenting with acute onset of fever, lethargy and anorexia with no respiratory signs. A two-step approach should be consider in which respiratory secretions and feces should be collected from such horses and submitted to a diagnostic laboratory. If the respiratory secretions test negative by qPCR for a panel of respiratory pathogens, feces already submitted to the laboratory should be tested for ECoV.

Phenotypes Associated with 16p11.2 Copy Number Gains and Losses at a Single Institution

2020 ◽  
Vol 51 (6) ◽  
pp. 642-648
Author(s):  
Caleb Chu ◽  
Haotian Wu ◽  
Fangling Xu ◽  
Joseph W Ray ◽  
Allison Britt ◽  
...  
Keyword(s):  
Behavioral Problems ◽  
Copy Number ◽  
Copy Number Variations ◽  
Molecular Diagnostic ◽  
Segmental Duplications ◽  
Diagnostic Laboratory ◽  
University Of Texas ◽  
Recombination Hotspots ◽  
Study Results ◽  
Gains And Losses

Abstract Chromosome 16p11.2 is one of the susceptible sites for recurrent copy number variations (CNVs) due to flanking near-identical segmental duplications. Five segmental duplications, named breakpoints 1 to 5 (BP1–BP5), have been defined as recombination hotspots within 16p11.2. Common CNVs on 16p11.2 include a proximal ~593 kb between BP4 and BP5, and a distal ~220 kb between BP2 and BP3. We performed a search for patients carrying 16p11.2 CNVs, as detected using chromosome microarray (CMA), in the Molecular Diagnostic Laboratory at the University of Texas Medical Branch (UTMB), in Galveston. From March 2013 through April 2018, a total of 1200 CMA results were generated for germline testing, and 14 patients tested positive for 16p11.2 CNVs, of whom 7 had proximal deletion, 2 had distal deletion, 4 had proximal duplication, and 1 had distal duplication. Herein, we provide detailed phenotype data for these patients. Our study results show that developmental delay, abnormal body weight, behavioral problems, and hypotonia are common phenotypes associated with 16p11.2 CNVs.

scholarly journals A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Aniela Wozniak ◽  
Ariel Cerda ◽  
Catalina Ibarra-Henríquez ◽  
Valentina Sebastian ◽  
Grace Armijo ◽  
...  
Keyword(s):  
Rna Extraction ◽  
Molecular Diagnostic ◽  
Nasopharyngeal Swab ◽  
Diagnostic Laboratory ◽  
Public Health Decision ◽  
Health Decision Making ◽  
Health Decision ◽  
Analytical Step ◽  
Commercial Kits ◽  
Novel Coronavirus

Abstract The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.

BRAF mutation testing with a novel, rapid, fully automated molecular diagnostics prototype platform.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 11086-11086
Author(s):  
Helen J. Huang ◽  
Benoit Devogelaere ◽  
Gerald Steven Falchook ◽  
Siqing Fu ◽  
Laura S. Angelo ◽  
...  
Keyword(s):  
Molecular Diagnostics ◽  
Braf Mutation ◽  
High Sensitivity ◽  
Complete Response ◽  
Molecular Diagnostic ◽  
Diagnostic Systems ◽  
Braf Mutations ◽  
Diagnostic Laboratory ◽  
Mek Inhibitors ◽  
Hands On

11086 Background: Mutations in the BRAF gene provide actionable targets for cancer therapy in melanoma and other tumor types. Novel, fast, and accurate diagnostic systems are needed for further implementation of personalized therapy. Methods: The molecular diagnostics (MDx) prototype platform (Biocartis, Mechelen, Belgium) is a fully integrated real-time PCR-based system with high sensitivity (1% mutant in wild-type [wt] background) and fast turnaround time (< 90 minutes), which requires no sample preparation and <2 min hands-on time. Archival formalin-fixed paraffin-embedded tumor samples (1 to 5 shavings of 10 µm) from patients (pts) with advanced cancers previously tested for V600 BRAF mutations in a CLIA-certified Molecular Diagnostic Laboratory (PCR-based sequencing or Sequenom MassARRAY) were tested for BRAF V600 mutations using the MDx prototype platform. Concordance between methods and treatment outcomes with BRAF/MEK inhibitors were analyzed. Results: Forty-seven pts (melanoma, n=26; colorectal, n=8; papillary thyroid, n=3; other cancers, n=10) with available tissue and CLIA laboratory BRAF results were selected (BRAF V600 mutant, n=37; BRAF V600 wt, n=10). Of the 40 pts for whom the same tissue block was used for MDx and CLIA, BRAF status was concordant in 38 (95%; kappa 0.87; 95% CI 0.69-1.05) of them. BRAF status by MDx was discordant with CLIA in 3 of 47 cases (mutant by CLIA, but not MDx); one discrepant case contained a different mutation subtype (resp. V600E vs. V600K/R), and in another case different tissue blocks were used for MDx vs. CLIA testing. Of 34 pts with BRAF mutations detected by MDx, 28 were treated on protocols (on the basis of the CLIA results) with BRAF/MEK inhibitors and 8 (29%) had a partial (n=7) or complete response (n=1). Of interest, 1 pt with prostate cancer (V600E by CLIA, wt by MDx) received a BRAF/MEK inhibitor and did not respond. Detailed patient characteristics, mutation types and discrepancy analysis will be presented. Conclusions: The BRAF V600 mutation MDx prototype assay is a fast (turn-around time about 1.5 hours) and simple (<2 minutes hands-on time) test to determine BRAF mutation status with 95% concordance with CLIA laboratory if identical tissue blocks are used.

scholarly journals Laboratory Diagnostic Techniques for Entamoeba Species

2007 ◽  
Vol 20 (3) ◽  
pp. 511-532 ◽  
Author(s):  
R. Fotedar ◽  
D. Stark ◽  
N. Beebe ◽  
D. Marriott ◽  
J. Ellis ◽  
...  
Keyword(s):  
Entamoeba Histolytica ◽  
Diagnostic Tests ◽  
New Technologies ◽  
Specific Antigen ◽  
Gastrointestinal Symptoms ◽  
Public Health Problem ◽  
Intestinal Lumen ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Diagnostic Laboratory

SUMMARY The genus Entamoeba contains many species, six of which (Entamoeba histolytica, Entamoeba dispar, Entamoeba moshkovskii, Entamoeba polecki, Entamoeba coli, and Entamoeba hartmanni) reside in the human intestinal lumen. Entamoeba histolytica is the causative agent of amebiasis and is considered a leading parasitic cause of death worldwide in humans. Although recent studies highlight the recovery of E. dispar and E. moshkovskii from patients with gastrointestinal symptoms, there is still no convincing evidence of a causal link between the presence of these two species and the symptoms of the host. New approaches to the identification of E. histolytica are based on detection of E. histolytica-specific antigen and DNA in stool and other clinical samples. Several molecular diagnostic tests, including conventional and real-time PCR, have been developed for the detection and differentiation of E. histolytica, E. dispar, and E. moshkovskii in clinical samples. The purpose of this review is to discuss different methods that exist for the identification of E. histolytica, E. dispar, and E. moshkovskii which are available to the clinical diagnostic laboratory. To address the need for a specific diagnostic test for amebiasis, a substantial amount of work has been carried out over the last decade in different parts of the world. The molecular diagnostic tests are increasingly being used for both clinical and research purposes. In order to minimize undue treatment of individuals infected with other species of Entamoeba such as E. dispar and E. moshkovskii, efforts have been made for specific diagnosis of E. histolytica infection and not to treat based simply on the microscopic examination of Entamoeba species in the stool. The incorporation of many new technologies into the diagnostic laboratory will lead to a better understanding of the public health problem and measures to control the disease.

scholarly journals Genetic Landscape of Myeloproliferative Neoplasms with an Emphasis on Molecular Diagnostic Laboratory Testing

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1158
Author(s):  
Arti Easwar ◽  
Alexa J. Siddon
Keyword(s):  
Laboratory Testing ◽  
Myeloproliferative Neoplasms ◽  
Philadelphia Chromosome ◽  
Chromatin Modification ◽  
Molecular Diagnostic ◽  
Diagnostic Laboratory ◽  
Hematopoietic Stem ◽  
Chronic Myeloproliferative Neoplasms ◽  
Molecular Alterations ◽  
Molecular Landscape

Chronic myeloproliferative neoplasms (MPNs) are hematopoietic stem cell neoplasms with driver events including the BCR-ABL1 translocation leading to a diagnosis of chronic myeloid leukemia (CML), or somatic mutations in JAK2, CALR, or MPL resulting in Philadelphia-chromosome-negative MPNs with constitutive activation of the JAK-STAT signaling pathway. In the Philadelphia-chromosome-negative MPNs, modern sequencing panels have identified a vast molecular landscape including additional mutations in genes involved in splicing, signal transduction, DNA methylation, and chromatin modification such as ASXL1, SF3B1, SRSF2, and U2AF1. These additional mutations often influence prognosis in MPNs and therefore are increasingly important for risk stratification. This review focuses on the molecular alterations within the WHO classification of MPNs and laboratory testing used for diagnosis.

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