scholarly journals Case Report: Next-Generation Sequencing in Diagnosis of Atypical Aspiration Pneumonia

2022 ◽  
Vol 9 ◽  
Author(s):  
Quan Zhang ◽  
Wei Xu ◽  
Fei Peng ◽  
Si Lei ◽  
Yanjun Zhong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Aspiration Pneumonia ◽  
Virus Disease ◽  
Correct Diagnosis ◽  
Ground Glass Opacity ◽  
Clinical History ◽  
Ground Glass ◽  
Careful Examination ◽  
Next Generation ◽  
Generation Sequencing

Since the pandemic of Corona Virus Disease 2019 (COVID-19), especially in the centers most affected, the symptoms such as fever, cough, myalgia or fatigue, and radioactive signs typically related to COVID-19 like ground-glass opacity (GGO) often distract the attention of physicians from other diseases. Aspiration pneumonia and COVID-19 share similarities in some aspects. There may be risk of misdiagnosis in the case of considering radiological patterns of pneumonia. Early diagnosis and treatment often greatly improve prognosis. We herein reported a case of 40-year-old patient who underwent chest CT scan with the discovery of ground-glass opacity, intralobular reticular opacity and interlobular septal thickening, consolidation, and air bronchogram sign, which were mainly located in the middle and upper lobes of the right lung. It was considered to be infection related pneumonia based on the negative reverse transcription-PCR (RT-PCR) result of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The next-generation sequencing (NGS) of bronchoalveolar lavage fluid (BALF) was performed and detected nucleic acid sequences of Klebsiella sp. Consequently, the patient accepted sensitive intravenous antibiotics therapy for 13 days and had a remarkable clinical and radiological improvement. His case was followed up through imaging procedures. Because of possible radiologic and clinical similarities between aspiration and COVID-19 pneumonia, COVID-19 can be of some value in proposing a differential diagnosis of aspiration pneumonia. Clinicians could suggest a correct diagnosis by careful examination of the CT images together with attention to the clinical history and judicious utilization of NGS, especially.

P0077A NEW MUTATION OF DNAJB11 AS A CAUSE OF CYSTIC KYDNEY DISEASE: THE FOURTH GENE OF ADPKD

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Isabella Pisani ◽  
Marco Allinovi ◽  
Viviana Palazzo ◽  
Micaela Gentile ◽  
Sabrina Giglio ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Kidney Disease ◽  
Autosomal Dominant ◽  
Renal Cysts ◽  
Clinical History ◽  
Pancreatic Cysts ◽  
Next Generation ◽  
Polycystic Kidney ◽  
New Mutation ◽  
Generation Sequencing

Abstract Background and Aims Monogenic inherited diseases are an underestimated but important cause of chronic kidney disease (CKD). Despite the increasing knowledge about their inheritance, they are identified in fewer than 10% of CKD patients. Among monogenic causes of CKD, polycystic kidney diseases (PKD) represent a group of disorders with a clinical and genetic heterogeneity and a variable phenotype (from early manifestations during pregnancy or childhood to the absence of clinical manifestations until adulthood). We here present a PKD family with 5 members displaying the disease (Figure 1). Method We revised patients clinical history, laboratory data and imaging exams. An accurate family history was recovered. Blood samples were collected from living patients to perform an exome analysis using next generation sequencing to analyze all possible genes involved in PKD. Results Each patient presented a clinical history of nephrolithiasis, a variable degree of CKD (from normal kidney function to renal transplant), urinary and blood parameters compatible with distal renal tubular acidosis (hypercalciuria, low urinary citrate excretion and hypokalemia). Imaging exams showed several renal cysts in the medulla or at the cortico-medullary junction with intracystic calcifications (Figure 2). Some patients displayed also large cortical renal cysts and also hepatic and pancreatic cysts. The genetic analysis performed using next generation sequencing in four patients showed a new mutation on the gene DNAJB11; the mutation introduced a stop codon and was identified as pathogenic by prediction programs. It was present in heterozygosity in all subjects and had an autosomal dominant pattern of inheritance. Conclusion DNAJB11 mutations were reported as a cause of PKD for the first time in 2018 by Cornec-Le-Gall and colleagues. The nephropathy derived from these mutations need to be differentiated from ADPKD (autosomal dominant polycystic kidney disease), from ADTKD (autosomal dominant tubulointerstitial kidney disease) and from medullary sponge kidney. DNAJB11 encodes a co-chaperone of the endoplasmic reticulum (ER) also called ERdj3. It is part of the HSP40 protein family and plays a central role in both intracellular and extracellular proteomic homeostasis (proteostasis). In the intracellular compartment it acts as a co-chaperone in the pathway of the unfolded protein response (UPR) in which it binds misfolded proteins which have to be secreted and activates BiP an HSP70 of ER whose function is to correct the misfolding. In the kidney it is mainly expressed in the thick ascending limb of Henle’s loop, in the distal tubule and in the collecting duct justifying the clinical presentation of nephropathy and differentiating the disease from ADPKD (Figure 3).

scholarly journals Metagenomic Next-Generation Sequencing of the 2014 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Tony Li ◽  
Placide Mbala-Kingebeni ◽  
Samia N. Naccache ◽  
Julien Thézé ◽  
Jerome Bouquet ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ebola Virus ◽  
Democratic Republic ◽  
Clinical Symptoms ◽  
Virus Disease ◽  
Hemorrhagic Fever ◽  
Next Generation ◽  
Qrt Pcr ◽  
Republic Of The Congo ◽  
Generation Sequencing

ABSTRACT We applied metagenomic next-generation sequencing (mNGS) to detect Zaire Ebola virus (EBOV) and other potential pathogens from whole-blood samples from 70 patients with suspected Ebola hemorrhagic fever during a 2014 outbreak in Boende, Democratic Republic of the Congo (DRC) and correlated these findings with clinical symptoms. Twenty of 31 patients (64.5%) tested in Kinshasa, DRC, were EBOV positive by quantitative reverse transcriptase PCR (qRT-PCR). Despite partial degradation of sample RNA during shipping and handling, mNGS followed by EBOV-specific capture probe enrichment in a U.S. genomics laboratory identified EBOV reads in 22 of 70 samples (31.4%) versus in 21 of 70 (30.0%) EBOV-positive samples by repeat qRT-PCR (overall concordance = 87.1%). Reads from Plasmodium falciparum (malaria) were detected in 21 patients, of which at least 9 (42.9%) were coinfected with EBOV. Other positive viral detections included hepatitis B virus (n = 2), human pegivirus 1 (n = 2), Epstein-Barr virus (n = 9), and Orungo virus (n = 1), a virus in the Reoviridae family. The patient with Orungo virus infection presented with an acute febrile illness and died rapidly from massive hemorrhage and dehydration. Although the patient’s blood sample was negative by EBOV qRT-PCR testing, identification of viral reads by mNGS confirmed the presence of EBOV coinfection. In total, 9 new EBOV genomes (3 complete genomes, and an additional 6 ≥50% complete) were assembled. Relaxed molecular clock phylogenetic analysis demonstrated a molecular evolutionary rate for the Boende strain 4 to 10× slower than that of other Ebola lineages. These results demonstrate the utility of mNGS in broad-based pathogen detection and outbreak surveillance.

scholarly journals Case Report: Next Generation Sequencing in Clinical Practice–A Real Tool for Ending the Protracted Diagnostic Odyssey

2022 ◽  
Vol 8 ◽  
Author(s):  
Alena S. Limonova ◽  
Alexandra I. Ershova ◽  
Alexey N. Meshkov ◽  
Anna V. Kiseleva ◽  
Mikhail G. Divashuk ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Correct Diagnosis ◽  
Clinical Manifestations ◽  
Disease Diagnosis ◽  
Next Generation ◽  
Lipid Clinic ◽  
Cholesterol Levels ◽  
Premature Cardiovascular Disease ◽  
Great Heterogeneity ◽  
Generation Sequencing

We reported a case of sitosterolemia, which is a rare genetic disease, characterized by increased plant sterol absorption and great heterogeneity of clinical manifestations. Our patient was initially referred to the lipid clinic due to high cholesterol levels and premature cardiovascular disease. Diagnosis of familial hypercholesterolemia was established in accordance with the Dutch Lipid Clinic Network criteria. Next-generation sequencing was later performed, which revealed a nonsense mutation in the ABCG8 gene, which led to the diagnosis of sitosterolemia. The aim of our report is to demonstrate, how genetic testing helped to make the correct diagnosis and to explain many of the patient's health problems, which etiology remained unclear for many years.

Labordiagnostik bei gastrointestinalen Tumoren

2020 ◽  
Vol 11 (05) ◽  
pp. 232-238
Author(s):  
Marcus Kleber
Keyword(s):  
Next Generation Sequencing ◽  
Kolorektales Karzinom ◽  
Next Generation ◽  
Generation Sequencing

ZUSAMMENFASSUNGDas kolorektale Karzinom (KRK) ist einer der häufigsten malignen Tumoren in Deutschland. Einer frühzeitigen Diagnostik kommt große Bedeutung zu. Goldstandard ist hier die Koloskopie. Die aktuelle S3-Leitlinie Kolorektales Karzinom empfiehlt zum KRK-Screening den fäkalen okkulten Bluttest. Für das Monitoring von Patienten vor und nach Tumorresektion werden die Messung des Carcinoembryonalen Antigens (CEA) und der Mikrosatellitenstabilität empfohlen. Für die Auswahl der korrekten Chemotherapie scheint derzeit eine Überprüfung des Mutationsstatus, mindestens des KRAS-Gens und des BRAF-Gens, sinnvoll zu sein. Eine Reihe an neuartigen Tumormarkern befindet sich momentan in der Entwicklung, hat jedoch noch nicht die Reife für eine mögliche Anwendung in der Routinediagnostik erreicht. Den schnellsten Weg in die breite Anwendung können Next-Generation-Sequencing-basierte genetische Tests finden.

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