What Is the Role of Molecular Techniques for Detection of Pathogen Deoxyribonucleic Acid (DNA) (Polymerase Chain Reaction [PCR] or Next-Generation Sequencing) in Patients With Infected Total Ankle Arthroplasty (TAA)?

2019 ◽  
Vol 40 (1_suppl) ◽  
pp. 29S-31S
Author(s):  
Khaled Emara ◽  
Amiethab Aiyer ◽  
Ryan Rogero
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Evidence ◽  
Molecular Techniques ◽  
Total Ankle Arthroplasty ◽  
Next Generation ◽  
Level Of Evidence ◽  
Ankle Arthroplasty ◽  
Polymerase Chain ◽  
Generation Sequencing

Recommendation: Molecular techniques, particularly next-generation sequencing and the Ibis T5000 technology, have the potential to be used as an important adjunct in the diagnosis of bacterial infection following total ankle arthroplasty (TAA), although sufficient clinical evidence is lacking. Level of Evidence: Limited. Delegate Vote: Agree: 100%, Disagree: 0%, Abstain: 0% (Unanimous, Strongest Consensus)

scholarly journals The Evolving Role of Next-Generation Sequencing in Screening and Diagnosis of Hemoglobinopathies

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahlem Achour ◽  
Tamara T. Koopmann ◽  
Frank Baas ◽  
Cornelis L. Harteveld
Keyword(s):  
Next Generation Sequencing ◽  
Large Scale ◽  
Genetic Diseases ◽  
Molecular Techniques ◽  
Added Value ◽  
Monogenic Disease ◽  
Clinical Genetics ◽  
Next Generation ◽  
Generation Sequencing

During the last few years, next-generation sequencing (NGS) has undergone a rapid transition from a research setting to a clinical application, becoming the method of choice in many clinical genetics laboratories for the detection of disease-causing variants in a variety of genetic diseases involving multiple genes. The hemoglobinopathies are the most frequently found Mendelian inherited monogenic disease worldwide and are composed of a complex group of disorders frequently involving the inheritance of more than one abnormal gene. This review aims to present the role of NGS in both screening and pre- and post-natal diagnostics of the hemoglobinopathies, and the added value of NGS is discussed based on the results described in the literature. Overall, NGS has an added value in large-scale high throughput carrier screening and in the complex cases for which common molecular techniques have some inadequacies. It is proven that the majority of thalassemia cases and Hb variants can be diagnosed using routine analysis involving a combined approach of hematology, hemoglobin separation, and classical DNA methods; however, we conclude that NGS can be a useful addition to the existing methods in the diagnosis of these disorders.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals Environmental Surveillance through Next-Generation Sequencing to Unveil the Diversity of Human Enteroviruses beyond the Reported Clinical Cases

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 120
Author(s):  
Andrés Lizasoain ◽  
Daiana Mir ◽  
Gisella Masachessi ◽  
Adrián Farías ◽  
Nélida Rodríguez-Osorio ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Echovirus 30 ◽  
Coxsackievirus B4 ◽  
Important Region ◽  
Enterovirus A71 ◽  
Wastewater Samples ◽  
Valuable Role ◽  
Generation Sequencing

The knowledge about circulation of Human Enteroviruses (EVs) obtained through medical diagnosis in Argentina is scarce. Wastewater samples monthly collected in Córdoba, Argentina during 2011–2012, and then in 2017–2018 were retrospectively studied to assess the diversity of EVs in the community. Partial VP1 gene was amplified by PCR from wastewater concentrates, and amplicons were subject of next-generation sequencing and genetic analyses. There were 41 EVs detected, from which ~50% had not been previously reported in Argentina. Most of the characterized EVs (60%) were detected at both sampling periods, with similar values of intratype nucleotide diversity. Exceptions were enterovirus A71, coxsackievirus B4, echovirus 14, and echovirus 30, which diversified in 2017–2018. There was a predominance of types from EV-C in 2017–2018, evidencing a common circulation of these types throughout the year in the community. Interestingly, high genetic similarity was evidenced among environmental strains of echovirus 30 circulating in 2011–2012 and co-temporal isolates obtained from patients suffering aseptic meningitis in different locations of Argentina. This study provides an updated insight about EVs circulating in an important region of South America, and suggests a valuable role of wastewater-based epidemiology in predicting outbreaks before the onset of cases in the community.

scholarly journals Next generation sequencing of RB1gene for the molecular diagnosis of ethnic minority with retinoblastoma in Yunnan

2020 ◽  
Author(s):  
Huaiyu Gu ◽  
Zhen Zhang ◽  
Yi-shuang Xiao ◽  
Ru Shen ◽  
Hong-chao Jiang ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Next Generation Sequencing ◽  
Low Income ◽  
Eastern China ◽  
Low Income Countries ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Bioinformatics Pipeline ◽  
Generation Sequencing

Abstract Background: Retinoblastoma is a rare intraocular malignancy and typically initiated by inactivating biallelic mutations of RB1 gene. Each year, ~8,000 children worldwide are diagnosed for retinoblastoma. In high-income countries, patient survival is over 95% while low-income countries is ~30%.If disease is diagnosed early and treated in centers specializing in retinoblastoma, the survival might exceed 95% and many eyes could be safely treated and support a lifetime of good vision. In China, approximate 1,100 newly diagnosed cases are expected annually and 28 hospitals covering 25 provinces established centers classified by expertise and resources for better treatment options and follow-up. Comparing with other province of eastern China, Yunnan province is remote geographically. This might result that healthcare staff have low awareness of the role of genetic testing in management and screening in families.Methods: The patients with retinoblastoma were selected in Yunnan. DNA from blood was used for targeted gene sequencing. Then, an in-house bioinformatics pipeline was done to detect both single nucleotide variants and small insertions/deletions. The pathogenic mutations were identified and further confirmed by conventional methods and cosegregation in families.Results: Using our approach, targeted next generation sequencing was used to detect the mutation of these 12 probands. Bioinformatic predictions showed that nine mutations were found in our study and four were novel pathogenic variants in these nine mutations.Conclusions: It’s the first report to describe RB1 mutations in Yunnan children with retinoblastoma. This study would improve role of genetic testing for management and family screening.

scholarly journals Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

2021 ◽  
Vol 11 ◽  
Author(s):  
Emilie Darrigues ◽  
Benjamin W. Elberson ◽  
Annick De Loose ◽  
Madison P. Lee ◽  
Ebonye Green ◽  
...  
Keyword(s):  
Brain Tumor ◽  
Next Generation Sequencing ◽  
Precision Medicine ◽  
Critical Role ◽  
First Year ◽  
Histopathological Diagnosis ◽  
Next Generation ◽  
Cancer Predisposition Syndrome ◽  
Generation Sequencing

Neuro-oncology biobanks are critical for the implementation of a precision medicine program. In this perspective, we review our first year experience of a brain tumor biobank with integrated next generation sequencing. From our experience, we describe the critical role of the neurosurgeon in diagnosis, research, and precision medicine efforts. In the first year of implementation of the biobank, 117 patients (Female: 62; Male: 55) had 125 brain tumor surgeries. 75% of patients had tumors biobanked, and 16% were of minority race/ethnicity. Tumors biobanked were as follows: diffuse gliomas (45%), brain metastases (29%), meningioma (21%), and other (5%). Among biobanked patients, 100% also had next generation sequencing. Eleven patients qualified for targeted therapy based on identification of actionable gene mutations. One patient with a hereditary cancer predisposition syndrome was also identified. An iterative quality improvement process was implemented to streamline the workflow between the operating room, pathology, and the research laboratory. Dedicated tumor bank personnel in the department of neurosurgery greatly improved standard operating procedure. Intraoperative selection and processing of tumor tissue by the neurosurgeon was integral to increasing success with cell culture assays. Currently, our institutional protocol integrates standard histopathological diagnosis, next generation sequencing, and functional assays on surgical specimens to develop precision medicine protocols for our patients. This perspective reviews the critical role of neurosurgeons in brain tumor biobank implementation and success as well as future directions for enhancing precision medicine efforts.

Characterizing the Microbiome of the Contracted Breast Capsule Using Next Generation Sequencing

2020 ◽  
Author(s):  
Jonathan Cook ◽  
Casey J Holmes ◽  
Roger Wixtrom ◽  
Martin I Newman ◽  
Jason N Pozner
Keyword(s):  
Next Generation Sequencing ◽  
Capsular Contracture ◽  
Bacterial Species ◽  
Fungal Species ◽  
Augmentation Mammoplasty ◽  
Next Generation ◽  
Level Of Evidence ◽  
Cutibacterium Acnes ◽  
Microbial Dna ◽  
Generation Sequencing

Abstract Background Recent work suggests that bacterial biofilms play a role in capsular contracture (CC). However, traditional culture techniques provide only a limited understanding of the bacterial communities present within the contracted breast. Next generation sequencing (NGS) represents an evolution of polymerase chain reaction technology that can sequence all DNA present in a given sample. Objectives The aim of this study was to utilize NGS to characterize the bacterial microbiome of the capsule in patients with CC following cosmetic breast augmentation. Methods We evaluated 32 consecutive patients with Baker grade III or IV CC following augmentation mammoplasty. Specimens were obtained from all contracted breasts (n = 53) during capsulectomy. Tissue specimens from contracted capsules as well as intraoperative swabs of the breast capsule and implant surfaces were obtained. Samples were sent to MicroGenDX Laboratories (Lubbock, TX) for NGS. Results Specimens collected from 18 of 32 patients (56%) revealed the presence of microbial DNA. The total number of positive samples was 22 of 53 (42%). Sequencing identified a total of 120 unique bacterial species and 6 unique fungal species. Specimens with microbial DNA yielded a mean [standard deviation] of 8.27 [4.8] microbial species per patient. The most frequently isolated species were Escherichia coli (25% of all isolates), Diaphorobacter nitroreducens (12%), Cutibacterium acnes (12%), Staphylococcus epidermidis (11%), fungal species (7%), and Staphylococcus aureus (6%). Conclusions NGS enables characterization of the bacterial ecosystem surrounding breast implants in unprecedented detail. This is a critical step towards understanding the role this microbiome plays in the development of CC. Level of Evidence: 4

scholarly journals Identification of an Emergent Pathogen, Bartonella vinsonii, Using Next-Generation Sequencing in a Patient With Culture-Negative Endocarditis

2020 ◽  
Author(s):  
Rachel D Downey ◽  
Susan M Russo ◽  
Sarmistha B Hauger ◽  
Donald K Murphey ◽  
Grace Marx ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Immunohistochemical Staining ◽  
Next Generation ◽  
Chain Reaction ◽  
Valve Tissue ◽  
Free Dna ◽  
Emergent Pathogen ◽  
Polymerase Chain ◽  
Culture Negative ◽  
Generation Sequencing

Abstract Diagnosis and treatment of culture negative endocarditis remains a challenge. This report describes a rare cause of endocarditis in humans, Bartonella vinsonii, identified through next generation sequencing of plasma microbial cell-free DNA with confirmation of cardiac valve tissue infection through immunohistochemical staining and polymerase chain reaction.

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