Primary Immunodeficiencies in India: Molecular Diagnosis and the Role of Next-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.

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Next-Generation Sequencing of Lung Cancer EGFR Exons 18-21 Allows Effective Molecular Diagnosis of Small Routine Samples (Cytology and Biopsy)

PLoS ONE ◽

10.1371/journal.pone.0083607 ◽

2013 ◽

Vol 8 (12) ◽

pp. e83607 ◽

Cited By ~ 53

Author(s):

Dario de Biase ◽

Michela Visani ◽

Umberto Malapelle ◽

Francesca Simonato ◽

Valentina Cesari ◽

...

Keyword(s):

Lung Cancer ◽

Next Generation Sequencing ◽

Molecular Diagnosis ◽

Next Generation ◽

Generation Sequencing

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The role of next generation sequencing in infection prevention in human parainfluenza virus 3 infections in immunocompromised patients

Journal of Clinical Virology ◽

10.1016/j.jcv.2017.05.010 ◽

2017 ◽

Vol 92 ◽

pp. 53-55 ◽

Cited By ~ 9

Author(s):

Atul Kothari ◽

Mary J. Burgess ◽

Juan Carlos Rico Crescencio ◽

Joshua L. Kennedy ◽

Jesse L. Denson ◽

...

Keyword(s):

Next Generation Sequencing ◽

Infection Prevention ◽

Parainfluenza Virus ◽

Immunocompromised Patients ◽

Next Generation ◽

Human Parainfluenza Virus ◽

Generation Sequencing

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

10.21203/rs.2.24190/v1 ◽

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.

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

Frontiers in Oncology ◽

10.3389/fonc.2021.662260 ◽

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.

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