scholarly journals The Role of Protein Structural Analysis in the Next Generation Sequencing Era

2012 ◽  
pp. 67-98 ◽  
Author(s):  
Wyatt W. Yue ◽  
D. Sean Froese ◽  
Paul E. Brennan
Keyword(s):  
Next Generation Sequencing ◽  
Structural Analysis ◽  
Next Generation ◽  
Protein Structural Analysis ◽  
Generation Sequencing

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

2017 ◽  
Vol 92 ◽  
pp. 53-55 ◽  
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

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.

Impact of Next‐generation Sequencing in Elucidating the Role of microRNA Related to Multiple Abiotic Stresses

2019 ◽  
pp. 389-426
Author(s):  
Kavita Goswami ◽  
Anita Tripathi ◽  
Budhayash Gautam ◽  
Neeti Sanan‐Mishra
Keyword(s):  
Next Generation Sequencing ◽  
Abiotic Stresses ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals P1805UNEXPECTD COMPLEMENT GENES ABNORALITIES IN CHILDREN WITH SECONDARY HEMOLITIC UREMIC SYNDROME

2020 ◽  
Vol 35 (Supplement_3) ◽  
Author(s):  
Luigi Cirillo ◽  
Francesca Becherucci ◽  
Francesco Guzzi ◽  
Carmela Errichiello ◽  
Elisa Buti ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Background ◽  
Case Series ◽  
Cobalamin Deficiency ◽  
Genetic Defects ◽  
Next Generation ◽  
Atypical Hus ◽  
Uremic Syndrome ◽  
Generation Sequencing

Abstract Background and Aims Secondary hemolytic-uremic syndrome (HUS) is currently defined in the absence of genetic defects in complement genes (primary or atypical HUS, aHUS) or Shiga-toxin producing E. Coli infection (STEC-HUS). However, the role of complement genes abnormalities in secondary HUS is still a matter of debate as results coming from studies performed in adults are controversial. Moreover, genetic defects of complement regulation have been recently described in children with STEC-HUS, thus challenging the current HUS classification. The identification of a role of complement genes abnormalities in these patients could have important clinical implications for diagnosis and treatment. In this study, we assessed the presence of complement genes abnormalities in children with secondary HUS. Method We describe a case series of pediatric patients diagnosed with secondary HUS. All patients were screened for the presence of ADAMTS13 auto-antibody and ADAMTS13 deficiency. We performed next-generation sequencing for a panel of complement genes reported in association with aHUS (CFH, CFI, MCP, C3, FB, and THBD). Copy number variations and hybrid genes assessment were included in the analysis. Results Four patients aged 1-4 years with a diagnosis of sporadic secondary HUS were included in the study. HUS was secondary to glomerulopathy, cobalamin deficiency, bone marrow transplantation, and pneumococcal pneumoniae. Two out of four patients showed hypocomplementaemia (both C3 and C4). Diarrhea was a common clinical feature in all patients at onset, and none of these patients showed neurologic involvement. Renal replacement therapy was required in two patients at onset. Only one patient did not recover kidney function, and subsequently underwent kidney transplantation. Next-generation sequencing showed genetic abnormalities in all the patients (Table 1). All but one genetic variants have already been described in association with atypical HUS. Interestingly, haplotypes in CHF and MCP were present in three patients, all of Caucasian ethnicity. Conclusion According to the current HUS classification, complement abnormalities are diagnostic of aHUS. However, results coming from pediatric cohorts of STEC-HUS patients already claimed a role for genetic background also outside the aHUS spectrum, suggesting that the current terminology lacks both specificity and suggestion of cause. In this case series, complement genes abnormalities were present in all patients. Whether confirmed in larger cohorts, these findings would support the role of genetic background even in secondary HUS, suggesting the need for a revision of the current HUS classification, in agreement with the pathogenic mechanisms, in order to tailor the optimal treatment.

Predicting prognosis in patients with acute myeloid leukemia: The role of next-generation sequencing and mutational profiling.

2014 ◽  
Vol 32 (15_suppl) ◽  
pp. 7068-7068
Author(s):  
Caroline E Sloan ◽  
Phyllis A. Gimotty ◽  
Anne M Boccuti ◽  
Alison Sehgal ◽  
Jianhua Zhao ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Next Generation Sequencing ◽  
Myeloid Leukemia ◽  
Next Generation ◽  
Mutational Profiling ◽  
Generation Sequencing ◽  
Acute Myeloid

Role of reverse phenotyping in interpretation of next generation sequencing data and a review of INPP5E related disorders

2016 ◽  
Vol 20 (2) ◽  
pp. 286-295 ◽  
Author(s):  
Christian de Goede ◽  
Wyatt W. Yue ◽  
Guanhua Yan ◽  
Shyamala Ariyaratnam ◽  
Kate E. Chandler ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Generation Sequencing

scholarly journals The Role of Next-Generation Sequencing in Enabling Personalized Oncology Therapy

2016 ◽  
Vol 9 (6) ◽  
pp. 283-292 ◽  
Author(s):  
CA Cummings ◽  
E Peters ◽  
L Lacroix ◽  
F Andre ◽  
MR Lackner
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Personalized Oncology ◽  
Generation Sequencing
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