scholarly journals Genetic Analysis of Gorlin Syndrome Using a Multiplex PCR Gene Panel, and Its Potential Clinical Utility for Liquid Biopsy

2021 ◽  
Author(s):  
Yuriko Nakamura ◽  
Shoko Onodera ◽  
Kazuhiko Hashimoto ◽  
Masayuki Takano ◽  
Akira Katakura ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Low Cost ◽  
Genetic Diagnosis ◽  
Gene Mutations ◽  
Gene Panel ◽  
Hereditary Diseases ◽  
Gorlin Syndrome ◽  
Prediction Tools ◽  
Multiple Organs ◽  
Target Ratio

Abstract Background: Gorlin syndrome is an autosomal dominant, rare disease caused by mutations in PTCH1, PTCH2, and SUFU with various symptoms in multiple organs making early diagnosis challenging. In this study, we generated a Gorlin syndrome gene panel that could help to overcome the difficulties in diagnosing Gorlin syndrome using a single test. Results: This gene panel is time- and cost-efficient and highly reliable with a high-quality score of 30, on-target ratio, and coverage depth, and could detect more mutations than whole-exome sequencing of the same patient. Although the current in silico prediction tools have a limited genetic database of gene mutations in rare hereditary diseases, five prediction tools were used to identify pathological mutations. Pathogenic gene mutations were detected not only in PTCH1 but also in PTCH2 in five out of 12 patients with Gorlin syndrome diagnosed based on clinical symptoms. Conclusions: Using this gene panel, we showed the same gene mutation in the patients and their asymptomatic relatives; hence, it has enabled a highly reliable genetic diagnosis of Gorlin syndrome at a low cost requiring only blood sample.

scholarly journals COT-07 HEREDITARY BRAIN TUMOR DISEASE MEDICINE IN THE CANCER GENOME MEDICAL AGE-IMPORTANCE OF MULTIDISCIPLINARY COLLABORATION AND GENETIC COUNSELING

2019 ◽  
Vol 1 (Supplement_2) ◽  
pp. ii42-ii42
Author(s):  
Shunsaku Takayanagi ◽  
Shota Tanaka ◽  
Masahiro Shin ◽  
Hirofumi Nakatomi ◽  
Kumiko Oseto ◽  
...  
Keyword(s):  
Genetic Counseling ◽  
Early Detection ◽  
Medical Treatment ◽  
Early Stage ◽  
Genetic Diagnosis ◽  
Cancer Genome ◽  
Hereditary Diseases ◽  
Multiple Organs ◽  
Vhl Disease ◽  
Cooperation System

Abstract INTRODUCTION Recently, the cancer genome medical system has been rapidly promoted in Japan, such as cancer related gene panel test as NCC oncopanel and Fonduation One being covered by insurance. At the same time, there is a great deal of attention now on hereditary tumor diseases caused by abnormalities in cancer-related genes and their medical treatment. Von Hippel-Lindau (VHL) disease and tuberous sclerosis (TSC) are one such hereditary tumor disease, and develop tumors in multiple organs such as kidney tumors and lung tumors as well as brain tumors. The University of Tokyo Hospital has been developing an in-hospital medical care system for VHL disease and TSC. [VHL disease] If VHL disease is diagnosed at an early stage and strives for early detection and treatment of tumor, it is said that the prognosis is not largely different from normal people. Therefore, our hospital opened a specialized outpatient for VHL disease from 2012, and has carried out genetic diagnosis of VHL disease and medical treatment based on it. [TSC] Recently, the use of Afinitor for SEGA was covered by insurance in Japan, and a system in which multiple departments involved in our hospital cooperated was established, and regular meetings were held to determine treatment policies. DISCUSSION It was the development of genetic counseling system and multidisciplinary cooperation system that was important in any disease. Genetic counseling helps patients with illness and their families to genetically understand and adapt to illness. In the case of hereditary diseases, the practice of genetic counseling was very useful. In addition, since it is a disease involving multiple organs, close cooperation with other in-hospital clinics has been extremely useful for early detection and treatment of patient’s lesions.

scholarly journals Nanopore Targeted Sequencing for Rapid Gene Mutations Detection in Acute Myeloid Leukemia

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1026 ◽  
Author(s):  
Cumbo ◽  
Minervini ◽  
Orsini ◽  
Anelli ◽  
Zagaria ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
Low Cost ◽  
Gene Mutations ◽  
Predictive Biomarkers ◽  
Molecular Testing ◽  
Sequencing Analysis ◽  
Cebpa Mutations ◽  
Targeted Gene Sequencing ◽  
Acute Myeloid

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy. Next generation sequencing offers the advantage of the simultaneous investigation of numerous genes, but these methods remain expensive and time consuming. In this context, we present a nanopore-based assay for rapid (24 h) sequencing of six genes (NPM1, FLT3, CEBPA, TP53, IDH1 and IDH2) that are recurrently mutated in AML. The study included 22 AML patients at diagnosis; all data were compared with the results of S5 sequencing, and discordant variants were validated by Sanger sequencing. Nanopore approach showed substantial advantages in terms of speed and low cost. Furthermore, the ability to generate long reads allows a more accurate detection of longer FLT3 internal tandem duplications and phasing double CEBPA mutations. In conclusion, we propose a cheap, rapid workflow that can potentially enable all basic molecular biology laboratories to perform detailed targeted gene sequencing analysis in AML patients, in order to define their prognosis and the appropriate treatment.

scholarly journals P040 Highly Sensitivity and Fast Genetic Diagnosis by Mean of a Novel NGS-Based Resequencing Gene Panel Underlying SCLC Patients

2018 ◽  
Vol 13 (12) ◽  
pp. S1066
Author(s):  
J. Wang ◽  
L. Zhao ◽  
X. Sun ◽  
F. Zhou ◽  
Y. Zhang ◽  
...  
Keyword(s):  
Genetic Diagnosis ◽  
Gene Panel

scholarly journals Self-assembled particulate vaccine elicits strong immune responses and reduces Mycobacterium avium subsp. paratuberculosis infection in mice

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sandeep K. Gupta ◽  
Natalie A. Parlane ◽  
Dongwen Luo ◽  
Bernd H. A. Rehm ◽  
Axel Heiser ◽  
...  
Keyword(s):  
Immune Responses ◽  
Fusion Protein ◽  
Mycobacterium Avium ◽  
Low Cost ◽  
Multiple Organs ◽  
T Cell Immune Responses ◽  
Protein Particle ◽  
Mycobacterium Avium Subsp Paratuberculosis ◽  
Eventual Death ◽  
Fusion Antigen

AbstractMycobacterium avium subspecies paratuberculosis (MAP) causes chronic progressive granulomatous enteritis leading to diarrhoea, weight loss, and eventual death in ruminants. Commercially available vaccines provide only partial protection against MAP infection and can compromise the use of bovine tuberculosis diagnostic tests. Here, we report the development of a protein-particle-based vaccine containing MAP antigens Ag85A202–347-SOD1–72-Ag85B173–330-74F1–148+669–786 as a fusion (‘MAP fusion protein particle’). The fusion antigen displayed on protein particles was identified using mass spectrometry. Surface exposure and accessibility of the fusion antigen was confirmed by flow cytometry and ELISA. The MAP fusion protein particle vaccine induced strong antigen-specific T-cell immune responses in mice, as indicated by increased cytokine (IFN-γ and IL-17A) and costimulatory signals (CD40 and CD86) in these animals. Following MAP-challenge, a significant reduction in bacterial burden was observed in multiple organs of the mice vaccinated with the MAP fusion protein particle vaccine compared with the PBS group. The reduction in severity of MAP infection conferred by the MAP fusion protein particle vaccine was similar to that of Silirum and recombinant protein vaccines. Overall, the results provide evidence that MAP antigens can be engineered as a protein particulate vaccine capable of inducing immunity against MAP infection. This utility offers an attractive platform for production of low-cost particulate vaccines against other intracellular pathogens.

scholarly journals CSF1R-related leukoencephalopathy

Neurology ◽  
2018 ◽  
Vol 91 (24) ◽  
pp. 1092-1104 ◽  
Author(s):  
Takuya Konno ◽  
Koji Kasanuki ◽  
Takeshi Ikeuchi ◽  
Dennis W. Dickson ◽  
Zbigniew K. Wszolek
Keyword(s):  
White Matter ◽  
Cultured Cells ◽  
Clinical Symptoms ◽  
Current Knowledge ◽  
Gene Mutations ◽  
Future Research ◽  
Primary Role ◽  
Extrapyramidal Signs ◽  
Underlying Mechanisms

Since the discovery of CSF1R gene mutations in families with hereditary diffuse leukoencephalopathy with spheroids in 2012, more than 70 different mutations have been identified around the world. Through the analyses of mutation carriers, CSF1R-related leukoencephalopathy has been distinctly characterized clinically, radiologically, and pathologically. Typically, patients present with frontotemporal dementia-like phenotype in their 40s–50s, accompanied by motor symptoms, including pyramidal and extrapyramidal signs. Women tend to develop the clinical symptoms at a younger age than men. On brain imaging, in addition to white matter abnormalities, thinning of the corpus callosum, diffusion-restricted lesions in the white matter, and brain calcifications are hallmarks. Primary axonopathy followed by demyelination was suggested by pathology. Haploinsufficiency of colony-stimulating factor-1 receptor (CSF1R) is evident in a patient with a frameshift mutation, facilitating the establishment of Csf1r haploinsufficient mouse model. These mice develop clinical, radiologic, and pathologic phenotypes consistent with those of human patients with CSF1R mutations. In vitro, perturbation of CSF1R signaling is shown in cultured cells expressing mutant CSF1R. However, the underlying mechanisms by which CSF1R mutations selectively lead to white matter degeneration remains to be elucidated. Given that CSF1R mainly expresses in microglia, CSF1R-related leukoencephalopathy is representative of primary microgliopathies, of which microglia have a pivotal and primary role in pathogenesis. In this review, we address the current knowledge of CSF1R-related leukoencephalopathy and discuss the putative pathophysiology, with a focus on microglia, as well as future research directions.

scholarly journals Genetic diagnosis of congenital hypopituitarism by a target gene panel: novel pathogenic variants in GLI2, OTX2 and GHRHR

2019 ◽  
Vol 8 (5) ◽  
pp. 590-595 ◽  
Author(s):  
Marilena Nakaguma ◽  
Fernanda A Correa ◽  
Lucas S Santana ◽  
Anna F F Benedetti ◽  
Ricardo V Perez ◽  
...  
Keyword(s):  
Target Gene ◽  
Gh Deficiency ◽  
Massively Parallel Sequencing ◽  
Genetic Diagnosis ◽  
Pituitary Hormones ◽  
Gene Panel ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Pathogenic Variants ◽  
Congenital Hypopituitarism

Aim Congenital hypopituitarism has an incidence of 1:3500–10,000 births and is defined by the impaired production of pituitary hormones. Early diagnosis has an impact on management and genetic counselling. The clinical and genetic heterogeneity of hypopituitarism poses difficulties to select the order of genes to analyse. The objective of our study is to screen hypopituitarism genes (candidate and previously related genes) simultaneously using a target gene panel in patients with congenital hypopituitarism. Methods Screening of 117 subjects with congenital hypopituitarism for pathogenic variants in 26 genes associated with congenital hypopituitarism by massively parallel sequencing using a customized target gene panel. Results We found three novel pathogenic variants in OTX2 c.295C>T:p.Gln99*, GLI2 c.1681G>T:p.Glu561* and GHRHR c.820_821insC:p.Asp274Alafs*113, and the previously reported variants in GHRHR c.57+1G>A and PROP1 [c.301_302delAG];[c.109+1G>A]. Conclusions Our results indicate that a custom-designed panel is an efficient method to screen simultaneously variants of biological and clinical relevance for congenital GH deficiency. A genetic diagnosis was possible in 5 out of 117 (4%) patients of our cohort. We identified three novel pathogenic variants in GHRHR, OTX2 and GLI2 expanding the spectrum of variants associated with congenital hypopituitarism.

scholarly journals RT-qPCR Assays for Rapid Detection of the N501Y, 69-70del, K417N, and E484K SARS-CoV-2 Mutations: A Screening Strategy to Identify Variants With Clinical Impact

2021 ◽  
Vol 11 ◽  
Author(s):  
Natali Vega-Magaña ◽  
Rocío Sánchez-Sánchez ◽  
Jorge Hernández-Bello ◽  
Alberto Antony Venancio-Landeros ◽  
Marcela Peña-Rodríguez ◽  
...  
Keyword(s):  
Biological Effects ◽  
Low Cost ◽  
Gene Mutations ◽  
High Specificity ◽  
Screening Strategy ◽  
Clinical Impact ◽  
Mexican Population ◽  
Rapid Screening ◽  
Clinical Samples ◽  
Reverse Transcription Pcr

BackgroundSeveral variants of the SARS-CoV-2 have been documented globally during the current COVID-19 pandemic. The N501Y, 69-70del, K417N, and E484K SARS-CoV-2 mutations have been documented among the most relevant due to their potential pathogenic biological effects. This study aimed to design, validate, and propose a fast real-time RT-qPCR assay to detect SARS-CoV-2 mutations with possible clinical and epidemiological relevance in the Mexican population.MethodsTargeting spike (S) gene mutations of SARS-CoV-2 (N501Y, 69-70del, K417N, and E484K), specific primers, and probes for three specific quantitative reverse transcription PCR (RT-qPCR) assays were designed, and validated using Sanger sequencing. These assays were applied in clinical samples of 1060 COVID-19 patients from Jalisco Mexico.ResultsIn silico analyzes showed high specificity of the three assays. Amplicons of samples were confirmed through sequencing. The screening of samples of COVID-19 patients allowed the identification of the E484K mutation in nine individuals and the identification of P.2 Brazilian variant in Mexico.ConclusionThis work provides low-cost RT-qPCR assays for rapid screening and molecular surveillance of mutations with potential clinical impact. This strategy allowed the detection of E484K mutation and P.2 variant for the first time in samples from the Mexican population.

scholarly journals Mosaicism in Tuberous Sclerosis Complex: A Case Report, Literature Review, and Original Data from Danish Hospitals

2021 ◽  
pp. 98-105
Author(s):  
Julie Loft Nagel ◽  
Maja Patricia Smerdel ◽  
Lisbeth Birk Møller ◽  
Lotte Andreasen ◽  
Anette Bygum
Keyword(s):  
Tuberous Sclerosis ◽  
Tuberous Sclerosis Complex ◽  
Molecular Genetic ◽  
Genetic Diagnosis ◽  
Original Data ◽  
Hereditary Disease ◽  
Loss Of Function ◽  
Low Level ◽  
Multiple Organs ◽  
Organ Systems

Tuberous sclerosis complex (TSC) is an autosomal dominant hereditary disease with hamartomatous growths in multiple organs due to loss-of-function variants in TSC1 or TSC2. In approximately 15% of patients with clinical TSC, no pathogenic variant can be identified, and low-level mosaicism is suggested to be one of the reasons. Mosaicism is well-known in TSC and challenges the molecular genetic diagnosis. The advent of next-generation sequencing has improved the diagnostics in TSC including in patients with mosaicism. The TSC phenotype varies widely, and mosaic patients with TSC are often considered to have a milder phenotype. Here, the authors describe a patient with mosaic TSC with a 10% variant allele fraction and manifestations in three organ systems (skin, eyes, and kidneys). Furthermore, the authors studied existing literature about phenotypic organ manifestations in patients with mosaic TSC. No clear definition of the phenotype of patients with mosaic TSC could be established, but unilateral angiofibromas and the absence of tubers and a subependymal nodule could indicate mosaicism. The case shows that patients with low-level mosaic TSC can have multiple affected organ systems though still a mild clinical picture.

scholarly journals Novel Approaches to Diagnose COVID-19

2020 ◽  
pp. 66-71
Author(s):  
Solaf Jawhar Ali
Keyword(s):  
Clinical Symptoms ◽  
Low Cost ◽  
Case Definition ◽  
Diagnostic Tools ◽  
Rt Pcr ◽  
Public Health Agencies ◽  
Health Agencies ◽  
Acute Respiratory Diseases ◽  
Diagnostic Approaches ◽  
Laboratory Examinations

An widespread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 has occurred worldwide.  Public health agencies are in need of developing diagnostic tools which will have a major impact in tracking the virus and suppressing the transmission. Diagnosis of the disease is based on clinical symptoms, epidemiological history and laboratory examinations. Severe acute respiratory diseases with fever and ,cough and dyspnea, are used as the case definition to select people for testing. Different samples taken from the human body such as oropharyngeal (OP) and nasopharyngeal (NP) swabs are used to detect the virus. SARS-CoV-2 can be detected with different methods in the laboratory including real time RT-PCR, chest CT scan and immunoassays. Viral nucleic acid testing has played important role in control COVIDI-19 outbreak.  More recently, a new CRISPR-based DETECTR assay has been developed to detect COVID-19. This test is rapid (~30 min), low-cost, and precise for identification of SARS-CoV-2. In addition, immunoassays and medical imaging can use as supplementary tests, combined with RT-PCR. This review is conducted to summarizes the current information on the present diagnostic approaches for SARS-CoV-2.

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