scholarly journals Melanoma Mimicking Malignant Peripheral Nerve Sheath Tumor with Spread to the Cerebellopontine Angle: Utility of Next-Generation Sequencing in Diagnosis

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Katie Fox Hanson ◽  
Paul Birinyi ◽  
Ronald Walker ◽  
Constantine Raptis ◽  
Rebecca Chernock ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Symptoms ◽  
Cranial Nerves ◽  
Melanocytic Lesion ◽  
Nerve Sheath Tumor ◽  
Next Generation ◽  
Parotid Region ◽  
Lentigo Maligna Melanoma ◽  
Clinically Significant ◽  
Generation Sequencing

Cutaneous spindle cell malignancy is associated with a broad differential diagnosis, particularly in the absence of a known primary melanocytic lesion. We present an unusually challenging patient who presented with clinical symptoms involving cranial nerves VII and VIII and a parotid-region mass, which was S100-positive while lacking in melanocytic pigment and markers. Over a year after resection of the parotid mass, both a cutaneous primary lentigo maligna melanoma and a metastatic CP angle melanoma were diagnosed in the same patient, prompting reconsideration of the diagnosis in the original parotid-region mass. Next-generation sequencing of a panel of cancer-associated genes demonstrated 19 identical, clinically significant mutations as well as a high tumor mutation burden in both the parotid-region and CP angle tumors, indicating a metastatic relationship between the two and a melanocytic identity of the parotid-region tumor.

scholarly journals A teljesexom-szekvenálás jelentősége a ritka neurológiai betegségek diagnosztikájában – saját tapasztalatok egy ataxiás eset kapcsán

2018 ◽  
Vol 159 (28) ◽  
pp. 1163-1169 ◽  
Author(s):  
Péter Balicza ◽  
Zoltán Grosz ◽  
Renáta Bencsik ◽  
Anett Illés ◽  
Anikó Gál ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Exome Sequencing ◽  
Cerebellar Ataxia ◽  
Clinical Symptoms ◽  
Spastic Paraparesis ◽  
Gene Panel ◽  
Next Generation ◽  
Hereditary Spastic Paraparesis ◽  
Disease Stratification ◽  
Generation Sequencing

Abstract: Next generation sequencing (NGS) technologies reshape the diagnostics of rare neurological diseases. In the background of certain neurological symptoms, such as ataxia, many acquired and genetic causes may be present. Variations in a given gene can present with variable phenotypes, too. Because of this phenomenon, the conventional one gene sequencing approach often fails to identify the genetic background of a disease. Next generation sequencing panels allow to sequence 50–100 genes simultaneously, and if the disease stratification is not possible based on the clinical symptoms, whole exome sequencing can help in the diagnostic of genetic disorders with atypical presentation. This case study is about the exome sequencing of a patient with cerebellar ataxia. Genetic investigations identified rare variants in the SPG11 gene in association with the clinical phenotype, which gene was originally described in the background of hereditary spastic paraparesis. Our article highlights that in certain cases the variability of the leading presenting symptom makes it hard to select the correct gene panel. In our case the variants in the gene, formerly associated to hereditary spastic paraparesis, resulted in cerebellar ataxia initially, so even an ataxia NGS gene panel would not detect those. Orv Hetil. 2018; 159(28): 1163–1169.

scholarly journals Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0243683
Author(s):  
Sun Hee Rosenthal ◽  
Anna Gerasimova ◽  
Charles Ma ◽  
Hai-Rong Li ◽  
Andrew Grupe ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myeloproliferative Neoplasms ◽  
Simultaneous Detection ◽  
Molecular Testing ◽  
Next Generation ◽  
Analytical Validation ◽  
Bioinformatics Pipeline ◽  
Myeloid Neoplasms ◽  
Clinically Significant ◽  
Generation Sequencing

Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9–99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.

scholarly journals A Rapid PCR-Free Next-Generation Sequencing Method for the Detection of Copy Number Variations in Prenatal Samples

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 98
Author(s):  
Xiya Zhou ◽  
Xiangbin Chen ◽  
Yulin Jiang ◽  
Qingwei Qi ◽  
Na Hao ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Next Generation Sequencing ◽  
Copy Number ◽  
Genomic Dna ◽  
Sex Chromosome ◽  
Copy Number Variations ◽  
Next Generation ◽  
Sequencing Data ◽  
Clinically Significant ◽  
Generation Sequencing

Next-generation sequencing (NGS) is emerging as a new method for the detection of clinically significant copy number variants (CNVs). In this study, we developed and validated rapid CNV-sequencing (rCNV-seq) for clinical application in prenatal diagnosis. Low-pass whole-genome sequencing was performed on PCR libraries prepared from amniocyte genomic DNA. From 10–40 ng of input DNA, PCR-free libraries consistently produced sequencing data with high unique read mapping ratios, low read redundancy, low coefficient of variation for all chromosomes and high genomic coverage. In validation studies, reliable and accurate CNV detection using PCR-free-based rCNV-seq was demonstrated for a range of common trisomies and sex chromosome aneuploidies as well as microdeletion and duplication syndromes. In reproducibility studies, CNV copy number and genomic intervals closely matched those defined by chromosome microarray analysis. Clinical testing of genomic DNA samples from 217 women referred for prenatal diagnosis identified eight samples (3.7%) with known chromosome disorders. We conclude that PCR-free-based rCNV-seq is a sensitive, specific, reproducible and efficient method that can be used in any NGS-based diagnostic laboratory for detection of clinically significant CNVs.

scholarly journals Molecular Diagnosis of Panel-Based Next-Generation Sequencing Approach and Clinical Symptoms in Patients With Glycogen Storage Disease: A Single Center Retrospective Study

2020 ◽  
Vol 8 ◽  
Author(s):  
Shen Ying ◽  
Zhang Zhihua ◽  
Zheng Yucan ◽  
Jin Yu ◽  
Lin Qian ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Glycogen Storage Disease ◽  
Storage Disease ◽  
Clinical Symptoms ◽  
Glycogen Storage ◽  
Next Generation ◽  
Mild Phenotype ◽  
Diagnostic Role ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Aim: The aim of this study was to investigate the clinical utility of panel-based next-generation sequencing (NGS) in the diagnostic approach of glycogen storage disease (GSD).Methods: We performed a retrospective review of the 32 cases with suspected GSDs between April 2013 and November 2019 through panel-based NGS, clinical and biochemical data and long-term complications.Results: Of the 32 clinical cases, we identified 41 different variants, including 24 missense (58.5%), one synonymous (2.4%), three nonsense (8%), one splice (2.4%), four frameshift (9.8%), one deletion (2.4%), four insertions (9.8%), two deletion-insertion (4.9%) and one duplication(2.4%), of which 13(31.7%) were previously unreported in the literature. In addition, patients with different types of GSDs showed important differences in biochemical parameters (i.e., CK, rGGT, TG, and UA).Conclusions: The panel-based NGS played an important diagnostic role in the suspicious GSDs patients, especially in the mild phenotype and ruled out detectable pathologic conditions. Besides, differences between our GSDs patients reflect biochemical heterogeneity.

scholarly journals European foulbrood in Czechia after 40 years: application of next-generation sequencing to analyze Melissococcus plutonius transmission and influence on the bacteriome of Apis mellifera

2016 ◽  
Author(s):  
Tomas Erban ◽  
Ondrej Ledvinka ◽  
Martin Kamler ◽  
Bronislava Hortova ◽  
Marta Nesvorna ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Clinical Symptoms ◽  
Rrna Gene ◽  
Next Generation ◽  
Colony Losses ◽  
Melissococcus Plutonius ◽  
European Foulbrood ◽  
Generation Sequencing

Worker honeybees (Apis mellifera) transmit Melissococcus plutonius between colonies. However, the transmission of M. plutonius, which causes European foulbrood (EFB), is poorly understood. To analyze the first EFB outbreak in 40 years in Czechia, we collected 49 hive worker samples from 18 beehives in two diseased apiaries for bacteriome analysis of the V1-V3 portion of the 16S rRNA gene. When we compared control samples obtained outside of the EFB zone, bees from an EFB apiaries containing colonies without clinical symptoms and bees from colonies with EFB clinical symptoms, there was a 100-fold higher occurrence of M. plutonius in colonies with EFB symptoms. The presence of M. plutonius in controls indicated that this pathogen exists in an enzootic state. EFB influenced the core bacteria in the worker bacteriome because the number of Snodgrassella alvi, Lactobacillus mellis, Lactobacillus melliventris, and Fructobacillus fructosus sequences increased, while Bartonella apis, Frischella perrara, and Commensalibacter intestine sequences decreased. Together, the results of this study suggest worker bees from EFB-diseased apiaries serve as vectors of M. plutonius, and eliminating such colonies is an appropriate method to overcome disease outbreaks. Because M. plutonius exists in honeybee colonies in an enzootic state, there may be similar abundances in control colonies outside the EFB zone to those in asymptomatic colonies from EFB apiaries. High-throughput Illumina next-generation sequencing permitted the quantitative interpretation of M. plutonius within the honeybee worker bacteriome. Future studies focusing on honeybee diseases, colony losses, detection of bacterial pathogens and interactions of bacteriome with pathogenic bacteria will benefit of this study.

scholarly journals European foulbrood in Czechia after 40 years: application of next-generation sequencing to analyze Melissococcus plutonius transmission and influence on the bacteriome of Apis mellifera

2016 ◽  
Author(s):  
Tomas Erban ◽  
Ondrej Ledvinka ◽  
Martin Kamler ◽  
Bronislava Hortova ◽  
Marta Nesvorna ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Next Generation Sequencing ◽  
Pathogenic Bacteria ◽  
Clinical Symptoms ◽  
Rrna Gene ◽  
Next Generation ◽  
Colony Losses ◽  
Melissococcus Plutonius ◽  
European Foulbrood ◽  
Generation Sequencing

Worker honeybees (Apis mellifera) transmit Melissococcus plutonius between colonies. However, the transmission of M. plutonius, which causes European foulbrood (EFB), is poorly understood. To analyze the first EFB outbreak in 40 years in Czechia, we collected 49 hive worker samples from 18 beehives in two diseased apiaries for bacteriome analysis of the V1-V3 portion of the 16S rRNA gene. When we compared control samples obtained outside of the EFB zone, bees from an EFB apiaries containing colonies without clinical symptoms and bees from colonies with EFB clinical symptoms, there was a 100-fold higher occurrence of M. plutonius in colonies with EFB symptoms. The presence of M. plutonius in controls indicated that this pathogen exists in an enzootic state. EFB influenced the core bacteria in the worker bacteriome because the number of Snodgrassella alvi, Lactobacillus mellis, Lactobacillus melliventris, and Fructobacillus fructosus sequences increased, while Bartonella apis, Frischella perrara, and Commensalibacter intestine sequences decreased. Together, the results of this study suggest worker bees from EFB-diseased apiaries serve as vectors of M. plutonius, and eliminating such colonies is an appropriate method to overcome disease outbreaks. Because M. plutonius exists in honeybee colonies in an enzootic state, there may be similar abundances in control colonies outside the EFB zone to those in asymptomatic colonies from EFB apiaries. High-throughput Illumina next-generation sequencing permitted the quantitative interpretation of M. plutonius within the honeybee worker bacteriome. Future studies focusing on honeybee diseases, colony losses, detection of bacterial pathogens and interactions of bacteriome with pathogenic bacteria will benefit of this study.

scholarly journals The Early Diagnosis of Scrub Typhus by Metagenomic Next-Generation Sequencing

2021 ◽  
Vol 9 ◽  
Author(s):  
Xianghong Liu ◽  
Ye Zhang ◽  
Jun Zhang ◽  
Zheng Lou ◽  
Han Xia ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Tract ◽  
Scrub Typhus ◽  
Clinical Symptoms ◽  
Early Stage ◽  
Febrile Illness ◽  
Diagnostic Methods ◽  
Chronic Obstructive ◽  
Next Generation ◽  
Generation Sequencing

Introduction: Scrub typhus is a mite-borne infection widespread in Southeast Asia, with clinical symptoms such as fever, chills, skin rash, eschar at the bite site, and other signs of acute febrile illness. The Rickettsia pathogen (Orientia tsutsugamushi) is always difficult to be diagnosed at an early stage by traditional clinical diagnostic methods, especially for patients without typical eschar. This greatly increases the mortality of patients with scrub typhus. A new approach should be introduced to improve its clinical diagnosis.Methods: During May 2018 to March 2021, 13 samples from 10 patients with suspected scrub typhus were collected. Metagenomic next-generation sequencing (mNGS) and other diagnostic methods (including serology using Weil–Felix reaction and indirect immunofluorescence test (IIFT) for scrub typhus and respiratory tract profile IgM as well as culture for routine bacteria) were used to identify the pathogens in this study.Results: The results of mNGS were all positive, with mapped reads of O. tsutsugamushi ranging from 1 to 460. Eight patients (80%) were diagnosed as scrub typhus. The other two were diagnosed as suspected scrub typhus due to the limited number of reads of the pathogen (one and two, respectively). According to clinical evidences, nine of the 10 patients were finally diagnosed as scrub typhus, except for patient 9 (suspected scrub typhus by mNGS with one specific reads of the pathogen) diagnosed as acute exacerbation of chronic obstructive pulmonary disease. For the five scrub typhus patients without typical eschar, mNGS gave all positive results (4–460 specific reads). For other methods, only Weil–Felix reaction of one patient detected the pathogen. In addition, the respiratory tract profile (IgM) detected various pathogens, but all were confirmed to be false positive.Conclusions: mNGS performed better than conventional clinical methods to early diagnose scrub typhus. This approach can be routinely carried out for early and precise diagnosis in clinical infections, especially for those hard to be identified by traditional diagnostic methods.

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