scholarly journals Detection of Coccidioides posadasii in a patient with meningitis using metagenomic next-generation sequencing: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuqiao Mao ◽  
Xia Li ◽  
Haibo Lou ◽  
Xiaoyu Shang ◽  
Yanjun Mai ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Los Angeles ◽  
Systemic Infection ◽  
High Sensitivity ◽  
Pathological Examination ◽  
Next Generation ◽  
Coccidioides Posadasii ◽  
Dimorphic Fungi ◽  
Almost All ◽  
Generation Sequencing

Abstract Background Coccidioidomycosis is a systemic infection caused by dimorphic fungi Coccidioides spp. endemic to Southwestern United States and Central and South America. A history of residence and travel in these areas is essential for the diagnostic of coccidioidomycosis, which has highly variable symptoms ranging from asymptomatic to severe, disseminated infection, and even death. Immunocompromised patients of coccidioidomycosis experience a high risk of dissemination, chronic infection, and mortality. Meningitis is one of the most deleterious coccidioidomycosis and can cause various life-threatening complications. Case presentation Here we report a case of Coccidioides posadasii meningitis in a 49-year-old female who returned to China after one and a half years residence in Los Angeles, USA. The repeated routine cultures using CSF for bacteria or fungi were all negative. To hunt for an infectious etiology, the state-of-the-art technology metagenomic next-generation sequencing (mNGS) was then utilized, suggesting Coccidioides posadasii. Organizational pathological examination and polymerase-chain-reaction (PCR) results subsequently confirmed the mNGS detection. Conclusion To our knowledge, cases for coccidioidal meningitis have been rarely reported in China. While global travelling may spread this disease across continents and make the diagnosis more difficult. mNGS can detect almost all known pathogens with high sensitivity and specificity, especially for uncommon pathogen, such as Coccidioides posadasii in China.

A Novel Method for Microsatellite Instability Detection by Liquid Biopsy Based on Next- Generation Sequencing

2020 ◽  
Vol 15 ◽  
Author(s):  
Zheng Jiang ◽  
Hui Liu ◽  
Siwen Zhang ◽  
Jia Liu ◽  
Weitao Wang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Instability ◽  
Liquid Biopsy ◽  
Tumor Tissue ◽  
High Sensitivity ◽  
Next Generation ◽  
Tissue Samples ◽  
Next Generation Sequencing Technology ◽  
Medication Selection ◽  
Generation Sequencing

Background: Microsatellite instability (MSI) is a prognostic biomarker used to guide medication selection in multiple cancers, such as colorectal cancer. Traditional PCR with capillary electrophoresis and next-generation sequencing using paired tumor tissue and leukocyte samples are the main approaches for MSI detection due to their high sensitivity and specificity. Currently, patient tissue samples are obtained through puncture or surgery, which causes injury and risk of concurrent disease, further illustrating the need for MSI detection by liquid biopsy. Methods: We propose an analytic method using paired plasma/leukocyte samples and MSI detection using next-generation sequencing technology. Based on the theoretical progress of oncogenesis, we hypothesized that the microsatellite site length in plasma equals the combination of the distribution of tumor tissue and leukocytes. Thus, we defined a window-judgement method to identify whether biomarkers were stable. Results: Compared to traditional PCR as the standard, we evaluated three methods in 20 samples (MSI-H:3/MSS:17): peak shifting method using tissue vs. leukocytes, peak shifting method using plasma vs. leukocytes, and our method using plasma vs. leukocytes. Compared to traditional PCR, we observed a sensitivity of 100%, 0%, and 100%, and a specificity of 100.00%, 94.12%, and 88.24%, respectively. Conclusion: Our method has the advantage of possibly detecting MSI in a liquid biopsy and provides a novel direction for future studies to increase the specificity of the method.

scholarly journals A case report of SMARCA4/BRG1-deficient non-small cell lung cancer with a spindle cell component found by next-generation sequencing of a brain metastasis

2020 ◽  
Author(s):  
Hiroko Ikeda ◽  
Takashi Sone ◽  
Kazuo Kasahara ◽  
Satoko Nakada ◽  
Kaori Yoshimura ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Spindle Cell ◽  
Small Cell ◽  
Pathological Examination ◽  
Next Generation ◽  
Small Cell Lung ◽  
Immunohistochemical Examination ◽  
The Brain ◽  
Generation Sequencing

Abstract Background: Several studies of different cancers have revealed mutations in switch/sucrose non-fermenting (SWI/SNF) complex genes. Brahma-related gene 1 (BRG1), which is encoded by SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), is a member of this complex. SMARCA4/BRG-1-deficient non-small cell lung carcinoma (NSCLC) has been considered a subset of lung cancer that has distinct clinical, pathological, and molecular characteristics, which implies its relationship with SMARCA4/BRG1-deficient thoracic sarcoma. Case presentation: We experienced a case of SMARCA4/BRG1-deficient lung cancer in a 40-year-old female patient with a history of smoking. Magnetic resonance imaging revealed a large mass in the right lung apex with an extension to the extrapulmonary region and cerebral metastasis. Histological analysis showed poorly differentiated carcinoma with spindle cell components. She was diagnosed with NSCLC (stage IV) at that point. An EGFR mutation and ALK and ROS1 rearrangement were not detected, and then treated with chemoradiotherapy. Overall, the tumors were resistant to chemotherapy, and therefore, after 2 years, the brain tumor was excised for histological and molecular analysis. Histologically, the brain mass was an undifferentiated tumor with round cells and glandular components. The mutation in SMARCA4 in the brain specimen was identified by next-generation sequencing. Immunohistochemical examination revealed a complete loss of BRG1. SMARCA4/BRG1-deficient thoracic sarcoma had been raised as a differential diagnosis, collectively, she was diagnosed with SMARCA4/BRG1-deficient NSCLC considering for the result of positivity for cytokeratin AE1/AE3 and claudin-4, and negativity for Sal-like protein 4, CD34, and SRY-box 2 by immunohistochemical examination. Regrettably, a definitive diagnosis required approximately 2 years. She is alive with disease at 30 months after the presentation. Conclusions: The diagnosis of SMARCA4/BRG1-deficient NSCLC is frequently difficult because of no specific morphology and necessity of discrimination from SMARCA4/BRG1-deficient thoracic sarcoma, which is the practical reason this disease is sometimes missed. Immunohistochemistry for BRG1 should be encouraged for the pathological examination of NSCLC with any histology for the prompt and precise diagnosis of SMARCA4/BRG1-deficient NSCLC.

scholarly journals Subacute Thyroiditis is Associated with HLA-B*18:01, -DRB1*01 and -C*04:01—The Significance of the New Molecular Background

2020 ◽  
Vol 9 (2) ◽  
pp. 534
Author(s):  
Magdalena Stasiak ◽  
Bogusław Tymoniuk ◽  
Renata Michalak ◽  
Bartłomiej Stasiak ◽  
Marek L. Kowalski ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Human Leukocyte ◽  
Subacute Thyroiditis ◽  
Control Group ◽  
Next Generation ◽  
Sequencing Method ◽  
Triggering Factor ◽  
Almost All ◽  
Generation Sequencing ◽  
Next Generation Sequencing Method

Subacute thyroiditis (SAT) is a thyroid inflammatory disease whose pathogenesis is still not completely defined. Previous viral infection is considered to be a triggering factor in genetically predisposed individuals. In about 70% of patients, susceptibility to SAT is associated with the HLA-B*35 allele. The correlation between SAT and other human leukocyte antigens (HLA) has not yet been unequivocally demonstrated and the genetic background is still unknown in about 30% of patients. The purpose of our study was to perform HLA genotyping using a next-generation sequencing method, to find out whether alleles other than HLA-B*35 are correlated with SAT morbidity. HLA-A, -B, -C, -DQB1, -DRB1 were genotyped using a next-generation sequencing method in 1083 subjects, including 60 SAT patients and 1023 healthy controls. Among 60 patients diagnosed with SAT, 81.7% of subjects were identified as having allele HLA-B*35, 23.3% had HLA-B*18:01, 28.3% had HLA-DRB1*01 and 75.5% had HLA-C*04:01. These alleles occurred in the control group at frequencies of 10.2%, 7.2%, 12.9% and 12.5%, respectively. The differences were statistically significant, with p < 0.05. In addition to its previously described relationship with HLA-B*35, genetic susceptibility to SAT was associated with the presence of HLA-B*18:01, DRB1*01 and C*04:01. The alleles HLA-B*18:01 and DRB1*01 were independent SAT risk factors. The assessment of these four alleles allows the confirmation of genetic predisposition in almost all patients with SAT.

A novel homozygous frameshift mutation in the FUCA1 gene causes both severe and mild fucosidosis

2018 ◽  
Vol 71 (9) ◽  
pp. 821-824 ◽  
Author(s):  
Nasrollah Saleh-Gohari ◽  
Kolsoum Saeidi ◽  
Roya Zeighaminejad
Keyword(s):  
Next Generation Sequencing ◽  
Frameshift Mutation ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Gene Mutations ◽  
Next Generation ◽  
Lysosomal Storage ◽  
Illumina Hiseq ◽  
Almost All ◽  
Generation Sequencing

AimsFucosidosis is a rare autosomal recessive lysosomal storage disorder caused by α-L-fucosidase deficiency as a result of FUCA1 gene mutations. Here, we studied clinical features and the molecular basis of fucosidosis in a family from Iran, including two probands and nine family members.MethodsDNA sample of two probands were screened for gene defects using a next generation sequencing technique. The sequencing processes were performed on an Illumina Hiseq 4000 platform. Sequence reads were analysed using BWA-GATK.ResultsNext generation sequencing revealed a frameshift mutation caused by 2 bp deletion (c.837_838 delTG; p.Cys279) in the FUCA1 gene. The identified mutation was tested in all participants. Homozygous patients had almost all the complications associated with fucosidosis, while heterozygous carriers were unaffected.ConclusionsThe variant c.837_838 delTG; p.Cys279 has not been reported previously and is predicted to be pathogenic due to a premature stop codon.

scholarly journals Highly sensitive and full-genome interrogation of SARS-CoV-2 using multiplexed PCR enrichment followed by next-generation sequencing

2020 ◽  
Author(s):  
Chenyu Li ◽  
David N. Debruyne ◽  
Julia Spencer ◽  
Vidushi Kapoor ◽  
Lily Y. Liu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Multiplex Pcr ◽  
High Sensitivity ◽  
Detection Methods ◽  
Next Generation ◽  
Rt Pcr ◽  
Copy Numbers ◽  
Virus Rna ◽  
Highly Sensitive ◽  
Generation Sequencing

AbstractMany detection methods have been used or reported for the diagnosis and/or surveillance of COVID-19. Among them, reverse transcription polymerase chain reaction (RT-PCR) is the most commonly used because of its high sensitivity, typically claiming detection of about 5 copies of viruses. However, it has been reported that only 47-59% of the positive cases were identified by some RT-PCR methods, probably due to low viral load, timing of sampling, degradation of virus RNA in the sampling process, or possible mutations spanning the primer binding sites. Therefore, alternative and highly sensitive methods are imperative. With the goal of improving sensitivity and accommodating various application settings, we developed a multiplex-PCR-based method comprised of 343 pairs of specific primers, and demonstrated its efficiency to detect SARS-CoV-2 at low copy numbers. The assay produced clean characteristic target peaks of defined sizes, which allowed for direct identification of positives by electrophoresis. We further amplified the entire SARS-CoV-2 genome from 8 to half a million viral copies purified from 13 COVID-19 positive specimens, and detected mutations through next generation sequencing. Finally, we developed a multiplex-PCR-based metagenomic method in parallel, that required modest sequencing depth for uncovering SARS-CoV-2 mutational diversity and potentially novel or emerging isolates.

scholarly journals Validation of a next-generation sequencing (NGS) panel to improve the diagnosis of X-linked hypophosphataemia (XLH) and other genetic disorders of renal phosphate wasting

2020 ◽  
Vol 183 (5) ◽  
pp. 497-504
Author(s):  
Susanne Thiele ◽  
Ralf Werner ◽  
Annika Stubbe ◽  
Olaf Hiort ◽  
Wolfgang Hoeppner
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Disorders ◽  
Fibroblast Growth Factor 23 ◽  
Somatic Mosaicism ◽  
High Sensitivity ◽  
Compound Heterozygous ◽  
Special Focus ◽  
Next Generation ◽  
Two Samples ◽  
Generation Sequencing

Background: Hypophosphataemic rickets (HR) comprise a clinically and genetically heterogeneous group of conditions, defined by renal-tubular phosphate wasting and consecutive loss of bone mineralisation. X-linked hypophosphataemia (XLH) is the most common form, caused by inactivating dominant mutations in PHEX, a gene encompassing 22 exons located at Xp22.1. XLH is treatable by anti-Fibroblast Growth Factor 23 antibody, while for other forms of HR such as therapy may not be indicated. Therefore, a genetic differentiation of HR is recommended. Objective: To develop and validate a next-generation sequencing panel for HR with special focus on PHEX. Design and methods: We designed an AmpliSeq gene panel for the IonTorrent PGM next-generation platform for PHEX and ten other HR-related genes. For validation of PHEX sequencing 50 DNA-samples from XLH-patients, in whom 42 different mutations in PHEX and 1 structural variation have been proven before, were blinded, anonymised and investigated with the NGS panel. In addition, we analyzed one known homozygous DMP1 mutation and two samples of HR-patients, where no pathogenic PHEX mutation had been detected by conventional sequencing. Results: The panel detected all 42 pathogenic missense/nonsense/splice-site/indel PHEX-mutations and in one the known homozygous DMP1 mutation. In the remaining two patients, we revealed a somatic mosaicism of a PHEX mutation in one; as well as two variations in DMP1 and a very rare compound heterozygous variation in ENPP1 in the second patient. Conclusions: This developed NGS panel is a reliable tool with high sensitivity and specificity for the diagnosis of XLH and related forms of HR.

scholarly journals A Customized Next-Generation Sequencing-Based Panel to Identify Novel Genetic Variants in Dementing Disorders: A Pilot Study

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Giuseppe Lanza ◽  
Francesco Calì ◽  
Mirella Vinci ◽  
Filomena Irene Ilaria Cosentino ◽  
Mariangela Tripodi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Variants ◽  
Ad Hoc ◽  
Cognitive Disorders ◽  
High Sensitivity ◽  
Future Application ◽  
Next Generation ◽  
Wide Range ◽  
Gene Panels ◽  
Generation Sequencing

Purpose. The advancements in the next-generation sequencing (NGS) techniques have allowed for rapid, efficient, and cost-time-effective genetic variant detection. However, in both clinical practice and research setting, sequencing is still often limited to the use of gene panels clinically targeted on the genes underlying the disease of interest. Methods. We performed a neurogenetic study through an ad hoc NGS-based custom sequencing gene panel in order to screen 16 genes in 8 patients with different types of degenerative cognitive disorders (Alzheimer’s disease, mild cognitive impairment, frontotemporal dementia, and dementia associated with Parkinson’s disease). The study protocol was based on previous evidence showing a high sensitivity and specificity of the technique even when the panel is limited to some hotspot exons. Results. We found variants of the TREM2 and APP genes in three patients; these have been previously identified as pathogenic or likely pathogenic and, therefore, considered “disease causing.” In the remaining subjects, the pathogenicity was evaluated according to the guidelines of the American College of Medical Genetics (ACMG). In one patient, the p.R205W variant in the CHMP2B gene was found to be likely pathogenic of the disease. A variant in the CSF1R and SERPINI1 genes found in two patients was classified as benign, whereas the other two (in the GRN and APP genes) were classified as likely pathogenic according to the ACMG. Conclusions. Notwithstanding the preliminary value of this study, some rare genetic variants with a probable disease association were detected. Although future application of NGS-based sensors and further replication of these experimental data are needed, this approach seems to offer promising translational perspectives in the diagnosis and management of a wide range of neurodegenerative disorders.

scholarly journals Analytical validation of a next generation sequencing liquid biopsy assay for high sensitivity broad molecular profiling

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0193802 ◽  
Author(s):  
Vincent Plagnol ◽  
Samuel Woodhouse ◽  
Karen Howarth ◽  
Stefanie Lensing ◽  
Matt Smith ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Liquid Biopsy ◽  
High Sensitivity ◽  
Molecular Profiling ◽  
Next Generation ◽  
Analytical Validation ◽  
Generation Sequencing
Sign in / Sign up

Export Citation Format

Share Document