scholarly journals Reevaluating the Mutation Classification in Genetic Studies of Bradycardia Using ACMG/AMP Variant Classification Framework

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Liting Cheng ◽  
Xiaoyan Li ◽  
Lin Zhao ◽  
Zefeng Wang ◽  
Junmeng Zhang ◽  
...  
Keyword(s):  
Clinical Manifestations ◽  
Sequence Variants ◽  
Variant Classification ◽  
Genetic Studies ◽  
Related Sequence ◽  
Classification Framework ◽  
Pubmed Database ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing

Purpose. Next-generation sequencing (NGS) has become more accessible, leading to an increasing number of genetic studies of familial bradycardia being reported. However, most of the variants lack full evaluation. The relationship between genetic factors and bradycardia should be summarized and reevaluated. Methods. We summarized genetic studies published in the PubMed database from 2008/1/1 to 2019/9/1 and used the ACMG/AMP classification framework to analyze related sequence variants. Results. We identified 88 articles, 99 sequence variants, and 34 genes after searching the PubMed database and classified ABCC9, ACTN2, CACNA1C, DES, HCN4, KCNQ1, KCNH2, LMNA, MECP2, LAMP2, NPPA, SCN5A, and TRPM4 as high-priority genes causing familial bradycardia. Most mutated genes have been reported as having multiple clinical manifestations. Conclusions. For patients with familial CCD, 13 high-priority genes are recommended for evaluation. For genetic studies, variants should be carefully evaluated using the ACMG/AMP variant classification framework before publication.

scholarly journals Detection of Listeria monocytogenes in a patient with meningoencephalitis using next-generation sequencing: a case report

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zi-Wei Lan ◽  
Min-Jia Xiao ◽  
Yuan-lin Guan ◽  
Ya-Jing Zhan ◽  
Xiang-Qi Tang
Keyword(s):  
Listeria Monocytogenes ◽  
Next Generation Sequencing ◽  
Mammalian Cells ◽  
Clinical Manifestations ◽  
Bacterial Pathogen ◽  
Next Generation ◽  
Accurate Treatment ◽  
The Central Nervous System ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Abstract Background Listeria monocytogenes (L. monocytogenes) is a facultative intracellular bacterial pathogen which can invade different mammalian cells and reach to the central nervous system (CNS), leading to meningoencephalitis and brain abscesses. In the diagnosis of L. monocytogenes meningoencephalitis (LMM), the traditional test often reports negative owing to the antibiotic treatment or a low number of bacteria in the cerebrospinal fluid. To date, timely diagnosis and accurate treatment remains a challenge for patients with listeria infections. Case presentation We present the case of a 66-year-old woman whose clinical manifestations were suspected as tuberculous meningoencephalitis, but the case was finally properly diagnosed as LMM by next-generation sequencing (NGS). The patient was successfully treated using a combined antibacterial therapy, comprising ampicillin and trimethoprim-sulfamethoxazole. Conclusion To improve the sensitivity of LMM diagnosis, we used NGS for the detection of L. monocytogenes. Hence, the clinical utility of this approach can be very helpful since it provides quickly and trust results.

scholarly journals Association of miR-1251-5p/miR-6892-5p Expression With Clinicopathological Factors in Premenopausal Endometrial Cancer

2021 ◽  
Author(s):  
Jing Zhang ◽  
Bin Li ◽  
Yang Liu ◽  
Fei Wang ◽  
Yu Zhang ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Target Genes ◽  
Tumor Grading ◽  
Node Metastasis ◽  
Predict Mirna Target ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing ◽  
Menarche Age ◽  
Selection Of

Abstract Background This study is aim to profile the differentially expressed microRNAs (DEMs) of premenopausal endometrial cancer (EC), identify their target genes and understand their roles in carcinogenesis. Methods Next-generation sequencing (NGS) was performed on 3 premenopausal EC and 3 premenopausal normal endometrial tissues. Selection of candidate miRNAs and subsequent validation were performed by qRT-PCR on 20 premenopausal EC, 30 premenopausal normal endometrial and 40 postmenopausal EC samples. The relationship between DEMs and clinical characteristics was analyzed. Moreover, bioinformatic software programs and databases were applied to predict miRNA target genes, molecular functions, and signaling pathways. Results 136 upregulated and 131 downregulated DEMs were identified. The expression of miR-1251-5p was highly upregulated in premenopausal EC samples compared with premenopausal normal endometrial samples and significantly downregulated compared with postmenopausal EC samples. The expression of miR-6892-5p was highly upregulated in premenopausal EC samples compared with premenopausal normal endometrial samples and postmenopausal EC samples. In the premenopausal EC group, miR-1251-5p expression was closely correlated with menarche age, number of pregnancies, tumor grading, myometrial infiltration and lymph node metastasis; miR-6892-5p expression was closely correlated with BMI, hypertension, tumor grading, and metastasis. Conclusions miR-1251-5p and miR-6892-5p may play important roles in tumorigenesis progression of premenopausal EC.

scholarly journals Tiered Somatic Variant Classification Adoption Has Increased Worldwide With Some Practice Differences Based on Location and Institutional Setting

2021 ◽  
Author(s):  
Frido K. Bruehl ◽  
Annette S. Kim ◽  
Marilyn M. Li ◽  
Neal I. Lindeman ◽  
Joel T. Moncur ◽  
...  
Keyword(s):  
Clinical Utility ◽  
Hematologic Malignancies ◽  
Classification Systems ◽  
Institutional Setting ◽  
Variant Classification ◽  
Somatic Variant ◽  
And Performance ◽  
American Society ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Context.— The 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (CAP) tier classification guideline provides a framework to standardize interpretation and reporting of somatic variants. Objective.— To evaluate the adoption and performance of the 2017 guideline among laboratories performing somatic next-generation sequencing (NGS). Design.— A survey was distributed to laboratories participating in NGS CAP proficiency testing for solid tumors (NGSST) and hematologic malignancies (NGSHM). Results.— Worldwide, 64.4% (152 of 236) of NGSST and 66.4% (87 of 131) of NGSHM participants used tier classification systems, of which the 2017 guideline was used by 84.9% (129 of 152) of NGSST and 73.6% (64 of 87) of NGSHM participants. The 2017 guideline was modified by 24.4% (30 of 123) of NGSST and 21.7% (13 of 60) of NGSHM laboratories. Laboratories implementing the 2017 guideline were satisfied or very satisfied (74.2% [89 of 120] NGSST and 69.5% [41 of 59] NGSHM), and the impression of tier classification reproducibility was high (mean of 3.9 [NGSST] and 3.6 [NGSHM] on a 5-point scale). Of nonusers, 35.2% (38 of 108) of NGSST and 39.4% (26 of 66) of NGSHM laboratories were planning implementation. For future guideline revisions, respondents favored including variants to monitor disease (63.9% [78 of 122] NGSST, 80.0% [48 of 60] NGSHM) and germline variants (55.3% [63 of 114] NGSST, 75.0% [45 of 60] NGSHM). Additional subtiers were not favored by academic laboratories compared to nonacademic laboratories (P < .001 NGSST and P = .02 NGSHM). Conclusions.— The 2017 guideline has been implemented by more than 50.0% of CAP laboratories. While most laboratories using the 2017 guideline report satisfaction, thoughtful guideline modifications may further enhance the quality, reproducibility, and clinical utility of the 2017 guideline for tiered somatic variant classification.

DEFICIENCY OF LRBA: BIBLIOGRAPHICAL REVIEW AND CASE REPORT

2021 ◽  
Vol 100 (2) ◽  
pp. 192-203
Author(s):  
I.V. Kondratenko ◽  
◽  
S.S. Vakhlayrskaya ◽  
D.V. Rogozhin ◽  
◽  
...  
Keyword(s):  
Case Report ◽  
Genetic Basis ◽  
Clinical Manifestations ◽  
Main Role ◽  
Principles Of Treatment ◽  
The Subject ◽  
Next Generation Sequencing Ngs ◽  
Lrba Deficiency ◽  
Generation Sequencing

Since the description of the first primary immunodeficiencies (PIDs) in the 50–60s of the last century, they have been the subject of intensive research aimed at elucidating their etiology and finding effective treatments. The development of next-generation sequencing (NGS) methods made it possible to reveal the genetic basis of many new forms of PID, which were previously attributed to various syndromes due to their clinical and immunological characteristics. An example of such a PID is the LRBA (the lipopolysaccharide-responsive and beige-like anchor protein) deficiency, sometimes called LATAIE [LRBA deficiency with autoantibodies, regulatory T (Treg) cell defects, autoimmune infiltration, and enteropathy]. The article provides information on the main role of the LRBA molecule in the functions of immunocompetent cells, describes immunological disorders and clinical manifestations of LRBA deficiency and the principles of treatment of diseases. Two own observations of LRBA deficiency are presented.

scholarly journals Eukaryotic and Prokaryotic Microbiota Interactions

2020 ◽  
Author(s):  
Aly Kodio ◽  
Estelle Menu ◽  
Stéphane Ranque
Keyword(s):  
Bacterial Communities ◽  
Current Knowledge ◽  
Experimental Models ◽  
Medical Practices ◽  
Host Genetics ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing ◽  
Health Applications

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites, and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g. antibiotic treatment), climate, season, and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths, and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

scholarly journals Copy number variations in female infertility in China

2019 ◽  
Vol 22 (1) ◽  
pp. 5-10
Author(s):  
W Huang ◽  
J Wang ◽  
M Pang ◽  
Q Zhao ◽  
L Kong ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variations ◽  
Female Infertility ◽  
Functional Genes ◽  
Chromosome X ◽  
Republic Of China ◽  
Number Variation ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing

AbstractCopy number variation (CNV) is a main cause of male infertility, yet its influence still remains elusive in that of females. To investigate the correlation between CNV and female infertility, we applied whole-genome CNV analyses by next generation Sequencing (NGS), and analyzed 324 female infertility samples in Xinjiang Province, People's Republic of China. We identified 29 CNVs in total, of which 10 were novel CNVs. We found these CNVs mostly in chromosome X. The CNVs from one sample overlapped the POF1B gene that was related to premature ovarian failure (POF). The rest of these CNVs overlapped important functional genes related to neuropathy, brain, skin and retina, and the relationship between these CNVs and fertility needs to be studied further. We also found recurrent CNVs located on Xp22.31 and 22ql 1.21 in five and three cases, respectively. Our study first identified and characterized CNVs (CNVs preference, recurrent CNVs) in female infertility, also provided genetic evidence and references for future study and infertility etiology research.

scholarly journals Next-Generation Sequencing Analysis of Root Canal Microbiota Associated with a Severe Endodontic-Periodontal Lesion

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1461
Author(s):  
Alessio Buonavoglia ◽  
Gianvito Lanave ◽  
Michele Camero ◽  
Marialaura Corrente ◽  
Antonio Parisi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Bacterial Population ◽  
Clinical Manifestations ◽  
Fusobacterium Nucleatum ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Bacterial Migration ◽  
Next Generation Sequencing Analysis ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

A patient with an unusual endo-periodontal lesion, without coronal decay or damage, likely caused by a deep periodontal lesion with subsequent endodontic bacterial migration, required medical care. Next-generation sequencing (NGS) was used to assess the endodontic microbiota in vestibular and palatal canals after tooth extraction, evidencing a predominant population (Fusobacterium nucleatum) in one endodontic canal, and a mixed bacterial population with six major populations almost equally distributed in the other endodontic canal (F. nucleatum, Porphyromonas gingivalis, P. endodontis, Parvimonas, Peptostreptococcus stomatis, Prevotella multiformis). These data could suggest different, separated ecologic niches in the same endodontic system, with potentially different pathogenicity levels, clinical manifestations and prognoses for every single canal of the same tooth.

scholarly journals Eukaryotic and Prokaryotic Microbiota Interactions

2020 ◽  
Vol 8 (12) ◽  
pp. 2018
Author(s):  
Aly Kodio ◽  
Estelle Menu ◽  
Stéphane Ranque
Keyword(s):  
Bacterial Communities ◽  
Current Knowledge ◽  
Experimental Models ◽  
Medical Practices ◽  
Host Genetics ◽  
Next Generation Sequencing Ngs ◽  
The Relationship ◽  
Generation Sequencing ◽  
Health Applications

The nature of the relationship between the communities of microorganisms making up the microbiota in and on a host body has been increasingly explored in recent years. Microorganisms, including bacteria, archaea, viruses, parasites and fungi, have often long co-evolved with their hosts. In human, the structure and diversity of microbiota vary according to the host’s immunity, diet, environment, age, physiological and metabolic status, medical practices (e.g., antibiotic treatment), climate, season and host genetics. The recent advent of next generation sequencing (NGS) technologies enhanced observational capacities and allowed for a better understanding of the relationship between distinct microorganisms within microbiota. The interaction between the host and their microbiota has become a field of research into microorganisms with therapeutic and preventive interest for public health applications. This review aims at assessing the current knowledge on interactions between prokaryotic and eukaryotic communities. After a brief description of the metagenomic methods used in the studies were analysed, we summarise the findings of available publications describing the interaction between the bacterial communities and protozoa, helminths and fungi, either in vitro, in experimental models, or in humans. Overall, we observed the existence of a beneficial effect in situations where some microorganisms can improve the health status of the host, while the presence of other microorganisms has been associated with pathologies, resulting in an adverse effect on human health.

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