Next Generation Sequencing
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Pathology ◽  
2021 ◽  
Vol 53 ◽  
pp. S32
Author(s):  
Sharron Liang ◽  
Min Li Huang ◽  
Bin Wang ◽  
Min R. Qiu

2021 ◽  
Vol 12 ◽  
Author(s):  
Isabelle Oliver-Petit ◽  
Thomas Edouard ◽  
Virginie Jacques ◽  
Marie Bournez ◽  
Audrey Cartault ◽  
...  

ContextCongenital hypothyroidism (CH) is related to dyshormonogenesis in 15% to 40% of the world population and associated with homozygous or heterozygous variants in the main genes of the hormone synthesis pathway. Emerging diagnostic tools, such as next-generation sequencing (NGS), have been used to efficiently explore panels of genes and identify complex mechanisms of pathogenesis.ObjectiveWe explored 19 candidate genes known to be causative for permanent or transient CH to evaluate the role of complex gene variations in CH phenotype.Patients, Design and SettingUsing the NGS approach, we studied 65 newborns with thyroid dyshormonogenesis (TDH). New variants were assessed in silico for pathogenicity.ResultsAmong the 65 infants, 56.9% presented a variant in one or more genes of the thyroid hormone synthesis axis. We identified homozygous or compound heterozygous variants in the TG, DUOX2, TPO, or SLC5A5 genes in 10 infants and heterozygous variants in DUOX2, TG, TPO, and TSHR in 19 others. In seven cases, a heterozygous variant in the TG gene was the unique anomaly detected, but related to disturbed hormonal balance. Oligogenic variants were found in eight infants associated with severe CH and goiter in five of them.ConclusionThe systematic exploration of genes involved in thyroid hormone synthesis by NGS in TDH showed high diagnostic relevance. Oligogenic inheritance could be related to phenotypic heterogeneity and a high frequency of goiter.


BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Chen ◽  
Zheng Chen ◽  
Yi-shu Yang ◽  
Gui-lan Cai ◽  
Xiao-jiao Xu ◽  
...  

Abstract Background Neurocysticercosis (NCC) is the most common helminthic infection of the central nervous system (CNS) caused by the larval stage of Taenia solium. Accurate and early diagnosis of NCC remains challenging due to its heterogeneous clinical manifestations, neuroimaging deficits, variable sensitivity, and specificity of serological tests. Next-generation sequencing (NGS)-based pathogen analysis in patient’s cerebrospinal fluid (CSF) with NCC infection has recently been reported indicating its diagnostic efficacy. In this case study, we report the diagnosis of a NCC patient with a symptomatic history of over 20 years using NGS analysis and further confirmation of the pathology by immunological tests. Case presentation This study reports the clinical imaging and immunological features of a patient with a recurrent headache for more than 20 years, which worsened gradually with the symptom of fever for more than 7 years and paroxysmal amaurosis for more than 1 year. By utilizing NGS technique, the pathogen was detected in patient’s CSF, and the presence of Taenia solium-DNA was confirmed by a positive immunological reaction to cysticercus IgG antibody in CSF and serum samples. The symptoms of the patient were alleviated, and the CSF condition was improved substantially after the anti-helminthic treatment. Conclusions This study suggests that combining CSF NGS with cysticercus IgG testing may be a highly promising approach for diagnosing the challenging cases of NCC. Further studies are needed to evaluate the parasitic DNA load in patients’ CSF for the diagnosis of disease severity, stage, and monitoring of therapeutic responses.


PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253541
Author(s):  
Miyoung Kim ◽  
Kibum Jeon ◽  
Kasey Hutt ◽  
Alyssa M. Zlotnicki ◽  
Hyo Jung Kim ◽  
...  

Introduction We assessed the applicability of next-generation sequencing (NGS)-based IGH/IGK clonality testing and analyzed the repertoire of immunoglobulin heavy chain (IGH) or immunoglobulin kappa light chain (IGK) gene usage in Korean patients with multiple myeloma (MM) for the first time. Methods Fifty-nine bone marrow samples from 57 Korean patients with MM were analyzed, and NGS-based clonality testing that targeted the IGH and IGK genes was performed using IGH FR1 and IGK primer sets. Results Clonal IGH and IGK rearrangements were observed in 74.2% and 67.7% of samples from Korean patients with kappa-restricted MM, respectively (90.3% had one or both), and in 60.7% and 95.5% of samples from those with lambda-restricted MM, respectively (85.7% had one or both). In total, 88.1% of samples from Koreans with MM had clonal IGH and/or IGK rearrangement. Clonal rearrangement was not significantly associated with the bone marrow plasma cells as a proportion of all BM lymphoid cells. IGHV3-9 (11.63%) and IGHV4-31 (9.30%) were the most frequently reported IGHV genes and were more common in Koreans with MM than in Western counterparts. IGHD3-10 and IGHD3-3 (13.95% each) were the most frequent IGHD genes; IGHD3-3 was more common in Koreans with MM. No IGK rearrangement was particularly prevalent, but single IGKV-J rearrangements were less common in Koreans with kappa-restricted MM than in Western counterparts. IGKV4-1 was less frequent in Koreans regardless of light chain type. Otherwise, the usages of the IGH V, D, and J genes and of the IGK gene were like those observed in previous Western studies. Conclusion NGS-based IGH/IGK clonality testing ought to be applicable to most Koreans with MM. The overrepresentation of IGHV3-9, IGHV4-31, and IGHD3-3 along with the underrepresentation of IGKV4-1 and the differences in IGK gene rearrangement types suggest the existence of ethnicity-specific variations in this disease.


2021 ◽  
Vol 10 (25) ◽  
Author(s):  
Masatoshi Tsukahara ◽  
Kotaro Ise ◽  
Maiko Nezuo ◽  
Haruna Azuma ◽  
Takeshi Akao ◽  
...  

We report here the draft genome sequence for Saccharomyces cerevisiae strain Awamori number 101, an industrial strain used for producing awamori, a distilled alcohol beverage. It was constructed by assembling the short reads obtained by next-generation sequencing. The 315 contigs constitute an 11.5-Mbp genome sequence coding 6,185 predicted proteins.


2021 ◽  
Vol 28 (4) ◽  
pp. 2326-2336
Author(s):  
Min-Ying Sun ◽  
Fang-Qin Lin ◽  
Lu-Jia Chen ◽  
Hong Li ◽  
Wei-Quan Lin ◽  
...  

Liquid biopsy through the detection of circulating tumor DNA (ctDNA) has potential advantages in cancer monitoring and prediction. However, most previous studies in this area were performed with a few hotspot genes, single time point detection, or insufficient sequencing depth. In this study, we performed targeted next-generation sequencing (NGS) with a customized panel in metastatic breast cancer (MBC) patients. Fifty-four plasma samples were taken before chemotherapy and after the third course of treatment for detection and analysis. Paired lymphocytes were also included to eliminate clonal hematopoiesis (CH)-related alternatives. A total of 1182 nonsynonymous mutations in 419 genes were identified. More ctDNA mutations were detected in patients with tumors > 3 cm (p = 0.035) and HER2(−) patients (p = 0.029). For a single gene, the distribution of ctDNA mutations was also correlated with clinical characteristics. Multivariate regression analysis revealed that HER2 status was significantly associated with mutation burden (OR 0.02, 95% CI 0–0.62, p = 0.025). The profiles of ctDNA mutations exhibited marked discrepancies between two time points, and baseline ctDNA was more sensitive and specific than that after chemotherapy. Finally, elevated ctDNA mutation level was positively correlated with poor survival (p < 0.001). Mutations in ctDNA could serve as a potential biomarker for the evaluation, prediction, and clinical management guidance of MBC patients with chemotherapy.


Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3148
Author(s):  
Youngjun Park ◽  
Dominik Heider ◽  
Anne-Christin Hauschild

The rapid improvement of next-generation sequencing (NGS) technologies and their application in large-scale cohorts in cancer research led to common challenges of big data. It opened a new research area incorporating systems biology and machine learning. As large-scale NGS data accumulated, sophisticated data analysis methods became indispensable. In addition, NGS data have been integrated with systems biology to build better predictive models to determine the characteristics of tumors and tumor subtypes. Therefore, various machine learning algorithms were introduced to identify underlying biological mechanisms. In this work, we review novel technologies developed for NGS data analysis, and we describe how these computational methodologies integrate systems biology and omics data. Subsequently, we discuss how deep neural networks outperform other approaches, the potential of graph neural networks (GNN) in systems biology, and the limitations in NGS biomedical research. To reflect on the various challenges and corresponding computational solutions, we will discuss the following three topics: (i) molecular characteristics, (ii) tumor heterogeneity, and (iii) drug discovery. We conclude that machine learning and network-based approaches can add valuable insights and build highly accurate models. However, a well-informed choice of learning algorithm and biological network information is crucial for the success of each specific research question.


2021 ◽  
Author(s):  
Ting Wang ◽  
Yinhuan Zhong ◽  
Xianzheng Li ◽  
Hanbiao Chen ◽  
Jian Lu ◽  
...  

Abstract Introductions: Complex chromosome rearrangement (CCR) is a structural rearrangement involving more than two breakpoints. CCR carriers are at high risk for phenotypic abnormalities or reproductive failure, such as chromosomal abnormalities in fetuses and infertility. In this study, we presented a carriers with chromosome (3,18) balanced translocation, whose fetus had duplications in chromosome 3 and deletions in chromosome 10 demonstrated by chromosomal microarray analysis (CMA).By revealing the cryptical translocation, we aimed to provide CCR carriers with more accurate risk assessment of abnormal pregnancy and better assisted reproduction with CMA and next generation sequencing(NGS).Results: By using the high resolution of GTG-banding technology, a cryptical translocation in chromosome 10 was found and the karyotype of the carrier was revised as 46,XY,t(3;10;18) (p26.3;q26.1;q21.1).In the cycle of preimplantation genetic diagnosis (PGD),21 oocytes were retrieved, and 15 were fertilized. At last 7 embryos were biospied and sent to diagnosis by next generation sequencing(NGS).Unfortunately, none of the NGS results from the 7 biopsy embryos were normal. Combining previous literature and our results, we assessed the odds of a balanced embryo in a CCR carrier to be about 9.3%(28/302).The transferable embryo rate was approximately 71.4%(20/28) and healthy live born delivery rate was 55%(11/20).Conclusions: NGS and CMA featured high automation, relatively low cost, high throughput, and high repeatability, which made them commonly used during prenatal diagnosis and PGD. The multiple technology combination can provide more accurate diagnosis and better fertility services for CCR patients.


2021 ◽  
Author(s):  
Chang Liu ◽  
Yanlin Huang ◽  
Yan Zhang ◽  
Hongke Ding ◽  
Lihua Yu ◽  
...  

Abstract Background: Hearing loss (HL) is a prevalent sensorineural disorder, and is among the most etiologically heterogeneous disorders. With the advent of next-generation sequencing (NGS) technologies, hundreds of candidate genes can be analyzed simultaneously in a cost-effective manner. Methods: 94 patients from 87 families diagnosed with non-syndromic or syndromic hearing loss were enrolled. A custom-designed HL panel and clinical exome sequencing (CES) were applied to explore molecular etiology in the cohort, and the efficacy of the two panels was examined. Results: The etiologic diagnosis for hearing loss has been arrived at 40 out of 94 patients (42.6%), 28 with an autosomal recessive (AR) inheritance pattern and 12 with an autosomal dominant (AD) pattern. Candidate variants in 19 different genes were identified in the study cohort, 11 with AR inheritance pattern and 8 with AD pattern. 14 of the variants identified in the study were novel. Compared with CES, the custom-designed HL panel has comparatively higher diagnostic yield (61.5% vs. 29.1%), less expensive price, similar turn-around time, and can be used as an efficient diagnostic tool for hearing loss in the clinical practice. Conclusions: Next-generation sequencing facilitates genetic diagnosis and improves the management of patients with hearing loss in the clinical practice.


Medicine ◽  
2021 ◽  
Vol 100 (25) ◽  
pp. e26388
Author(s):  
Assaf Moore ◽  
Yael Bar ◽  
Corinne Maurice-Dror ◽  
Inbar Finkel ◽  
Hadar Goldvaser ◽  
...  

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