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https://www.readbyqxmd.com/read/29778030/retrospective-genotype-phenotype-analysis-in-a-305-patient-cohort-referred-for-testing-of-a-targeted-epilepsy-panel
#1
Andrew N Hesse, Jennifer Bevilacqua, Kritika Shankar, Honey V Reddi
PURPOSE: Epilepsy is a diverse neurological condition with extreme genetic and phenotypic heterogeneity. The introduction of next-generation sequencing into the clinical laboratory has made it possible to investigate hundreds of associated genes simultaneously for a patient, even in the absence of a clearly defined syndrome. This has resulted in the detection of rare and novel mutations at a rate well beyond our ability to characterize their effects. This retrospective study reviews genotype data in the context of available phenotypic information on 305 patients spanning the epileptic spectrum to identify established and novel patterns of correlation...
May 16, 2018: Epilepsy Research
https://www.readbyqxmd.com/read/29777593/degradation-of-recombinant-proteins-by-cho-host-cell-proteases-is-prevented-by-matriptase-1-knock-out
#2
Holger Laux, Sandrine Romand, Sandro Nuciforo, Christopher J Farady, Joel Tapparel, Stine Buechmann-Moeller, Benjamin Sommer, Edward J Oakeley, Ursula Bodendorf
An increasing number of non-antibody format proteins are entering the clinical development. However, one of the major hurdles for the production of non-antibody glycoproteins is host cell-related proteolytic degradation, which can drastically impact developability and timelines of pipeline projects. Chinese hamster ovary (CHO) cells are the preferred production host for recombinant therapeutic proteins. Using protease inhibitors, transcriptomics and genetic knockdowns we have identified, out of the more than 700 known proteases in rodents, Matriptase-1 as the major protease involved in degradation of recombinant proteins expressed in CHO-K1 cells...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777376/comprehensive-molecular-diagnosis-of-epstein-barr-virus-associated-lymphoproliferative-diseases-using-next-generation-sequencing
#3
Shintaro Ono, Manabu Nakayama, Hirokazu Kanegane, Akihiro Hoshino, Saeko Shimodera, Hirofumi Shibata, Hisanori Fujino, Takahiro Fujino, Yuta Yunomae, Tsubasa Okano, Motoi Yamashita, Takahiro Yasumi, Kazushi Izawa, Masatoshi Takagi, Kohsuke Imai, Kejian Zhang, Rebecca Marsh, Capucine Picard, Sylvain Latour, Osamu Ohara, Tomohiro Morio
Epstein-Barr virus (EBV) is associated with several life-threatening diseases, such as lymphoproliferative disease (LPD), particularly in immunocompromised hosts. Some categories of primary immunodeficiency diseases (PIDs) including X-linked lymphoproliferative syndrome (XLP), are characterized by susceptibility and vulnerability to EBV infection. The number of genetically defined PIDs is rapidly increasing, and clinical genetic testing plays an important role in establishing a definitive diagnosis. Whole-exome sequencing is performed for diagnosing rare genetic diseases, but is both expensive and time-consuming...
May 18, 2018: International Journal of Hematology
https://www.readbyqxmd.com/read/29776865/gut-microbiota-in-patients-with-parkinson-s-disease-in-southern-china
#4
Aiqun Lin, Wenxia Zheng, Yan He, Wenli Tang, Xiaobo Wei, Rongni He, Wei Huang, Yuying Su, Yaowei Huang, Hongwei Zhou, Huifang Xie
INTRODUCTION: Accumulating evidence has revealed alterations in the communication between the gut and brain in patients with Parkinson's disease (PD), and previous studies have confirmed that alterations in the gut microbiome play an important role in the pathogenesis of numerous diseases, including PD. The aim of this study was to determine whether the faecal microbiome of PD patients in southern China differs from that of control subjects and whether the gut microbiome composition alters among different PD motor phenotypes...
May 16, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29774027/clinical-remission-of-sight-threatening-non-infectious-uveitis-is-characterized-by-an-upregulation-of-peripheral-t-regulatory-cell-polarized-towards-t-bet-and-tigit
#5
Rose M Gilbert, Xiaozhe Zhang, Robert D Sampson, Michael R Ehrenstein, Dao X Nguyen, Mahid Chaudhry, Charles Mein, Nadiya Mahmud, Grazyna Galatowicz, Oren Tomkins-Netzer, Virginia L Calder, Sue Lightman
Background: Non-infectious uveitis can cause chronic relapsing and remitting ocular inflammation, which may require high dose systemic immunosuppression to prevent severe sight loss. It has been classically described as an autoimmune disease, mediated by pro-inflammatory Th1 and Th17 T-cell subsets. Studies suggest that natural immunosuppressive CD4+ CD25+ FoxP3+ T-regulatory cells (Tregs) are involved in resolution of inflammation and may be involved in the maintenance of clinical remission...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29773649/ptap-motif-duplication-in-the-p6-gag-protein-confers-a-replication-advantage-on-hiv-1-subtype-c
#6
Shilpee Sharma, Prabhu S Arunachalam, Malini Menon, Viswanath Ragupathy, Ravi Vijaya Satya, Joshua Jebaraj, Shambhu Ganeshappa Aralaguppe, Chaitra Rao, Sreshtha Pal, Shanmugam Saravanan, Kailapuri G Murugavel, Pachamuthu Balakrishnan, Suniti Solomon, Indira Hewlett, Udaykumar Ranga
HIV-1 subtype C (HIV-1C) may duplicate longer amino acid stretches in the p6 Gag protein, leading to the creation of an additional Pro-Thr/Ser-Ala-Pro (PTAP) motif necessary for viral packaging. However, the biological significance of a duplication of the PTAP motif for HIV-1 replication and pathogenesis has not been experimentally validated. In a longitudinal study of two different clinical cohorts of select HIV-1 seropositive, drug-naive individuals from India, we found that 8 of 50 of these individuals harbored a mixed infection of viral strains discordant for the PTAP duplication...
May 17, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29773090/vsita-an-improved-approach-of-target-amplification-in-the-identification-of-viral-pathogens
#7
Yi Zhang, Chen Zhang, Bo Li, Yang Li, Xiao Zhou He, Acher Li, Wei Wu, Su Xia Duan, Fang Zhou Qiu, Ji Wang, Xin Xin Shen, Meng Jie Yang, De Xin Li, Xue Jun Ma
OBJECTIVE: Unbiased next generation sequencing (NGS) is susceptible to interference from host or environmental sequences. Consequently, background depletion and virome enrichment techniques are usually needed for clinical samples where viral load is much lower than background sequences. METHODS: A viral Sequence Independent Targeted Amplification (VSITA) approach using a set of non-ribosomal and virus-enriched octamers (V8) was developed and compared with traditionally used random hexamers (N6)...
April 2018: Biomedical and Environmental Sciences: BES
https://www.readbyqxmd.com/read/29771234/an-observational-clinical-case-of-zika-virus-associated-neurological-disease-is-associated-with-primary-igg-response-and-enhanced-tnf-levels
#8
Edson Delatorre, Milene Miranda, Diogo A Tschoeke, Patrícia Carvalho de Sequeira, Simone Alves Sampaio, Giselle Barbosa-Lima, Yasmine Rangel Vieira, Luciana Leomil, Fernando A Bozza, José Cerbino-Neto, Patricia T Bozza, Rita Maria Ribeiro Nogueira, Patrícia Brasil, Fabiano L Thompson, Ana M B de Filippis, Thiago Moreno L Souza
Descriptive clinical data help to reveal factors that may provoke Zika virus (ZIKV) neuropathology. The case of a 24-year-old female with a ZIKV-associated severe acute neurological disorder was studied. The levels of ZIKV in the cerebrospinal fluid (CSF) were 50 times higher than the levels in other compartments. An acute anti-flavivirus IgG, together with enhanced TNF-alpha levels, may have contributed to ZIKV invasion in the CSF, whereas the unbiased genome sequencing [obtained by next-generation sequencing (NGS)] of the CSF revealed that no virus mutations were associated with the anatomic compartments (CSF, serum, saliva and urine)...
May 17, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29767702/long-reads-their-purpose-and-place
#9
Martin O Pollard, Deepti Gurdasani, Alexander J Mentzer, Tarryn Porter, Manjinder S Sandhu
In recent years long read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing (NGS), the cost of sequencing using long read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterising genomes at high resolution. In this article, we will endeavour to present an introduction to long read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful; and how they are being used...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29766049/interleukin-1%C3%AE-deficient-mice-have-an-altered-gut-microbiota-leading-to-protection-from-dextran-sodium-sulfate-induced-colitis
#10
Moran Nunberg, Nir Werbner, Hadar Neuman, Marina Bersudsky, Alex Braiman, Moshe Ben-Shoshan, Meirav Ben Izhak, Yoram Louzoun, Ron N Apte, Elena Voronov, Omry Koren
Inflammatory bowel diseases (IBD) are a group of chronic inflammatory disorders of the intestine, with as-yet-unclear etiologies, affecting over a million people in the United States alone. With the emergence of microbiome research, numerous studies have shown a connection between shifts in the gut microbiota composition (dysbiosis) and patterns of IBD development. In a previous study, we showed that interleukin 1α (IL-1α) deficiency in IL-1α knockout (KO) mice results in moderate dextran sodium sulfate (DSS)-induced colitis compared to that of wild-type (WT) mice, characterized by reduced inflammation and complete healing, as shown by parameters of weight loss, disease activity index (DAI) score, histology, and cytokine expression...
May 2018: MSystems
https://www.readbyqxmd.com/read/29765558/the-fallopian-tube-microbiome-implications-for-reproductive-health
#11
Elise S Pelzer, Dana Willner, Melissa Buttini, Louise M Hafner, Christina Theodoropoulos, Flavia Huygens
Objective: There is a paucity of data characterizing the microbiota of the female upper genital tract, which controversially is described as a sterile site. We examine whether the fallopian tube harbours an endogenous microbial community. Design: This prospective study collected from women undergoing total hysterectomy or salpingectomy-oophorectomy. Setting: Private hospital gynaecology department. Patients: Fallopian tubes were collected from women diagnosed with benign disease or for prophylaxis...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765525/clinical-characteristics-of-non-small-cell-lung-cancer-harboring-mutations-in-exon-20-of-egfr-or-her2
#12
Masayuki Takeda, Kazuko Sakai, Hidetoshi Hayashi, Kaoru Tanaka, Junko Tanizaki, Takayuki Takahama, Koji Haratani, Kazuto Nishio, Kazuhiko Nakagawa
Unlike common epidermal growth factor receptor gene ( EGFR ) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), mutations in exon 20 of either EGFR or the human EGFR2 gene ( HER2 ) are associated with insensitivity to EGFR-TKIs, with treatment options for patients with such mutations being limited. Clinical characteristics, outcome of EGFR-TKI or nivolumab treatment, and the presence of coexisting mutations were reviewed for NSCLC patients with exon-20 mutations of EGFR or HER2 as detected by routine application of an amplicon-based next-generation sequencing panel...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765283/integration-of-multigene-panels-for-the-diagnosis-of-hereditary-retinal-disorders-using-next-generation-sequencing-and-bioinformatics-approaches
#13
Chiara Di Resta, Ivana Spiga, Silvia Presi, Stefania Merella, Giovanni Battista Pipitone, Maria Pia Manitto, Giuseppe Querques, Maurizio Battaglia Parodi, Maurizio Ferrari, Paola Carrera
In recent years, Next-Generation Sequencing (NGS) opened a new way for the study of pathogenic mechanisms and for molecular diagnosis of inherited disorders. In the present work, we focused our attention on the inherited retinal dystrophies (IRDs), a group of specific disorders of the retina, displaying a very high clinical and genetic heterogeneity, whose genetic diagnosis is not easily feasible. It represents a paradigmatic example for the integration of clinical and molecular examination toward precision medicine...
April 2018: EJIFCC
https://www.readbyqxmd.com/read/29765282/next-generation-sequencing-approach-for-the-diagnosis-of-human-diseases-open-challenges-and-new-opportunities
#14
Chiara Di Resta, Silvia Galbiati, Paola Carrera, Maurizio Ferrari
The rapid evolution and widespread use of next generation sequencing (NGS) in clinical laboratories has allowed an incredible progress in the genetic diagnostics of several inherited disorders. However, the new technologies have brought new challenges. In this review we consider the important issue of NGS data analysis, as well as the interpretation of unknown genetic variants and the management of the incidental findings. Moreover, we focus the attention on the new professional figure of bioinformatics and the new role of medical geneticists in clinical management of patients...
April 2018: EJIFCC
https://www.readbyqxmd.com/read/29764856/-tp53-stk11-and-egfr-mutations-predict-tumor-immune-profile-and-the-response-to-anti-pd-1-in-lung-adenocarcinoma
#15
Jerome Biton, Audrey Mansuet-Lupo, Nicolas Pécuchet, Marco Alifano, Hanane Ouakrim, Jennifer Arrondeau, Pascaline Boudou-Rouquette, Francois Goldwasser, Karen Leroy, Jeremy Goc, Marie Wislez, Claire Germain, Pierre Laurent-Puig, Marie-Caroline Dieu-Nosjean, Isabelle Cremer, Ronald Herbst, Hélène F Blons, Diane Damotte
PURPOSE: By unlocking anti-tumor immunity, antibodies targeting programmed cell death 1 (PD-1) exhibit impressive clinical results in non-small cell lung cancer, underlining the strong interactions between tumor and immune cells. However, factors that can robustly predict long-lasting responses are still needed. EXPERIMENTAL DESIGN: We performed in depth immune profiling of lung adenocarcinoma using an integrative analysis based on immunohistochemistry, flow-cytometry and transcriptomic data...
May 15, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29764581/-clinical-application-of-minimal-residual-disease-detection-in-childhood-acute-leukemia
#16
Yan-Qin Cheng, Xiao-Wen Zhai
In recent years, great progress has been made in the treatment outcome of childhood acute leukemia with the improvement of chemotherapy regimens and the introduction of risk-stratified therapy; however, minimal residual disease (MRD) is still a difficult problem which affects the prognosis of acute leukemia. MRD influences the selection of chemotherapy regimens and recurrence risk stratification, and meanwhile, it can be used for prognostic prediction. At present, flow cytometry and polymerase chain reaction are mainly used for MRD detection...
May 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/29764494/precision-medicine-becomes-reality-tumor-type-agnostic-therapy
#17
REVIEW
Li Yan, Wei Zhang
Precision medicine just witnessed two breakthroughs in oncology in 2017. Pembrolizumab (Keytruda), Merck's anti-programmed cell death-1 (PD-1) monoclonal antibody (mAb), received accelerated approval in May 2017 by the US Food and Drug Administration for the treatment of adult and pediatric patients with unresectable or metastatic solid tumors that have been identified as having microsatellite instability-high (MSI-H) or deficient DNA mismatch repair (dMMR). Shortly after, nivolumab (Opdivo), Bristol-Myers Squibb's anti-PD-1 mAb, gained an accelerated approval in August 2017 for adult and pediatric patients with MSI-H or dMMR metastatic colorectal cancer that has progressed after standard chemotherapy...
March 31, 2018: Cancer communications
https://www.readbyqxmd.com/read/29764212/the-clinical-application-of-single-sperm-based-snp-haplotyping-for-pgd-of-osteogenesis-imperfecta
#18
Linjun Chen, Zhenyu Diao, Zhipeng Xu, Jianjun Zhou, Guijun Yan, Haixiang Sun
Osteogenesis imperfecta (OI) is a genetically heterogeneous disorder, presenting either autosomal dominant, autosomal recessive or X-linked inheritance patterns. The majority of OI cases are autosomal dominant and are caused by heterozygous mutations in either the COL1A1 or COL1A2 gene. In these dominant disorders, allele dropout (ADO) can lead to misdiagnosis in preimplantation genetic diagnosis (PGD). Polymorphic markers linked to the mutated genes have been used to establish haplotypes for identifying ADO and ensuring the accuracy of PGD...
May 15, 2018: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/29763627/evaluation-of-minion-nanopore-sequencing-for-rapid-enterovirus-genotyping
#19
Emily Rames, Joanne Macdonald
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new methods for EV genome amplification, and subsequent genotyping using the miniaturised MinION sequencing device. Importantly, this next-generation sequencer enabled correct strain-level assignment of identity for the EV-A71 isolate assessed, where strains with up to 99...
May 12, 2018: Virus Research
https://www.readbyqxmd.com/read/29762727/development-of-targeted-therapy-and-immunotherapy-for-treatment-of-small-cell-lung-cancer
#20
Motonobu Saito, Kouya Shiraishi, Akiteru Goto, Hiroyuki Suzuki, Takashi Kohno, Koji Kono
Targeted therapy against druggable genetic aberrations has shown a significantly positive response rate and longer survival in various cancers, including lung cancer. In lung adenocarcinoma (LADC), specific thyroxin kinase inhibitors against EGFR mutations and ALK fusions are used as a standard treatment regimen and show significant positive efficacy. On the other hand, targeted therapy against driver gene aberrations has not been adapted yet in small cell lung cancer (SCLC). This is because driver genes and druggable aberrations are rarely identified by next generation sequencing in SCLC...
May 14, 2018: Japanese Journal of Clinical Oncology
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