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Next generation sequencing review

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https://www.readbyqxmd.com/read/29674443/recent-advances-in-the-treatment-of-peripheral-t-cell-lymphoma
#1
REVIEW
Kamel Laribi, Mustapha Alani, Catherine Truong, Alix Baugier de Materre
Peripheral T-cell lymphoma (PTCL) is a heterogeneous group of clinically aggressive diseases associated with poor outcome. Despite progress in the last several years, resulting in a deeper understanding of the natural history and biology of PTCL based on molecular profiling and next-generation sequencing, there is a need for improvement in efficacy of chemotherapeutic regimens for newly diagnosed patients. Treatment in the front-line setting is most often cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) or CHOP-like regimens, which are associated with a high failure rate and frequent relapses...
April 19, 2018: Oncologist
https://www.readbyqxmd.com/read/29673906/interest-of-next-generation-sequencing-in-bcg-treated-high-risk-bladder-cancer
#2
C Jungels, N Martinez Chanza, S Albisinni, M Mercier, N d'Haene, S Rorive, T Roumeguère
OBJECTIVES: There are only few predictive factors for response of non-musculo-invasive bladder cancer (NMIBC) to Bacillus Calmette-Guérin (BCG) therapy. Our study analyzed the results of the sequencing of new generation (NGS) targeted on 50 genes of oncological interest obtained on bladder resection parts in high-risk NMIBC patients treated with BCG, to describe this population from a molecular point of view and try to correlate these results in patients who present or not recurrence after BCG...
April 16, 2018: Progrès en Urologie
https://www.readbyqxmd.com/read/29673712/update-on-systemic-prostate-cancer-therapies-management-of-metastatic-castration-resistant-prostate-cancer-in-the-era-of-precision-oncology
#3
REVIEW
Philipp Nuhn, Johann S De Bono, Karim Fizazi, Stephen J Freedland, Maurizio Grilli, Philip W Kantoff, Guru Sonpavde, Cora N Sternberg, Srinivasan Yegnasubramanian, Emmanuel S Antonarakis
CONTEXT: Introduction of novel agents for the management of advanced prostate cancer provides a range of treatment options with notable benefits for men with metastatic castration-resistant prostate cancer (mCRPC). At the same time, understanding of optimal patient selection, effective sequential use, and development of resistance patterns remains incomplete. OBJECTIVE: To review current systemic therapies and recent advances in drug development for mCRPC and strategies to aid in patient selection and optimal sequencing...
April 16, 2018: European Urology
https://www.readbyqxmd.com/read/29673048/emerging-diagnostic-tests-for-vitreoretinal-lymphoma
#4
REVIEW
Abby C Dawson, Keryn A Williams, Binoy Appukuttan, Justine R Smith
Vitreoretinal lymphoma, which most commonly is diffuse large B cell non-Hodgkin in type, is a rare cancer with high morbidity and high mortality. Making a tissue diagnosis of vitreoretinal lymphoma is a major challenge for clinicians due to biological and technical factors. Yet, the delay in start of treatment may have vision- and life- threatening consequences, and there is considerable interest in the application of molecular assays to improve the accuracy of the diagnostic process: detection of a clonal immunoglobulin heavy chain rearrangements in lymphoma cells by polymerase chain reaction; measurement of vitreous or aqueous interleukin-10 protein levels in ocular fluids; and identification of mutations in the myeloid differentiation primary response gene 88 in tumour cells...
April 19, 2018: Clinical & Experimental Ophthalmology
https://www.readbyqxmd.com/read/29669169/genetic-testing-for-hereditary-prostate-cancer-current-status-and-limitations
#5
REVIEW
Jun Tu Zhen, Jamil Syed, Kevin Anh Nguyen, Michael S Leapman, Neeraj Agarwal, Karina Brierley, Xavier Llor, Erin Hofstatter, Brian Shuch
A significant proportion of prostate cancer diagnoses may be associated with a strong hereditary component. Men who have multiple single-gene polymorphisms and a family history of prostate cancer have a significantly greater risk of developing prostate cancer. Numerous single-gene alterations have been confirmed to increase the risk of prostate cancer. These include breast cancer genes 1 and 2 (BRCA1 and BRCA2, respectively), mutL homolog 1 (MLH1), mutS homologs 2 and 6 (MSH2 and MSH6, respectively), postmeiotic segregation increased 2 (PMS2), homeobox B13 (HOXB13), checkpoint kinase 2 (CHEK2), nibrin (NBN), BRCA1-interacting protein C-terminal helicase 1 (BRIP1), and ataxia telangiectasia mutated (ATM)...
April 18, 2018: Cancer
https://www.readbyqxmd.com/read/29666441/using-biology-to-guide-the-treatment-of-sarcomas-and-aggressive-connective-tissue-tumours
#6
REVIEW
Armelle Dufresne, Mehdi Brahmi, Marie Karanian, Jean-Yves Blay
Sarcomas are a heterogeneous group of malignancies that arise from cells of a mesenchymal origin. Surgery forms the mainstay of the treatment of most patients with localized sarcoma and might be followed or preceded by chemotherapy and/or radiotherapy. In the metastatic setting, systemic treatments tend to improve survival and control symptoms. However, the adverse events and sometimes disappointing outcomes associated with these empirical approaches to treatment indicate a need for new approaches. The advent of next-generation sequencing (NGS) has enabled more targeted treatment of many malignancies based on the presence of specific alterations...
April 17, 2018: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/29661707/the-genetic-architecture-of-long-qt-syndrome-a-critical-reappraisal
#7
REVIEW
John R Giudicessi, Arthur A M Wilde, Michael J Ackerman
Collectively, the completion of the Human Genome Project and subsequent development of high-throughput next-generation sequencing methodologies have revolutionized genomic research. However, the rapid sequencing and analysis of thousands upon thousands of human exomes and genomes has taught us that most genes, including those known to cause heritable cardiovascular disorders such as long QT syndrome, harbor an unexpected background rate of rare, and presumably innocuous, non-synonymous genetic variation. In this Review, we aim to reappraise the genetic architecture underlying both the acquired and congenital forms of long QT syndrome by examining how the clinical phenotype associated with and background genetic variation in long QT syndrome-susceptibility genes impacts the clinical validity of existing gene-disease associations and the variant classification and reporting strategies that serve as the foundation for diagnostic long QT syndrome genetic testing...
March 30, 2018: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/29661468/successful-treatment-of-cytogenetically-normal-acute-myeloid-leukemia-with-ten-eleven-translocation-2-isocitrate-dehydrogenase-2-and-additional-sex-comb-like-1-nucleophosmin-co-mutations-by-hla-haploidentical-stem-cell-transplantation-a-case-report-and-literature
#8
Y Liu, Y Cao, Y Lin, W-M Dong, R-R Lin, Q Gu, X-B Xie, W-Y Gu
The presence of recurrent gene mutations is increasingly important in acute myeloid leukemia (AML) and sheds new insights into the understanding of leukemogenesis, prognostic evaluation, and clinical therapeutic efficacy. Until now, ten-eleven translocation 2 (TET2) and isocitrate dehydrogenase 2 (IDH2) mutations were reported to be mutually exclusive in AML patients. Similarly, nucleophosmin (NPM1) and additional sex comb-like 1 (ASXL1) mutations were rarely coexisted in AML. A 47-year-old man diagnosed with high-risk AML presented simultaneous mutations of TET2-IDH2 and NPM1-ASXL1 revealed by next-generation sequencing...
April 2018: Transplantation Proceedings
https://www.readbyqxmd.com/read/29659698/molecular-subtyping-of-cancer-current-status-and-moving-toward-clinical-applications
#9
Lan Zhao, Victor H F Lee, Michael K Ng, Hong Yan, Maarten F Bijlsma
Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Molecular subtyping studies have allowed the allocation of cancer into homogeneous groups that are considered to harbor similar molecular and clinical characteristics...
April 12, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29656758/feasibility-of-endobronchial-ultrasound-transbronchial-needle-aspiration-for-massively-parallel-next-generation-sequencing-in-thoracic-cancer-patients
#10
Simon R Turner, Darren Buonocore, Patrice Desmeules, Natasha Rekhtman, Snjezana Dogan, Oscar Lin, Maria E Arcila, David R Jones, James Huang
INTRODUCTION: Next-generation sequencing (NGS) allows for the identification of a growing number of therapeutic and prognostic molecular targets. However, NGS typically requires greater quantities of DNA than traditional molecular testing does. Endobronchial ultrasound transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive procedure used to sample central thoracic lesions, but it is not well established whether this technique provides sufficient material for NGS. METHODS: We performed a retrospective review of EBUS-TBNA at our institution (3/1/14-9/28/16)...
May 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29656376/human-genetics-of-sclerosing-bone-disorders
#11
REVIEW
Raphaël De Ridder, Eveline Boudin, Geert Mortier, Wim Van Hul
PURPOSE OF REVIEW: The group of sclerosing bone disorders encompasses a variety of disorders all marked by increased bone mass. In this review, we give an overview of the genetic causes of this heterogeneous group of disorders and briefly touch upon the value of these findings for the development of novel therapeutic agents. RECENT FINDINGS: Advances in the next-generation sequencing technologies are accelerating the molecular dissection of the pathogenic mechanisms underlying skeletal dysplasias...
April 14, 2018: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/29655603/new-technologies-to-uncover-the-molecular-basis-of-disorders-of-sex-development
#12
REVIEW
Hayk Barseghyan, Emmanuèle C Délot, Eric Vilain
The elegant developmental biology experiments conducted in the 1940s by French physiologist Alfred Jost demonstrated that the sexual phenotype of a mammalian embryo depended whether the embryonic gonad develops into a testis or not. In humans, anomalies in the processes that regulate development of chromosomal, gonadal or anatomic sex result in a spectrum of conditions termed Disorders/Differences of Sex Development (DSD). Each of these conditions is rare, and understanding of their genetic etiology is still incomplete...
April 12, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29653267/emerging-landscape-of-circular-rnas-in-lung-cancer
#13
Wei Hu, Zhuo-Yue Bi, Zhen-Long Chen, Cong Liu, Lin-Lin Li, Feng Zhang, Qun Zhou, Wei Zhu, Yang-Yi-Yan Song, Bo-Tao Zhan, Qian Zhang, Yong-Yi Bi, Cheng-Cao Sun, De-Jia Li
Lung cancer, the leading cause of cancer deaths worldwide, is characterized with malignant cell growth. Advances in next-generation sequencing has helped us further understand RNA and identify novel circular RNAs (circRNAs) that may be useful in the early diagnosis and treatment of lung cancer. Similar to other noncoding RNAs, circRNAs present diverse biological functions in normal and disease states, including various types of cancers. This review focuses mainly on the poorly understood functions of circRNA in lung cancer...
April 10, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29651275/structural-and-functional-motifs-in-influenza-virus-rnas
#14
REVIEW
Damien Ferhadian, Maud Contrant, Anne Printz-Schweigert, Redmond P Smyth, Jean-Christophe Paillart, Roland Marquet
Influenza A viruses (IAV) are responsible for recurrent influenza epidemics and occasional devastating pandemics in humans and animals. They belong to the Orthomyxoviridae family and their genome consists of eight (-) sense viral RNA (vRNA) segments of different lengths coding for at least 11 viral proteins. A heterotrimeric polymerase complex is bound to the promoter consisting of the 13 5'-terminal and 12 3'-terminal nucleotides of each vRNA, while internal parts of the vRNAs are associated with multiple copies of the viral nucleoprotein (NP), thus forming ribonucleoproteins (vRNP)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29650893/-towards-development-of-innovative-cancer-therapies-trans-omics-approach
#15
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29644010/value-based-genomics
#16
REVIEW
Jun Gong, Kathy Pan, Marwan Fakih, Sumanta Pal, Ravi Salgia
Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge...
March 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29642968/review-historical-and-futuristic-developments-in-bovine-semen-technology
#17
P Lonergan
Up to the 18th century, the prevailing view of reproduction, or 'generation' as it was referred to, was that organisms develop from miniatures of themselves, termed preformation. The alternative theory, epigenesis, proposed that the structure of an animal emerges gradually from a relatively formless egg. The teachings of the Ancient Greeks who argued either that both sexes each contributed 'semen' to form the embryo, or held a more male-centred view that the female merely provided fertile ground for the male seed to grow, dominated thinking until the 17th century, when the combined work of numerous scholars led to the theory that all female organisms, including humans, produced eggs...
April 12, 2018: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29642462/new-challenges-in-targeting-signaling-pathways-in-acute-lymphoblastic-leukemia-by-ngs-approaches-an-update
#18
REVIEW
Adrián Montaño, Maribel Forero-Castro, Darnel Marchena-Mendoza, Rocío Benito, Jesús María Hernández-Rivas
The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures...
April 7, 2018: Cancers
https://www.readbyqxmd.com/read/29628935/neurodevelopmental-genetic-diseases-associated-with-microdeletions-and-microduplications-of-chromosome-17p13-3
#19
REVIEW
Sara M Blazejewski, Sarah A Bennison, Trevor H Smith, Kazuhito Toyo-Oka
Chromosome 17p13.3 is a region of genomic instability that is linked to different rare neurodevelopmental genetic diseases, depending on whether a deletion or duplication of the region has occurred. Chromosome microdeletions within 17p13.3 can result in either isolated lissencephaly sequence (ILS) or Miller-Dieker syndrome (MDS). Both conditions are associated with a smooth cerebral cortex, or lissencephaly, which leads to developmental delay, intellectual disability, and seizures. However, patients with MDS have larger deletions than patients with ILS, resulting in additional symptoms such as poor muscle tone, congenital anomalies, abnormal spasticity, and craniofacial dysmorphisms...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29628515/state-of-the-antiretroviral-therapy-in-human-immunodeficiency-virus-drug-resistance-science-and-technology-knowledge-gap
#20
Charles A Boucher, Marina R Bobkova, Anna Maria Geretti, Chien-Ching Hung, Rolf Kaiser, Anne-Geneviève Marcelin, Adrian Streinu-Cercel, Jean van Wyk, Pat Dorr, Anne-Mieke Vandamme
Resistance to antiretroviral therapy (ART) threatens the efficacy of human immunodeficiency virus type 1 (HIV-1) treatment. We present a review of knowledge gaps in the science and technologies of acquired HIV-1 drug resistance (HIVDR) in an effort to facilitate research, scientific exchange, and progress in clinical management. The expert authorship of this review convened to identify data gaps that exist in the field of HIVDR and discuss their clinical implications. A subsequent literature review of trials and current practices was carried out to provide supporting evidence...
January 2018: AIDS Reviews
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