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Next generation sequencing review

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https://www.readbyqxmd.com/read/28078645/parp-inhibitors-in-reproductive-system-cancers-current-use-and-developments
#1
REVIEW
Geraldine O'Sullivan Coyne, Alice P Chen, Robert Meehan, James H Doroshow
The repair of DNA damage is a critical cellular process governed by multiple biochemical pathways that are often found to be defective in cancer cells. The poly(ADP-ribose) polymerase (PARP) family of proteins controls response to single-strand DNA breaks by detecting these damaged sites and recruiting the proper factors for repair. Blocking this pathway forces cells to utilize complementary mechanisms to repair DNA damage. While PARP inhibition may not, in itself, be sufficient to cause tumor cell death, inhibition of DNA repair with PARP inhibitors is an effective cytotoxic strategy when it is used in patients who carry other defective DNA-repair mechanisms, such as mutations in the genes BRCA 1 and 2...
January 11, 2017: Drugs
https://www.readbyqxmd.com/read/28078112/molecular-spectrum-of-kras-nras-braf-pik3ca-tp53-and-apc-somatic-gene-mutations-in-arab-patients-with-colorectal-cancer-determination-of-frequency-and-distribution-pattern
#2
Humaid O Al-Shamsi, Jeremy Jones, Yazan Fahmawi, Ibrahim Dahbour, Aziz Tabash, Reham Abdel-Wahab, Ahmed O S Abousamra, Kenna R Shaw, Lianchun Xiao, Manal M Hassan, Benjamin R Kipp, Scott Kopetz, Amr S Soliman, Robert R McWilliams, Robert A Wolff
BACKGROUND: The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features. METHODS: Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed...
December 2016: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28068482/metabolic-reprogramming-in-brain-tumors
#3
Sriram Venneti, Craig B Thompson
Next-generation sequencing has substantially enhanced our understanding of the genetics of primary brain tumors by uncovering several novel driver genetic alterations. How many of these genetic modifications contribute to the pathogenesis of brain tumors is not well understood. An exciting paradigm emerging in cancer biology is that oncogenes actively reprogram cellular metabolism to enable tumors to survive and proliferate. We discuss how some of these genetic alterations in brain tumors rewire metabolism...
December 21, 2016: Annual Review of Pathology
https://www.readbyqxmd.com/read/28062412/plant-genome-and-transcriptome-annotations-from-misconceptions-to-simple-solutions
#4
Marie E Bolger, Borjana Arsova, Björn Usadel
Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources...
January 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28061482/genomic-mutation-driven-metastatic-breast-cancer-therapy-a-single-center-experience
#5
Yuan Yuan, Susan E Yost, Yate-Ching Yuan, Nicola M Solomon, Isa Mambetsariev, Sumanta Pal, Paul Frankel, Ravi Salgia, Susan L Neuhausen, Joanne Mortimer
BACKGROUND: Next-Generation Sequencing (NGS) has made genomic mutation-driven therapy feasible for metastatic breast cancer (MBC) patients. We frequently submit tumor tissue from MBC patients for targeted NGS of tumor using the Illumina HiSeq 2000 platform (FoundationOne®, Foundation Medicine, MA). Herein, we report the results and clinical impact of this test in MBC patients. PATIENTS AND METHODS: We identified patients with MBC treated at City of Hope from January 2014 to May 2016 who underwent NGS...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060710/a-review-of-machine-learning-and-statistical-approaches-for-detecting-snp-interactions-in-high-dimensional-genomic-data
#6
Suneetha Uppu, Aneesh Krishna, Raj Gopalan
In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature...
December 2, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28059958/future-technologies-for-monitoring-hiv-drug-resistance-and-cure
#7
Urvi M Parikh, Kevin McCormick, Gert van Zyl, John W Mellors
PURPOSE OF REVIEW: Sensitive, scalable and affordable assays are critically needed for monitoring the success of interventions for preventing, treating and attempting to cure HIV infection. This review evaluates current and emerging technologies that are applicable for both surveillance of HIV drug resistance (HIVDR) and characterization of HIV reservoirs that persist despite antiretroviral therapy and are obstacles to curing HIV infection. RECENT FINDINGS: Next-generation sequencing (NGS) has the potential to be adapted into high-throughput, cost-efficient approaches for HIVDR surveillance and monitoring during continued scale-up of antiretroviral therapy and rollout of preexposure prophylaxis...
January 5, 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/28055035/dna-sequencing-technologies-2006-2016
#8
Elaine R Mardis
Recent advances in the field of genomics have largely been due to the ability to sequence DNA at increasing throughput and decreasing cost. DNA sequencing was first introduced in 1977, and next-generation sequencing technologies have been available only during the past decade, but the diverse experiments and corresponding analyses facilitated by these techniques have transformed biological and biomedical research. Here, I review developments in DNA sequencing technologies over the past 10 years and look to the future for further applications...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28050628/epigenetic-modifications-and-reprogramming-in-paternal-pronucleus-sperm-preimplantation-embryo-and-beyond
#9
REVIEW
Yuki Okada, Kosuke Yamaguchi
Pronuclear/zygotic stage is the very first stage of life. In this period, paternal pronucleus undergoes massive chromatin remodeling called "paternal reprogramming" including protamine-histone replacement and subsequent acquisition of epigenetic modifications. Although these consecutive events are required for the initiation of maternal-zygotic transition, the precise role of paternal reprogramming and its effect on subsequent embryonic development has been largely unknown to date. Recently, various new techniques, especially next-generation sequencing (NGS) and RNAi microinjection contribute to unveil the epigenetic transition from both paternal and maternal to early preimplantation embryos, suggesting not only the simple transcriptional regulation by transcription factors but also dynamic structural alteration of chromatin to initiate the wave of zygotic gene transcription...
January 3, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28049366/primary-thyroid-carcinoma-with-low-risk-histology-and-distant-metastases-clinico-pathologic-and-molecular-characteristics
#10
Bin Xu, R Michael Tuttle, Mona Sabra, Ian Ganly, Ronald Ghossein
BACKGROUND: Distant metastases (DM) are a rare occurrence in well differentiatedwell-differentiated thyroid carcinoma. The aim of our study was to analyze the clinical, pathologic, and molecular features of primary thyroid carcinoma with low risk histology that develop DM. METHODS: Detailed clinico-pathologic review and targeted next generation sequencing were performed on a cohort of well-differentiatedwell-differentiated thyroid carcinoma lacking gross extrathyroidal extension, extensive vascular invasion or significant lymph node metastases but exhibiting distant metastases...
January 3, 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/28043904/liver-cancer-cell-of-origin-molecular-class-and-effects-on-patient-prognosis
#11
REVIEW
Daniela Sia, Augusto Villanueva, Scott L Friedman, Josep M Llovet
Primary liver cancer is the second leading cause of cancer-related death worldwide and therefore a major public health challenge. We review hypotheses of the cell of origin of liver tumorigenesis, and clarify the classes of liver cancer, based on molecular features and how these affect patient prognosis. Primary liver cancer comprises hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (iCCA), and other rare tumors, notably fibrolamellar carcinoma and hepatoblastoma. The molecular and clinical features of HCC vs iCCA are distinct, although they have overlapping risk factors and pathways of oncogenesis...
December 30, 2016: Gastroenterology
https://www.readbyqxmd.com/read/28042011/application-of-next-generation-sequencing-in-clinical-microbiology-and-infection-prevention
#12
Ruud H Deurenberg, Erik Bathoorn, Monika A Chlebowicz, Natacha Couto, Mithila Ferdous, Silvia García-Cobos, Anna M D Kooistra-Smid, Erwin C Raangs, Sigrid Rosema, Alida C M Veloo, Kai Zhou, Alexander W Friedrich, John W A Rossen
Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test...
December 29, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/28039028/genome-wide-association-studies-in-maize-praise-and-stargaze
#13
REVIEW
Yingjie Xiao, Haijun Liu, Liuji Wu, Marilyn Warburton, Jianbing Yan
Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to technical advances in next-generation sequencing (NGS) applications. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review aims to summarize current GWAS efforts in maize functional genomics, and discuss future prospects in the omics era. The general goal of a GWAS analysis is to link genotypic variantions to corresponding differences in phenotype using the most appropriate statistical model in a given population...
December 27, 2016: Molecular Plant
https://www.readbyqxmd.com/read/28035232/back-into-the-wild-apply-untapped-genetic-diversity-of-wild-relatives-for-crop-improvement
#14
REVIEW
Hengyou Zhang, Neha Mittal, Larry J Leamy, Oz Barazani, Bao-Hua Song
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges...
January 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28034498/genomic-sequencing-and-precision-medicine-in-head-and-neck-cancers
#15
REVIEW
R C Hoesli, M L Ludwig, N L Michmerhuizen, A J Rosko, M E Spector, J C Brenner, A C Birkeland
Head and neck squamous cell carcinoma (HNSCC) remains a common and deadly disease. Historically, surgical and chemoradiation treatments have been met with modest success, and understanding of genetic drivers of HNSCC has been limited. With recent next generation sequencing studies focused on HNSCC, we are beginning to understand the genetic landscape of HNSCCs and are starting to identify and advance targeted options for patients. In this review, we describe current knowledge and recent advances in sequencing studies of HNSCC, discuss current limitations and future directions for further genomic analysis, and highlight the translational advances being undertaken to treat this important disease...
December 15, 2016: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28031556/advances-in-the-molecular-genetics-of-gliomas-implications-for-classification-and-therapy
#16
REVIEW
Guido Reifenberger, Hans-Georg Wirsching, Christiane B Knobbe-Thomsen, Michael Weller
Genome-wide molecular-profiling studies have revealed the characteristic genetic alterations and epigenetic profiles associated with different types of gliomas. These molecular characteristics can be used to refine glioma classification, to improve prediction of patient outcomes, and to guide individualized treatment. Thus, the WHO Classification of Tumours of the Central Nervous System was revised in 2016 to incorporate molecular biomarkers - together with classic histological features - in an integrated diagnosis, in order to define distinct glioma entities as precisely as possible...
December 29, 2016: Nature Reviews. Clinical Oncology
https://www.readbyqxmd.com/read/28025978/immune-targets-and-neoantigens-for-cancer-immunotherapy-and-precision-medicine
#17
REVIEW
Rong-Fu Wang, Helen Y Wang
Harnessing the immune system to eradicate malignant cells is becoming a most powerful new approach to cancer therapy. FDA approval of the immunotherapy-based drugs, sipuleucel-T (Provenge), ipilimumab (Yervoy, anti-CTLA-4), and more recently, the programmed cell death (PD)-1 antibody (pembrolizumab, Keytruda), for the treatment of multiple types of cancer has greatly advanced research and clinical studies in the field of cancer immunotherapy. Furthermore, recent clinical trials, using NY-ESO-1-specific T cell receptor (TCR) or CD19-chimeric antigen receptor (CAR), have shown promising clinical results for patients with metastatic cancer...
January 2017: Cell Research
https://www.readbyqxmd.com/read/28025179/measuring-the-diversity-of-the-human-microbiota-with-targeted-next-generation-sequencing
#18
Francesca Finotello, Eleonora Mastrorilli, Barbara Di Camillo
The human microbiota is a complex ecological community of commensal, symbiotic and pathogenic microorganisms harboured by the human body. Next-generation sequencing (NGS) technologies, in particular targeted amplicon sequencing of the 16S ribosomal RNA gene (16S-seq), are enabling the identification and quantification of human-resident microorganisms at unprecedented resolution, providing novel insights into the role of the microbiota in health and disease. Once microbial abundances are quantified through NGS data analysis, diversity indices provide valuable mathematical tools to describe the ecological complexity of a single sample or to detect species differences between samples...
December 26, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28017915/natural-recombination-in-alphaherpesviruses-insights-into-viral-evolution-through-full-genome-sequencing-and-sequence-analysis
#19
REVIEW
Carlos A Loncoman, Paola K Vaz, Mauricio Jc Coppo, Carol A Hartley, Francisco J Morera, Glenn F Browning, Joanne M Devlin
Recombination in alphaherpesviruses was first described more than sixty years ago. Since then, different techniques have been used to detect recombination in natural (field) and experimental settings. Over the last ten years, next-generation sequencing (NGS) technologies and bioinformatic analyses have greatly increased the accuracy of recombination detection, particularly in field settings, thus contributing greatly to the study of natural alphaherpesvirus recombination in both human and veterinary medicine...
December 22, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28012982/clostridium-difficile-infection-evolution-phylogeny-and-molecular-epidemiology
#20
REVIEW
Briony Elliott, Grace O Androga, Daniel R Knight, Thomas V Riley
Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications...
December 22, 2016: Infection, Genetics and Evolution
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