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Next generation sequencing review

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https://www.readbyqxmd.com/read/29230532/rna-mediated-transgenerational-inheritance-in-ciliates-and-plants
#1
REVIEW
Zachary T Neeb, Mariusz Nowacki
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction...
December 11, 2017: Chromosoma
https://www.readbyqxmd.com/read/29227308/medical-bioinformatics-in-melanoma
#2
Phil F Cheng
PURPOSE OF REVIEW: Bioinformatic insights from next-generation sequencing has been integral in understanding melanoma biology, resistance to treatment and provided new avenues for melanoma treatment. Whole-genome sequencing, whole-exome sequencing and RNA sequencing has redefined the molecular classification of melanoma, revealed distinct genetic aberrations that define clinical subtypes of melanoma and uncovered the diverse heterogeneity that resides in an individual tumor. RECENT FINDINGS: In this review, we will summarize the recent whole-genome study that catalogs the genomic landscape across many melanoma subtypes, the single-cell RNA sequencing studies that interrogates tumor heterogeneity and the personalized vaccine approaches to melanoma treatment...
December 8, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29226910/towards-personalized-tumour-specific-therapeutic-vaccines-for-cancer
#3
REVIEW
Zhuting Hu, Patrick A Ott, Catherine J Wu
Cancer vaccines, which are designed to amplify tumour-specific T cell responses through active immunization, have long been envisioned as a key tool of effective cancer immunotherapy. Despite a clear rationale for such vaccines, extensive past efforts were unsuccessful in mediating clinically relevant antitumour activity in humans. Recently, however, next-generation sequencing and novel bioinformatics tools have enabled the systematic discovery of tumour neoantigens, which are highly desirable immunogens because they arise from somatic mutations of the tumour and are therefore tumour specific...
December 11, 2017: Nature Reviews. Immunology
https://www.readbyqxmd.com/read/29226007/houston-methodist-variant-viewer-an-application-to-support-clinical-laboratory-interpretation-of-next-generation-sequencing-data-for-cancer
#4
Paul A Christensen, Yunyun Ni, Feifei Bao, Heather L Hendrickson, Michael Greenwood, Jessica S Thomas, S Wesley Long, Randall J Olsen
Introduction: Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/29225610/horizontal-gene-transfer-contributes-to-plant-evolution-the-case-of-agrobacterium-t-dnas
#5
REVIEW
Dora G Quispe-Huamanquispe, Godelieve Gheysen, Jan F Kreuze
Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29224747/next-generation-sequencing-identifies-three-novel-missense-variants-in-ildr1-and-myo6-genes-in-an-iranian-family-with-hearing-loss-with-review-of-the-literature
#6
Farah Talebi, Farideh Ghanbari Mardasi, Javad Mohammadi Asl, Masoomeh Sayahi
OBJECTIVES: Hearing impairment is the most common sensorineural disorder and is genetically heterogeneous. Identification of the pathogenic mutations underlying hearing impairment is difficult, since causative mutations in 127 different genes have so far been reported. METHODS: In this study, we performed Next-generation sequencing (NGS) in 2 individuals from a consanguineous family with hearing loss. RESULTS: Three novel mutations in known deafness genes were identified in the family; MYO6-p...
December 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/29222241/inherited-bone-marrow-failure-syndromes-considerations-pre-and-posttransplant
#7
REVIEW
Blanche P Alter
Patients with inherited bone marrow failure syndromes are usually identified when they develop hematologic complications such as severe bone marrow failure, myelodysplastic syndrome, or acute myeloid leukemia. They often have specific birth defects or other physical abnormalities that suggest a syndrome, and sequencing of specific genes or next-generation sequencing can determine or confirm the particular syndrome. The 4 most frequent syndromes are Fanconi anemia, dyskeratosis congenita, Diamond Blackfan anemia, and Shwachman Diamond syndrome...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29221448/next-generation-sequencing-recent-applications-to-the-analysis-of-colorectal-cancer
#8
REVIEW
Filippo Del Vecchio, Valentina Mastroiaco, Antinisca Di Marco, Chiara Compagnoni, Daria Capece, Francesca Zazzeroni, Carlo Capalbo, Edoardo Alesse, Alessandra Tessitore
Since the establishment of the Sanger sequencing method, scientists around the world focused their efforts to progress in the field to produce the utmost technology. The introduction of next-generation sequencing (NGS) represents a revolutionary step and promises to lead to massive improvements in our understanding on the role of nucleic acids functions. Cancer research began to use this innovative and highly performing method, and interesting results started to appear in colorectal cancer (CRC) analysis. Several studies produced high-quality data in terms of mutation discovery, especially about actionable or less frequently mutated genes, epigenetics, transcriptomics...
December 8, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29218397/can-we-better-predict-the-biologic-behavior-of-incidental-ipmn-a-comprehensive-analysis-of-molecular-diagnostics-and-biomarkers-in-intraductal-papillary-mucinous-neoplasms-of-the-pancreas
#9
Kiara A Tulla, Ajay V Maker
PURPOSE: Predicting the biologic behavior of intraductal papillary mucinous neoplasm (IPMN) remains challenging. Current guidelines utilize patient symptoms and imaging characteristics to determine appropriate surgical candidates. However, the majority of resected cysts remain low-risk lesions, many of which may be feasible to have under surveillance. We herein characterize the most promising and up-to-date molecular diagnostics in order to identify optimal components of a molecular signature to distinguish levels of IPMN dysplasia...
December 7, 2017: Langenbeck's Archives of Surgery
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#10
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29209992/cost-effectiveness-of-karyotyping-chromosomal-microarray-analysis-and-targeted-next-generation-sequencing-of-patients-with-unexplained-global-developmental-delay-or-intellectual-disability
#11
Yonghong Li, Lori A Anderson, Edward I Ginns, James J Devlin
BACKGROUND: Genetic diagnosis of unexplained global developmental delay and intellectual disability (GDD/ID) often ends the diagnostic odyssey and can lead to changes in clinical management. OBJECTIVE: The objective of this study was to investigate the cost effectiveness of testing scenarios involving several methods used to diagnose GDD/ID: karyotyping, chromosomal microarray analysis (CMA), and targeted next-generation sequencing (NGS). METHODS: We used decision-tree models to estimate the number of genetic diagnoses, the cost from a payers' perspective in the USA, and the incremental cost per additional genetic diagnosis...
December 5, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/29209898/clinical-application-of-next-generation-sequencing-in-hereditary-spinocerebellar-ataxia-increasing-the-diagnostic-yield-and-broadening-the-ataxia-spasticity-spectrum-a-retrospective-analysis
#12
REVIEW
Daniele Galatolo, Alessandra Tessa, Alessandro Filla, Filippo M Santorelli
One of the hardest challenges in medical genetics is to reach a molecular diagnosis in the presence of rare brain disorders. Hereditary spinocerebellar ataxia (HA), characterized by high clinical and genetic heterogeneity, is among the diseases that present this challenge. HA can have features overlapping with those of other neurological diseases, especially hereditary spastic paraplegia (HSP), as routine clinical application of next generation sequencing (NGS) has confirmed. This article reviews different NGS methods applied in heterogeneous cohorts of patients with suspected HA and suggests that exome sequencing should be considered the first-tier genetic approach in this setting...
December 6, 2017: Neurogenetics
https://www.readbyqxmd.com/read/29206925/exploring-fish-microbial-communities-to-mitigate-emerging-diseases-in-aquaculture
#13
Irene de Bruijn, Yiying Liu, Geert F Wiegertjes, Jos M Raaijmakers
Aquaculture is the fastest-growing animal food sector worldwide and expected to further increase to feed the growing human population. However, existing and (re-)emerging diseases are hampering fish and shellfish cultivation and yield. For many diseases, vaccination protocols are not in place and the excessive use of antibiotics and other chemicals is of substantial concern. A more sustainable disease control strategy to protect fish and shellfish from (re-)emerging diseases could be achieved by introduction or augmentation of beneficial microbes...
November 29, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29206688/current-developments-in-the-genetics-of-rett-and-rett-like-syndrome
#14
Friederike Ehrhart, Nasim Bahram Sangani, Leopold M G Curfs
PURPOSE OF REVIEW: This article reviews the current molecular genetic studies, which investigate the genetic causes of Rett syndrome or Rett-like phenotypes without a classical MECP2 mutation. RECENT FINDINGS: As next generation sequencing becomes broadly available, especially whole exome sequencing is used in clinical diagnosis of the genetic causes of a wide spectrum of intellectual disability, autism, and encephalopathies. Patients who were diagnosed with Rett syndrome or Rett-like syndrome because of their phenotype but were negative for mutations in the MECP2, CDKL5 or FOXG1 genes were subjected to whole exome sequencing and the results of the last few years revealed yet 69 different genes...
December 4, 2017: Current Opinion in Psychiatry
https://www.readbyqxmd.com/read/29206173/histone-macroh2a1-a-chromatin-point-of-intersection-between-fasting-senescence-and-cellular-regeneration
#15
REVIEW
Oriana Lo Re, Manlio Vinciguerra
Histone variants confer chromatin unique properties. They have specific genomic distribution, regulated by specific deposition and removal machineries. Histone variants, mostly of canonical histones H2A, H2B and H3, have important roles in early embryonic development, in lineage commitment of stem cells, in the converse process of somatic cell reprogramming to pluripotency and, in some cases, in the modulation of animal aging and life span. MacroH2A1 is a variant of histone H2A, present in two alternatively exon-spliced isoforms macroH2A1...
December 5, 2017: Genes
https://www.readbyqxmd.com/read/29205437/mrna-traffic-control-reviewed-n6-methyladenosine-m6-a-takes-the-driver-s-seat
#16
REVIEW
Abhirami Visvanathan, Kumaravel Somasundaram
Messenger RNA is a flexible tool box that plays a key role in the dynamic regulation of gene expression. RNA modifications variegate the message conveyed by the mRNA. Similar to DNA and histone modifications, mRNA modifications are reversible and play a key role in the regulation of molecular events. Our understanding about the landscape of RNA modifications is still rudimentary in contrast to DNA and histone modifications. The major obstacle has been the lack of sensitive detection methods since they are non-editing events...
December 4, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29202942/microbiome-at-the-frontier-of-personalized-medicine
#17
REVIEW
Purna C Kashyap, Nicholas Chia, Heidi Nelson, Eran Segal, Eran Elinav
The genomic revolution promises to transform our approach to treat patients by individualizing treatments, reducing adverse events, and decreasing health care costs. The early advances using this have been realized primarily by optimizing preventive and therapeutic approaches in cancer using human genome sequencing. The ability to characterize the microbiome, which includes all the microbes that reside within and upon us and all their genetic elements, using next-generation sequencing allows us to now incorporate this important contributor to human disease into developing new preventive and therapeutic strategies...
December 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/29198847/first-delivery-in-a-leukemia-survivor-after-transplantation-of-cryopreserved-ovarian-tissue-evaluated-for-leukemia-cells-contamination
#18
Moran Shapira, Hila Raanani, Iris Barshack, Ninette Amariglio, Sanaz Derech-Haim, Meital Nagar Marciano, Eyal Schiff, Raoul Orvieto, Dror Meirow
OBJECTIVE: To describe a successful autologous ovarian tissue re-transplantation in a sterile leukemia survivor after evaluation for minimal residual disease and provide a review of the current literature. DESIGN: Presentation of a carefully designed workup taken to evaluate tissue for minimal residual disease, its limitations, and applicability to other patients. To date, there have not been any publications of auto-transplantations in leukemia survivors, owing to an estimated high risk for malignancy induction...
November 29, 2017: Fertility and Sterility
https://www.readbyqxmd.com/read/29196276/next-generation-sequencing-of-the-cerebrospinal-fluid-in-the-diagnosis-of-neurobrucellosis
#19
Siyuan Fan, Haitao Ren, Yanping Wei, Chenhui Mao, Zhenzi Ma, Lu Zhang, Li Wang, Ying Ge, Taisheng Li, Liying Cui, Honglong Wu, Hongzhi Guan
BACKGROUNDS: Brucellosis is the most common zoonotic infection in the world. Brucellosis with nervous system involvement is known as 'neurobrucellosis' (NB). The diagnosis of NB is difficult because its clinical manifestations are nonspecific and the sensitivity of routine culture tests is low. METHODS: Next-generation sequencing (NGS) of cerebrospinal fluid (CSF) was used to detect pathogens in patients with clinically suspected central nervous system (CNS) infections in a tertiary referral center in China between June 1, 2016 and June 1, 2017...
November 28, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29193310/bacterial-modulators-of-bone-remodeling-in-the-periodontal-pocket
#20
REVIEW
Brian Henderson, Frank Kaiser
The signaling network involved in the pathogenesis of periodontal disease is not yet fully understood. This review aims to describe possible mechanisms through which the bacterial modulators may be linked directly or indirectly to the process of alveolar bone loss in periodontitis. From the late 1970s to present, new paradigm shifts have been developed regarding our understanding of pathological bone remodeling in periodontal disease. Upcoming evidence suggests that in periodontal disease the local immune response is exacerbated and involves the existence of signaling pathways that have been shown to modulate bone-cell function leading to alveolar bone loss...
November 30, 2017: Periodontology 2000
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