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Next generation sequencing review

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https://www.readbyqxmd.com/read/28212287/big-data-analytics-for-genomic-medicine
#1
REVIEW
Karen Y He, Dongliang Ge, Max M He
Genomic medicine attempts to build individualized strategies for diagnostic or therapeutic decision-making by utilizing patients' genomic information. Big Data analytics uncovers hidden patterns, unknown correlations, and other insights through examining large-scale various data sets. While integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a Big Data infrastructure exhibit challenges, they also provide a feasible opportunity to develop an efficient and effective approach to identify clinically actionable genetic variants for individualized diagnosis and therapy...
February 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28211564/the-genomics-of-inherited-bone-marrow-failure-from-mechanism-to-the-clinic
#2
REVIEW
Talia Wegman-Ostrosky, Sharon A Savage
The inherited bone marrow failure syndromes (IBMFS) typically present with significant cytopenias in at least one haematopoietic cell lineage that may progress to pancytopenia, and are associated with increased risk of cancer. Although the clinical features of the IBMFS are often diagnostic, variable disease penetrance and expressivity may result in diagnostic dilemmas. The discovery of the genetic aetiology of the IBMFS has been greatly facilitated by next-generation sequencing methods. This has advanced understanding of the underlying biology of the IBMFS and been essential in improving clinical management and genetic counselling for affected patients...
February 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28202655/constraints-in-cancer-evolution
#3
REVIEW
Subramanian Venkatesan, Nicolai J Birkbak, Charles Swanton
Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28193548/advances-in-understanding-tumour-evolution-through-single-cell-sequencing
#4
Jack Kuipers, Katharina Jahn, Niko Beerenwinkel
The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes...
February 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28193154/opportunities-and-challenges-of-whole-genome-and-exome-sequencing
#5
REVIEW
Britt-Sabina Petersen, Broder Fredrich, Marc P Hoeppner, David Ellinghaus, Andre Franke
Recent advances in the development of sequencing technologies provide researchers with unprecedented possibilities for genetic analyses. In this review, we will discuss the history of genetic studies and the progress driven by next-generation sequencing (NGS), using complex inflammatory bowel diseases as an example. We focus on the opportunities, but also challenges that researchers are facing when working with NGS data to unravel the genetic causes underlying diseases.
February 14, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28188229/the-human-long-interspersed-element-1-retrotransposon-an-emerging-biomarker-of-neoplasia
#6
REVIEW
Daniel Ardeljan, Martin S Taylor, David T Ting, Kathleen H Burns
BACKGROUND: A large portion of intronic and intergenic space in our genome consists of repeated sequences. One of the most prevalent is the long interspersed element-1 (LINE-1, L1) mobile DNA. LINE-1 is rightly receiving increasing interest as a cancer biomarker. CONTENT: Intact LINE-1 elements are self-propagating. They code for RNA and proteins that function to make more copies of the genomic element. Our current understanding is that this process is repressed in most normal cells, but that LINE-1 expression is a hallmark of many types of malignancy...
February 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28182618/the-evolving-landscape-of-hiv-drug-resistance-diagnostics-for-expanding-testing-in-resource-limited-settings
#7
Seth C Inzaule, Raph L Hamers, Roger Paredes, Chunfu Yang, Rob Schuurman, Tobias F Rinke de Wit
Global scale-up of antiretroviral treatment (ART) has dramatically changed the prospects of HIV/AIDS disease rendering life-long chronic care and treatment a reality for millions of HIV-infected patients. Affordable technologies to monitor ART are needed to ensure long-term durability of limited available drug regimens. HIV drug resistance tests can complement existing strategies in optimizing clinical decision-making for patients with treatment failure, in addition to facilitating population-based surveillance of HIV drug resistance...
February 9, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28181911/molecular-diagnostics-of-periodontitis
#8
Izabela Korona-Głowniak, Radosław Siwiec, Marcin Berger, Anna Malm, Jolanta Szymańska
The microorganisms that form dental plaque are the main cause of periodontitis. Their identification and the understanding of the complex relationships and interactions that involve these microorganisms, environmental factors and the host's health status enable improvement in diagnostics and targeted therapy in patients with periodontitis. To this end, molecular diagnostics techniques (both techniques based on the polymerase chain reaction and those involving nucleic acid analysis via hybridization) come increasingly into use...
January 28, 2017: Postȩpy Higieny i Medycyny Doświadczalnej
https://www.readbyqxmd.com/read/28180024/ciliopathies-genetics-in-pediatric-medicine
#9
REVIEW
Machteld M Oud, Ideke J C Lamers, Heleen H Arts
Ciliary disorders, which are also referred to as ciliopathies, are a group of hereditary disorders that result from dysfunctional cilia. The latter are cellular organelles that stick up from the apical plasma membrane. Cilia have important roles in signal transduction and facilitate communications between cells and their surroundings. Ciliary disruption can result in a wide variety of clinically and genetically heterogeneous disorders with overlapping phenotypes. Because cilia occur widespread in our bodies many organs and sensory systems can be affected when they are dysfunctional...
March 2017: Journal of Pediatric Genetics
https://www.readbyqxmd.com/read/28178700/genetic-profiling-of-cancers-of-the-digestive-system-biological-insights-and-clinical-implications
#10
Albrecht Stenzinger, Wilko Weichert
Massive parallel sequencing technologies (next-generation sequencing) have enabled us to draw a comprehensive landscape of the genomic aberrations underlying common cancers of the digestive system, and they have thus revolutionized our understanding of the genomic makeup and biology of these tumors. Apart from the commonly mutated founder genes, e.g., KRAS and TP53, we now have detailed information on additional and less frequent genomic events for every major digestive system cancer. However, many challenging issues remain when it comes to translating these findings into clinical applications...
February 9, 2017: Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28176435/fish-intestinal-microbiome-diversity-and-symbiosis-unraveled-by-metagenomics
#11
REVIEW
Andrea M Tarnecki, Francisca A Burgos, Candis L Ray, Covadonga R Arias
The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition, and outcompeting opportunistic pathogens. Development of next-generation sequencing (NGS) technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically-significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility...
February 7, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28173653/-coenzyme-q-10-treatment-for-one-child-with-coq6-gene-mutation-induced-nephrotic-syndrome-and-literature-review
#12
Q Cao, G M Li, H Xu, Q Shen, L Sun, X Y Fang, H M Liu, W Guo, Y H Zhai, B B Wu
Objective: To summarize the clinical manifestation and molecular characteristics of COQ6 mutation induced nephrotic syndrome, and to evaluate efficacy of CoQ(10) therapy. Method: Clinical data of the case with infantile nephrotic syndrome was summarized, including clinical manifestations, laboratory findings and family investigation. The patient received CoQ(10) 30 mg/(kg·d) therapy. Urine protein/creatinine ratio, serum albumin and creatinine were detected to assess the efficacy of the therapy. Result: (1) The 10 months old boy was presented with nephrotic level proteinuria and hypoalbuminemia...
February 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28161773/clinicopathological-differences-exist-between-calr-and-jak2-mutated-myeloproliferative-neoplasms-despite-a-similar-molecular-landscape-data-from-targeted-next-generation-sequencing-in-the-diagnostic-laboratory
#13
Rishu Agarwal, Piers Blombery, Michelle McBean, Kate Jones, Andrew Fellowes, Ken Doig, Cecily Forsyth, David A Westerman
Mutations in CALR have recently been detected in JAK2-negative myeloproliferative neoplasms (MPNs) and are key pathological drivers in these diseases. CALR-mutated MPNs are shown to have numerous clinicopathological differences to JAK2-mutated MPNs. The basis of these differences is poorly understood. It is unknown whether these differences result directly from any differences in intracellular signalling abnormalities induced by JAK2/CALR mutations or whether they relate to other phenomena such as a differing spectrum of genetic lesions between the two groups...
February 4, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/28160876/neurology-individualized-medicine-when-to-use-next-generation-sequencing-panels
#14
REVIEW
Christopher J Klein, Tatiana M Foroud
Next-generation sequencing (NGS) is increasingly being applied to clinical testing. This practice is predicted to grow especially in neurology clinics because many of their patients have monogenetic causes for their "diagnostic odyssey." The cost of sequencing has been steadily decreasing, but the cost of DNA sequencing is a minor part of the total cost. Downstream data analysis, storage, and interpretation account for most of the total expense. In patients with nonspecific neurologic disorders in which an extensive number of genetic differential diagnoses exist, whole-genome sequencing (WGS) or whole-exome sequencing (WES) has shown promise in the identification of genetic causes...
February 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/28157722/genotype-guided-diagnosis-in-familial-hypercholesterolemia-clinical-management-and-concerns
#15
Paul N Hopkins, Stacey R Lane
PURPOSE OF REVIEW: In this review, we examine benefits and concerns associated with genetic testing in the clinical management of familial hypercholesterolemia (FH). RECENT FINDINGS: Application of next-generation sequencing and other advances provide improved yield of causal mutations compared with older methods and help disclose underlying pathophysiology in many instances. Concerns regarding clinical application of genetic testing remain. SUMMARY: More widespread application of genetic testing for FH in the USA may be forthcoming...
February 2, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/28156484/molecular-tumor-profiling-ordering-trends-in-cancer-patients
#16
Winnie S Wang, Warren Yau, Chelsea Hagmann, Carolyn Revta, Janet M Armstrong, Eric Roeland
: 165 Background: Molecular tumor profiling may provide information as to whether to initiate or not initiate a targeted therapy. As to the timing of when the tumor profiling is ordered relative to date of diagnosis, date of death, and palliative care (PC) consultations are unknown. The primary objective of this study was to examine molecular tumor profiling ordering trends in the course of cancer illness. METHODS: A preliminary, retrospective chart review was conducted in a cohort of patients with a confirmed diagnosis of cancer at an academic, NCI-designated comprehensive cancer center...
October 9, 2016: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28155656/2016-update-on-apbionet-s-annual-international-conference-on-bioinformatics-incob
#17
EDITORIAL
Christian Schönbach, Chandra Verma, Lawrence Jin Kiat Wee, Peter John Bond, Shoba Ranganathan
InCoB became since its inception in 2002 one of the largest annual bioinformatics conferences in the Asia-Pacific region with attendance ranging between 150 and 250 delegates depending on the venue location. InCoB 2016 in Singapore was attended by almost 220 delegates. This year, sessions on structural bioinformatics, sequence and sequencing, and next-generation sequencing fielded the highest number of oral presentation. Forty-four out 96 oral presentations were associated with an accepted manuscript in supplemental issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics or BMC Systems Biology...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28155230/further-delineation-of-a-rare-recessive-encephalomyopathy-linked-to-mutations-in-gfer-thanks-to-data-sharing-of-whole-exome-sequencing-data
#18
S Nambot, D Gavrilov, J Thevenon, A L Bruel, M Bainbridge, M Rio, C Goizet, A Rötig, J Jaeken, N Niu, F Xia, A Vital, N Houcinat, F Mochel, P Kuentz, D Lehalle, Y Duffourd, J B Rivière, C Thauvin-Robinet, A L Beaudet, L Faivre
Alterations in GFER gene have been associated with progressive mitochondrial myopathy, congenital cataracts, hearing loss, developmental delay, lactic acidosis and respiratory chain deficiency in 3 siblings born to consanguineous Moroccan parents by homozygosity mapping and candidate gene approach (OMIM#613076). Next generation sequencing recently confirmed this association by the finding of compound heterozygous variants in 19-year-old girl with a strikingly similar phenotype, but this ultra-rare entity remains however unknown from most of the scientific community...
February 2, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28154920/high-grade-serous-ovarian-cancer-the-clone-wars
#19
REVIEW
Aleksander Salomon-Perzyński, Magdalena Salomon-Perzyńska, Bogdan Michalski, Violetta Skrzypulec-Plinta
BACKGROUND: The last 5 years' studies using next-generation sequencing provided evidences that many types of solid tumors present spatial and temporal genetic heterogeneity and are composed of multiple populations of genetically distinct subclones that evolve over time following a pattern of branched evolution. The evolutionary nature of cancer has been proposed as the major contributor to drug resistance and treatment failure. In this review, we present the current state of knowledge about the clonal evolution of high-grade serous ovarian cancer and discuss the challenge that clonal evolution poses for efforts to achieve an optimal cancer control...
February 3, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28153948/extremely-fast-and-incredibly-close-co-transcriptional-splicing-in-budding-yeast
#20
Edward W J Wallace, Jean D Beggs
RNA splicing, an essential part of eukaryotic pre-messenger RNA processing, can be simultaneous with transcription by RNA polymerase II. Here, we compare and review independent next-generation sequencing methods that jointly quantify transcription and splicing in budding yeast. For many yeast transcripts, splicing is fast, taking place within seconds of intron transcription, while polymerase is within a few dozens of nucleotides of the 3' splice site. Ribosomal protein transcripts are spliced particularly fast and co-transcriptionally...
February 2, 2017: RNA
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