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Genomics review

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https://www.readbyqxmd.com/read/29045549/emerging-treatment-paradigms-in-brain-metastasis-in-non-small-cell-lung-cancer-an-overview-of-the-current-landscape-and-challenges-ahead
#1
D Ulahannan, J Khalifa, C Faivre-Finn, S M Lee
Advances in the last decade in genomic profiling and the identification of druggable targets amenable to biological agents, has transformed the management and survival of a subgroup of patients with brain metastasis in non-small cell lung cancer. In parallel, clinicians have re-evaluated the role of whole brain radiotherapy in selected patients with brain metastases to reduce neurocognitive toxicity. Continual progress in this understudied field is required: optimisation of the sequence of schedules for therapies in patients with brain metastases of differing genomic profiles, focusing on new strategies to overcome mechanisms of biological resistance and increasing drug penetrability into the central nervous system...
October 17, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045506/clinical-and-molecular-characterization-of-patients-with-cancers-of-unknown-primary-in-the-modern-era
#2
A M Varghese, A Arora, M Capanu, N Camacho, H H Won, A Zehir, J Gao, D Chakravarty, N Schultz, D S Klimstra, M Ladanyi, D M Hyman, D B Solit, M F Berger, L B Saltz
Background: On the basis of historical data, patients with cancers of unknown primary (CUP) are generally assumed to have a dismal prognosis with overall survival of less than one year. Treatment is typically cytotoxic chemotherapy guided by histologic features and the pattern of metastatic spread. The purpose of this study was to provide a clinical and pathologic description of patients with CUP in the modern era, to define the frequency of clinically actionable molecular alterations in this population, to determine how molecular testing can alter therapeutic decisions, and to investigate novel uses of next generation sequencing in the evaluation and treatment of patients with CUP...
September 26, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29045504/molecular-tumor-boards-current-practice-and-future-needs
#3
D L van der Velden, C M L van Herpen, H W M van Laarhoven, E F Smit, H J M Groen, S M Willems, P M Nederlof, M H G Langenberg, E Cuppen, S Sleijfer, N Steeghs, E E Voest
Background: due to rapid technical advances, steeply declining sequencing costs, and the ever-increasing number of targeted therapies, it can be expected that extensive tumor sequencing such as Whole Exome- and -Genome Sequencing will soon be applied in standard care. Clinicians will thus be confronted with increasingly complex genetic information and multiple test-platforms to choose from. General medical training, meanwhile, can hardly keep up with the pace of innovation. Consequently, there is a rapidly growing gap between clinical knowledge and genetic potential in cancer care...
September 27, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29043643/imaging-of-dna-ultrafine-bridges-in-budding-yeast
#4
Oliver Quevedo, Michael Lisby
DNA ultrafine bridges (UFBs) are a type of chromatin-free DNA bridges that connect sister chromatids in anaphase and pose a threat to genome stability. However, little is known about the origin of these structures, and how they are sensed and resolved by the cell. In this chapter, we review tools and methods for studying UFBs by fluorescence microscopy including chemical and genetic approaches to induce UFBs in the model organism Saccharomyces cerevisiae.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043642/the-detection-and-analysis-of-chromosome-fragile-sites
#5
Victoria A Bjerregaard, Özgün Özer, Ian D Hickson, Ying Liu
A fragile site is a chromosomal locus that is prone to form a gap or constriction visible within a condensed metaphase chromosome, particularly following exposure of cells to DNA replication stress. Based on their frequency, fragile sites are classified as either common (CFSs; present in all individuals) or rare (RFSs; present in only a few individuals). Interest in fragile sites has remained high since their discovery in 1965, because of their association with human disease. CFSs are recognized as drivers of oncogene activation and genome instability in cancer cells, while some RFSs are associated with neurodegenerative diseases...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29043570/towards-precision-nephrology-the-opportunities-and-challenges-of-genomic-medicine
#6
REVIEW
Jordan G Nestor, Emily E Groopman, Ali G Gharavi
The expansion of genomic medicine is furthering our understanding of many human diseases. This is well illustrated in the field of nephrology, through the characterization, discovery, and growing insight into various renal diseases through use of Next Generation Sequencing (NGS) technologies. This review will provide an overview of the diagnostic opportunities of using genetic testing in the clinical setting by describing notable discoveries regarding inherited forms of renal disease that have advanced the field and by highlighting some of the potential benefits of establishing a molecular diagnosis in a clinical practice...
October 17, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/29043379/copy-number-variation-and-disease-resistance-in-plants
#7
REVIEW
Aria Dolatabadian, Dhwani Apurva Patel, David Edwards, Jacqueline Batley
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning...
October 17, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29043205/an-extremely-rare-case-of-concurrent-braf-v600e-mutation-driven-hairy-cell-leukemia-and-melanoma-case-report-and-review-of-literature
#8
Amir Ghorbani-Aghbolaghi, Mirna Lechpammer, Saba F Ali, Nam K Ku, Denis M Dwyre, Hooman H Rashidi
BRAF protein is a serine/threonine kinase with 766 amino acids. Approximately 15% of human cancers harbor BRAF mutations as well as other BRAF anomalies (amplifications, fusions). Somatic mutations mainly occur in the catalytic kinase domain (CR3), and the predominant mutation is p.V600E which is the substitution of glutamic acid (E) for valine (V) as result of a mutation at codon 600 of the kinase domain. To our knowledge, the vast majority of the cancers have non-germline BRAF mutations. Here we describe a case of a 60-year-old female with a history of hairy cell leukemia (HCL) who presented with aphasia and forgetfulness...
July 2017: Autopsy & case reports
https://www.readbyqxmd.com/read/29043074/recent-advances-in-eosinophilic-esophagitis
#9
REVIEW
Sandy Durrani, Marc Rothenberg
Eosinophilic esophagitis is a chronic, antigen-driven, eosinophil-predominant inflammatory disease of the esophagus and affects both children and adults. Cutting-edge technologies, such as genome-wide association studies, have advanced our understanding of the disease pathogenesis at a remarkable rate. Recent insights from genetic and mechanistic studies have concluded that a complex interplay between genetic and environmental risk factors, allergic sensitization, and esophageal-specific pathways leads to disease pathogenesis...
2017: F1000Research
https://www.readbyqxmd.com/read/29042476/the-three-dimensional-genome-regulating-gene-expression-during-pluripotency-and-development
#10
REVIEW
Guillaume Andrey, Stefan Mundlos
The precise expression of genes in time and space during embryogenesis is largely influenced by communication between enhancers and promoters, which is propagated and governed by the physical proximity of these elements in the nucleus. Here, we review how chromatin domains organize the genome by guiding enhancers to their target genes thereby preventing non-specific interactions with other neighboring regions. We also discuss the dynamics of chromatin interactions between enhancers and promoters, as well as the consequent changes in gene expression, that occur in pluripotent cells and during development...
October 15, 2017: Development
https://www.readbyqxmd.com/read/29042475/mitotic-bookmarking-in-development-and-stem-cells
#11
REVIEW
Nicola Festuccia, Inma Gonzalez, Nick Owens, Pablo Navarro
The changes imposed on the nucleus, chromatin and its regulators during mitosis lead to the dismantlement of most gene regulatory processes. However, an increasing number of transcriptional regulators are being identified as capable of binding their genomic targets during mitosis. These so-called 'mitotic bookmarking factors' encompass transcription factors and chromatin modifiers that are believed to convey gene regulatory information from mother to daughter cells. In this Primer, we review mitotic bookmarking processes in development and stem cells and discuss the interest and potential importance of this concept with regard to epigenetic regulation and cell fate transitions involving cellular proliferation...
October 15, 2017: Development
https://www.readbyqxmd.com/read/29040782/egfr-heterogeneity-and-implications-for-therapeutic-intervention-in-glioblastoma
#12
Eskil Eskilsson, Gro V Røsland, Gergely Solecki, Qianghu Wang, Patrick N Harter, Grazia Graziani, Roel G W Verhaak, Frank Winkler, Rolf Bjerkvig, Hrvoje Miletic
Patients with glioblastoma (GBM) have a universally poor prognosis and are in urgent need of effective treatment strategies. Recent advances in sequencing techniques unraveled the complete genomic landscape of GBMs and revealed profound heterogeneity of individual tumors even at the single cell level. Genomic profiling has detected epidermal growth factor receptor (EGFR) gene alterations in more than half of GBMs. Major genetic events include amplification and mutation of EGFR. Yet, treatment strategies targeting EGFR have thus far failed in clinical trials...
October 10, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29040673/assimilation-of-omics-strategies-to-study-the-cuticle-layer-and-suberin-lamellae-in-plants
#13
Hagai Cohen, Jedrzej Szymanski, Asaph Aharoni, Eva Dominguez
The assembly of the lipophilic cuticle layer and suberin lamellae, approximately 450 million years ago, was a major evolutionary development that enabled plants to colonize terrestrial habitats. The cuticle layer is composed of cutin polyester and embedded cuticular waxes, whereas the suberin lamellae consist of very long chain fatty acid derivatives, glycerol, and phenolics cross-linked with alkyl ferulate-embedded waxes. Due to their substantial biological roles in plant life, the mechanisms underlying the assembly of these structures have been extensively investigated...
October 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29040510/genomic-fragmentation-and-extrachromosomal-telomeric-repeats-impact-assessment-of-telomere-length-in-human-spermatozoa-quantitative-experiments-and-systematic-review
#14
P Kurjanowicz, S Moskovtsev, C Librach
STUDY QUESTION: Can differences in DNA isolation alter assessment of sperm telomere length (spTL) and do they account for conflicting results in the literature on spTL and male fertility? SUMMARY ANSWER: DNA isolation methods preferentially include or exclude short, extrachromosomal (EC) telomere-specific sequences that alter spTL measurements, and are responsible for a proportion of the disparity observed between investigations. WHAT IS KNOWN ALREADY: The relationship between spTL and male fertility has become an active area of research...
September 29, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29040422/pharmacogenetics-a-general-review-on-progress-to-date
#15
Ann K Daly
Background: Pharmacogenetics is not a new subject area but its relevance to drug prescribing has become clearer in recent years due to developments in gene cloning and DNA genotyping and sequencing. Sources of data: There is a very extensive published literature concerned with a variety of different genes and drugs. Areas of agreement: There is general agreement that pharmacogenetic testing is essential for the safe use of drugs such as the thiopurines and abacavir...
October 11, 2017: British Medical Bulletin
https://www.readbyqxmd.com/read/29040395/human-genome-sequencing-at-the-population-scale-a-primer-on-high-throughput-dna-sequencing-and-analysis
#16
Rachel L Goldfeder, Dennis P Wall, Muin J Khoury, John P A Ioannidis, Euan A Ashley
Most human diseases have underlying genetic causes. To better understand the impact of genes on disease and its implications for medicine and public health, researchers have pursued methods for determining the sequences of individual genes, then all genes, and now complete human genomes. Massively parallel high-throughput sequencing technology, where DNA is sheared into smaller pieces, sequenced, and then computationally reordered and analyzed, enables fast and affordable sequencing of full human genomes. As the price of sequencing continues to decline, more and more individuals are having their genomes sequenced...
October 15, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/29040258/prognostic-and-therapeutic-implications-of-dna-repair-gene-mutations-in-advanced-prostate-cancer
#17
Michael T Schweizer, Emmanuel S Antonarakis
Recent work directed toward understanding the molecular features of advanced prostate cancers has revealed a relatively high incidence of both germline and somatic alterations in genes involved in DNA damage repair (DDR). Many of these alterations likely play a critical role in the pathogenesis of more aggressive prostate cancers-leading to genomic instability and an increased probability of the development of lethal disease. However, because the ability to repair DNA damage with a high degree of fidelity is critical to an individual cell's survival, tumor cells harboring alterations in DDR pathway genes are also more susceptible to drugs that induce DNA damage or impair alternative DNA repair pathways...
October 2017: Clinical Advances in Hematology & Oncology: H&O
https://www.readbyqxmd.com/read/29040257/current-challenges-in-the-management-of-essential-thrombocythemia
#18
Ariel Kleman, Arun K Singavi, Laura C Michaelis
Essential thrombocythemia (ET), an uncommon blood cancer, is one of the classic myeloproliferative neoplasms, a category that also includes polycythemia vera and primary myelofibrosis. All 3 diseases are clonal hematopoietic stem cell disorders. Since 2005, when scientists discovered a molecular aberration driving clonal hematopoiesis in polycythemia vera, our understanding of the genomic underpinnings of these conditions has increased rapidly. Over the last decades, primary prevention of thrombotic and hemorrhagic complications has improved the lives of patients with ET, and the ability to characterize the disease by the presence or absence of molecular mutations has lent precision to our prognostic models...
October 2017: Clinical Advances in Hematology & Oncology: H&O
https://www.readbyqxmd.com/read/29039812/molecular-aspects-of-circadian-pharmacology-and-relevance-for-cancer-chronotherapy
#19
REVIEW
Narin Ozturk, Dilek Ozturk, Ibrahim Halil Kavakli, Alper Okyar
The circadian timing system (CTS) controls various biological functions in mammals including xenobiotic metabolism and detoxification, immune functions, cell cycle events, apoptosis and angiogenesis. Although the importance of the CTS is well known in the pharmacology of drugs, it is less appreciated at the clinical level. Genome-wide studies highlighted that the majority of drug target genes are controlled by CTS. This suggests that chronotherapeutic approaches should be taken for many drugs to enhance their effectiveness...
October 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29039455/cell-penetrating-peptides-and-their-utility-in-genome-function-modifications-review
#20
Maciej Gagat, Wioletta Zielińska, Alina Grzanka
For almost 30 years, studies have confirmed the effectiveness of cell-penetrating peptides (CPPs) in the facilitation of the intracellular delivery of various cargo molecules, including RNA, DNA, plasmids, proteins or nanoparticles, under in vitro and in vivo conditions. The cellular uptake of CPPs occurs via energy-dependent, as well as -independent mechanisms. In this relatively new direction of research, studies have attempted to introduce genome modification systems into cells by CPPs. Cellular uptake of CPPs carrying either covalently bound or electrostatically conjugated cargo, has several advantages over viral delivery systems, as it does not lead to any significant cytotoxicity or immunogenicity, and simultaneously it is more efficient than other non-viral systems...
October 4, 2017: International Journal of Molecular Medicine
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