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https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#1
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28544474/breast-cancer-and-transplantation
#2
Germaine Wong, Eric Au, Sunil V Badve, Wai H Lim
Breast cancer is an important cancer among solid organ transplant recipients. While the incidence of breast cancer in solid organ transplant recipients is comparable to the age matched general population, the outcomes are generally poor. Interventions such as cancer screening which preclude the development of late stage disease through early detection are not well-studied, and clinical practice guidelines for cancer screening rely solely on recommendations from the general population. Among those with a prior breast cancer history, disease recurrence after transplantation is a rare but fearful event...
May 19, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28544285/salmonella-typhi-genomics-envisaging-the-future-of-typhoid-eradication
#3
REVIEW
Kien-Pong Yap, Kwai Lin Thong
Next-generation whole genome sequencing has revolutionized the study of infectious diseases in recent years. The availability of genome sequences and its understanding have transformed the field of molecular microbiology, epidemiology, infection treatments and vaccine developments. We review the key findings of the publicly accessible genomes of Salmonella enterica serovar Typhi since the first complete genome to the most recent release of thousands of S. typhi genomes, which remarkably shape the genomic research of S...
May 24, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#4
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28543993/genetic-background-of-hirschsprung-disease-a-bridge-between-basic-science-and-clinical-application
#5
Afsane Bahrami, Marjan Joodi, Mehrdad Ahmadi, Mina Maftouh, Seyed Mahdi Hassanian, Gordon A Ferns, Amir Avan
Hirschsprung's disease (HSCR) is a congenital disorder, defined by partial or complete loss of the neuronal ganglion cells in the intestinal tract, which is caused by the failure of neural crest cells to migrate completely during intestinal development during fetal life. HSCR has a multifactorial etiology, and genetic factors play a key role in its pathogenesis; these include mutations within several gene loci. These have been identified by screening candidate genes, or by conducting genome wide association (GWAS) studies...
May 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28543693/somatic-driver-mutations-in-melanoma
#6
REVIEW
Bobby Y Reddy, David M Miller, Hensin Tsao
Melanoma has one of the highest somatic mutational burdens among solid malignancies. Although the rapid progress in genomic research has contributed immensely to our understanding of the pathogenesis of melanoma, the clinical significance of the vast array of genomic alterations discovered by next-generation sequencing is far from being fully characterized. Most mutations prevalent in melanoma are simply neutral "passengers," which accompany functionally significant "drivers" under transforming conditions. The delineation of driver mutations from passenger mutations is critical to the development of targeted therapies...
June 1, 2017: Cancer
https://www.readbyqxmd.com/read/28542881/genetic-susceptibility-in-cervical-cancer-from-bench-to-bedside
#7
Afsane Bahrami, Malihe Hasanzadeh, Soodabeh Shahidsales, Marjaneh Farazestanian, Seyed Mahdi Hassanian, Mehrdad Ahmadi, Mina Maftouh, Masoumeh Gharib, Zohre Yousefi, Sima Kadkhodayan, Gordon A Ferns, Amir Avan
Cervical cancer (CC) is the third most common malignancy in women globally, and persistent infection with the oncogenic human papillomaviruses (HPV) is recognized as the major risk factor. The pathogenesis of CC relies on the interplay between the tumorigenic properties of the HPV and host factors. Host-related genetic factors, including the presence of susceptibility loci for cervix tumor is substantial importance. Preclinical and genome-wide association studies (GWAS) have reported the associations of genetic variations in several susceptibility loci for the development of cervical cancer...
May 19, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28542676/detailed-clinical-phenotype-and-molecular-genetic-findings-in-cln3-associated-isolated-retinal-degeneration
#8
Cristy A Ku, Sarah Hull, Gavin Arno, Ajoy Vincent, Keren Carss, Robert Kayton, Douglas Weeks, Glenn W Anderson, Ryan Geraets, Camille Parker, David A Pearce, Michel Michaelides, Robert E MacLaren, Anthony G Robson, Graham E Holder, Elise Heon, F Lucy Raymond, Anthony T Moore, Andrew R Webster, Mark E Pennesi
Importance: Mutations in genes traditionally associated with syndromic retinal disease are increasingly found to cause nonsyndromic inherited retinal degenerations. Mutations in CLN3 are classically associated with juvenile neuronal ceroid lipofuscinosis, a rare neurodegenerative disease with early retinal degeneration and progressive neurologic deterioration, but have recently also been identified in patients with nonsyndromic inherited retinal degenerations. To our knowledge, detailed clinical characterization of such cases has yet to be reported...
May 25, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/28541858/the-pathologic-finding-of-combined-lobular-carcinoma-in-situ-and-invasive-lobular-cancer-may-indicate-more-than-just-a-high-risk-marker-role-of-lobular-carcinoma-in-situ
#9
Christopher J Jean-Louis, Joshua Masdon, Betsy Smith, Oscar Battles, Paul Dale
For years, lobular carcinoma In Situ (LCIS) has been considered a high-risk marker for developing breast cancer. It is well known that ductal carcinoma In Situ is a precursor for the development of invasive ductal carcinoma, and ductal carcinoma In Situ is reported to be present in invasive ductal carcinoma in at least 40 per cent of cases. A similar relationship between LCIS and invasive lobular carcinoma (ILC) remains in question. This study evaluates the incidence of synchronous LCIS and ILC at our institution...
May 1, 2017: American Surgeon
https://www.readbyqxmd.com/read/28541389/cell-cycle-dependent-control-of-homologous-recombination
#10
Xin Zhao, Chengwen Wei, Jingjing Li, Poyuan Xing, Jingyao Li, Sihao Zheng, Xuefeng Chen
DNA double-strand breaks (DSBs) are among the most deleterious type of DNA lesions threatening genome integrity. Homologous recombination (HR) and non-homologous end joining (NHEJ) are two major pathways to repair DSBs. HR requires a homologous template to direct DNA repair, and is generally recognized as a high-fidelity pathway. In contrast, NHEJ directly seals broken ends, but the repair product is often accompanied by sequence alterations. The choice of repair pathways is strictly controlled by the cell cycle...
May 25, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28541025/structural-genomic-variations-and-parkinson-s-disease
#11
Sara Bandrés-Ciga, Clara Ruz, Francisco J Barrero, Francisco Escamilla-Sevilla, Javier Pelegrina, Francisco Vives, Raquel Duran
Parkinson's disease (PD) is the second most common neurodegenerative disease, whose prevalence is projected to be between 8.7 and 9.3 million by 2030. Until about 20 years ago, PD was considered to be the textbook example of a "nongenetic" disorder. Nowadays, PD is generally considered a multifactorial disorder that arises from the combination and complex interaction of genes and environmental factors. To date, a total of 7 genes including SNCA, LRRK2, PARK2, DJ-1, PINK 1, VPS35 and ATP13A2 have been seen to cause unequivocally Mendelian PD...
May 25, 2017: Minerva Medica
https://www.readbyqxmd.com/read/28540673/micrornas-long-noncoding-rnas-and-their-functions-in-human-disease
#12
Min Xue, Ying Zhuo, Bin Shan
Majority of the human genome is transcribed into RNAs with absent or limited protein-coding potential. microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two major families of the non-protein-coding transcripts. miRNAs and lncRNAs can regulate fundamental cellular processes via diverse mechanisms. The expression and function of miRNAs and lncRNAs are tightly regulated in development and physiological homeostasis. Dysregulation of miRNAs and lncRNAs is critical to pathogenesis of human disease. Moreover, recent evidence indicates a cross talk between miRNAs and lncRNAs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540671/multidisciplinary-management-of-mycosis-fungoides-s%C3%A3-zary-syndrome
#13
REVIEW
Sara Berg, Jennifer Villasenor-Park, Paul Haun, Ellen J Kim
PURPOSE OF REVIEW: Diagnosis and management of mycosis fungoides and Sézary syndrome (MF/SS) require accurate clinicopathological correlation and a multidisciplinary approach. We reviewed major advances in the field regarding diagnostic and prognostic tools as well as skin-directed therapies (SDTs) and systemic agents for MF/SS published in the past 2 years. RECENT FINDINGS: Improved technology (T-cell receptor high-throughput sequencing) and increased multicenter collaboration (Cutaneous Lymphoma International Consortium) have led to diagnostic/prognostic advances...
May 24, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/28540512/a-molecular-insight-into-papaya-leaf-curl-a-severe-viral-disease
#14
REVIEW
Priyanka Varun, S A Ranade, Sangeeta Saxena
Papaya leaf curl disease (PaLCuD) caused by papaya leaf curl virus (PaLCuV) not only affects yield but also plant growth and fruit size and quality of papaya and is one of the most damaging and economically important disease. Management of PaLCuV is a challenging task due to diversity of viral strains, the alternate hosts, and the genomic complexities of the viruses. Several management strategies currently used by plant virologists to broadly control or eliminate the viruses have been discussed. In the absence of such strategies in the case of PaLCuV at present, the few available options to control the disease include methods like removal of affected plants from the field, insecticide treatments against the insect vector (Bemisia tabaci), and gene-specific control through transgenic constructs...
May 25, 2017: Protoplasma
https://www.readbyqxmd.com/read/28539834/complex-relationship-between-obesity-and-the-fat-mass-and-obesity-locus
#15
REVIEW
Qingyun Yang, Tiancun Xiao, Jiao Guo, Zhengquan Su
In the 21st century, obesity has become a serious problem because of increasing obese patients and numerous metabolic complications. The primary reasons for this situation are environmental and genetic factors. In 2007, FTO (fat mass and obesity associated) was the first gene identified through a genome-wide association study (GWAS) associated with obesity in humans. Subsequently, a cluster of single nucleotide polymorphisms (SNPs) in the first intron of the FTO gene was discovered to be associated with BMI and body composition...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/28539503/mycoplasma-pneumoniae-from-the-respiratory-tract-and-beyond
#16
REVIEW
Ken B Waites, Li Xiao, Yang Liu, Mitchell F Balish, T Prescott Atkinson
Mycoplasma pneumoniae is an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests for M. pneumoniae detection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms...
July 2017: Clinical Microbiology Reviews
https://www.readbyqxmd.com/read/28538216/the-emerging-view-of-aging-as-a-reversible-epigenetic-process
#17
Micaela López-León, Rodolfo G Goya
The achievement of animal cloning and subsequent development of cell reprogramming technology are having a profound impact on our view of the mechanisms of aging in complex organisms. The experimental evidence showing that an adult somatic nucleus implanted into an enucleated oocyte can give rise to a whole new individual strongly suggests that the integrity of the genome of an adult nucleus is fully preserved. Here, we will review recent experimental evidence showing that pluripotency gene-based cell reprogramming can erase the epigenetic marks of aging and rejuvenate cells from old individuals reversing most signs of aging and that when induced pluripotent stem cells are differentiated back to the cell type of origin, the rejuvenated cells share many of the features of wild-type counterparts from young donors...
May 25, 2017: Gerontology
https://www.readbyqxmd.com/read/28537880/biological-effects-and-epidemiological-consequences-of-arsenic-exposure-and-reagents-that-can-ameliorate-arsenic-damage-in-vivo
#18
REVIEW
Chinthalapally V Rao, Sanya Pal, Altaf Mohammed, Mudassir Farooqui, Mark P Doescher, Adam S Asch, Hiroshi Y Yamada
Through contaminated diet, water, and other forms of environmental exposure, arsenic affects human health. There are many U.S. and worldwide "hot spots" where the arsenic level in public water exceeds the maximum exposure limit. The biological effects of chronic arsenic exposure include generation of reactive oxygen species (ROS), leading to oxidative stress and DNA damage, epigenetic DNA modification, induction of genomic instability, and inflammation and immunomodulation, all of which can initiate carcinogenesis...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28537574/mechanisms-of-dna-replication-termination
#19
REVIEW
James M Dewar, Johannes C Walter
Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation...
May 24, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28537231/-viral-component-of-the-human-genome
#20
V M Blinov, V V Zverev, G S Krasnov, F P Filatov, A V Shargunov
Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent...
March 2017: Molekuliarnaia Biologiia
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