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Genetic markers

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https://www.readbyqxmd.com/read/28335509/novel-diagnostic-and-predictive-biomarkers-in-pancreatic-adenocarcinoma
#1
REVIEW
John C Chang, Madappa Kundranda
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease for a multitude of reasons including very late diagnosis. This in part is due to the lack of understanding of the biological behavior of PDAC and the ineffective screening for this disease. Significant efforts have been dedicated to finding the appropriate serum and imaging biomarkers to help early detection and predict response to treatment of PDAC. Carbohydrate antigen 19-9 (CA 19-9) has been the most validated serum marker and has the highest positive predictive value as a stand-alone marker...
March 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#2
Michael T Eadon, Ronald J Hause, Amy L Stark, Ying-Hua Cheng, Heather E Wheeler, Kimberly S Burgess, Eric A Benson, Patrick N Cunningham, Robert L Bacallao, Pierre C Dagher, Todd C Skaar, M Eileen Dolan
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines...
March 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335091/assessment-of-genetic-diversity-and-phylogenetic-relationships-of-korean-native-chicken-breeds-using-microsatellite-markers
#3
Joo Hee Seo, Jun-Heon Lee, Hong Sik Kong
In this study, the genetic diversity and phylogenetic relationships of 445 Korean native chickens from five different breeds(Korean Native Chicken (NC), Leghorn (LH), Cornish (CS), Rhode Island Red (RIR), and Hanhyup(HH) commercial line) were studied by performing genotyping using 20 microsatellite (MS) markers. Among the 20 MS markers selected for the genotyping, the number of alleles ranged from 5 (ADL0268) to 20 (MCW0127). The observed heterozygosity (Hobs) ranged from 0.349 (GCT0016) to 0.683 (MCW0145)...
March 21, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28335009/open-chromatin-profiling-of-human-postmortem-brain-infers-functional-roles-for-non-coding-schizophrenia-loci
#4
John F Fullard, Claudia Giambartolomei, Mads E Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T Dudley, Manuel Mattheisen, Nikolaos K Robakis, Vahram Haroutunian, Panos Roussos
Open chromatin provides access to DNA binding proteins for the correct spatiotemporal regulation of gene expression. Mapping chromatin accessibility has been widely used to identify the location of cis regulatory elements (CREs) including promoters and enhancers. CREs show tissue- and cell-type specificity and disease-associated variants are often enriched for CREs in the tissues and cells that pertain to a given disease. To better understand the role of CREs in neuropsychiatric disorders we applied the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq) to neuronal and non-neuronal nuclei isolated from frozen postmortem human brain by fluorescence-activated nuclear sorting (FANS)...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334355/a-zoom-focus-algorithm-zfa-to-locate-the-optimal-testing-region-for-rare-variant-association-tests
#5
Maggie Haitian Wang, Haoyi Weng, Rui Sun, Jack Lee, William Ka Kei Wu, Ka Chun Chong, Benny Chung-Ying Zee
Motivation: Increasing amounts of whole exome or genome sequencing data present the challenge of analysing rare variants with extremely small minor allele frequencies. Various statistical tests have been proposed, which are specifically configured to increase power for rare variants by conducting the test within a certain bin, such as a gene or a pathway. However, a gene may contain from several to thousands of markers, and not all of them are related to the phenotype. Combining functional and non-functional variants in an arbitrary genomic region could impair the testing power...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334284/genomic-diversity-guides-conservation-strategies-among-rare-terrestrial-orchid-species-when-taxonomy-remains-uncertain
#6
Collin W Ahrens, Megan A Supple, Nicola C Aitken, David J Cantrill, Justin O Borevitz, Elizabeth A James
Background and Aims: Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia...
March 15, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334280/origin-and-genetic-differentiation-of-pink-flowered-sorbus-hybrids-in-the-western-carpathians
#7
Veronika Uhrinová, Judita Zozomová-Lihová, Dana Bernátová, Juraj Paule, Ladislav Paule, Dušan Gömöry
Background and Aims: Diversity of the genus Sorbus has been affected by interspecific hybridizations. Pink-flowered hybrid species have been insufficiently studied so far. They comprise bigenomic hybrid species derived from crosses S. aria s.l. × S. chamaemespilus and trigenomic ones, where S. aucuparia was involved as well. The main objective of the present study was to reconstruct their hybrid origins as well as to assess genetic distinction among several morphologically recognized hybrid species...
March 13, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#8
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334169/characterization-of-saccharomyces-uvarum-beijerinck-1898-and-related-hybrids-assessment-of-molecular-markers-that-predict-the-parent-and-hybrid-genomes-and-a-proposal-to-name-yeast-hybrids
#9
Huu-Vang Nguyen, Teun Boekhout
The use of the nuclear-DNA re-association technique has led taxonomists to consider Saccharomyces uvarum a synonym of S. bayanus. The latter, however, is not a species but a hybrid harbouring S. eubayanus (Seu) and S. uvarum (Su) sub-genomes with a minor DNA contribution from S. cerevisiae (Sc). To recognize genetically pure lines of S. uvarum and putative interspecies hybrids among so-called S. bayanus strains present in public culture collections, we propose the use of four markers that were defined from the S...
March 3, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28334091/landscape-level-patterns-of-elevated-fs1-asian-allele-frequencies-in-populations-of-gypsy-moth-lepidoptera-erebidae-at-a-northern-u-s-boundary
#10
Marissa A Streifel, Patrick C Tobin, Lucia Hunt, Hannah Nadel, John J Molongoski, Brian H Aukema
From a regulatory perspective, Asian gypsy moth is a species complex consisting of three species of Lymantria and two subspecies of Lymantria dispar (L.), differing from the European subspecies, L. dispar dispar (L.), by having consistently flight-capable females. As such, the invasion potential in North America is thought to exceed that of European gypsy moth. USDA-APHIS therefore has a monitoring program to detect Asian gypsy moth at high-risk introduction pathways. Molecular markers are used to improve the diagnosis of Asian gypsy moth...
February 17, 2017: Environmental Entomology
https://www.readbyqxmd.com/read/28332837/molecular-recognition-based-dna-nanoassemblies-on-the-surfaces-of-nanosized-exosomes
#11
Shuo Wan, Liqin Zhang, Sai Wang, Yuan Liu, Cuichen Wu, Cheng Cui, Hao Sun, Muling Shi, Ying Jiang, Long Li, Liping Qiu, Weihong Tan
Exosomes are membrane-enclosed extracellular vesicles derived from cells, carrying biomolecules that include pro-teins and nucleic acids for intercellular communication. Owning to their advantages of size, structure, stability and biocompatibility, exosomes have been used widely as natu-ral nanocarriers for intracellular delivery of theranostic agents. Meanwhile, surface modifications needed to endow exosomes with additional functionalities remain challeng-ing by their small size and the complexity of their mem-brane surfaces...
March 23, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28332274/time-course-expression-qtl-atlas-of-the-global-transcriptional-response-of-wheat-to-fusarium-graminearum
#12
Mina Samad-Zamini, Wolfgang Schweiger, Thomas Nussbaumer, Klaus F X Mayer, Hermann Buerstmayr
Fusarium head blight is a devastating disease of small grain cereals such as bread wheat (Triticum aestivum). The pathogen switches from a biotrophic to a nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. Using a genetical genomics approach we illustrate genome-wide reconfigurations of genetic control over transcript abundances between two decisive time points after inoculation with the causative pathogen Fusarium graminearum. Whole transcriptome measurements have been recorded for 163 lines of a wheat doubled haploid population segregating for several resistance genes yielding 15 552 at 30 hours and 15 888 eQTL at 50 hours after inoculation...
March 23, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28331626/osteosarcoma-inheritance-in-two-families-of-scottish-deerhounds
#13
John E Dillberger, Sara Ann McAtee
BACKGROUND: Osteosarcoma is the most common neoplastic disease in Scottish Deerhounds. For Deerhounds, a 2007 population-based study concluded that a single dominant genetic factor largely governed disease risk. For Greyhounds, Rottweilers, and Irish Wolfhounds, a 2013 genome-wide association study found multiple genetic markers in each breed, with each marker only weakly associated with the disease. We obtained from two breeders the pedigrees, age (if alive) or age at death, and osteosarcoma status for two families of Scottish Deerhounds, designated Cohorts K and T...
2017: Canine Genetics and Epidemiology
https://www.readbyqxmd.com/read/28331559/tumor-suppressor-genes-in-familial-adenomatous-polyposis
#14
REVIEW
Nahal Eshghifar, Naser Farrokhi, Tahereh Naji, Mohammadreza Zali
Colorectal cancer (CRC) is mostly due to a series of genetic alterations that are being greatly under the influence of the environmental factors. These changes, mutational or epigenetic modifications at transcriptional forefront and/or post-transcriptional effects via miRNAs, include inactivation and the conversion of proto-oncogene to oncogenes, and/or inactivation of tumor suppressor genes (TSG). Here, a thorough review was carried out on the role of TSGs with the focus on the APC as the master regulator, mutated genes and mal-/dysfunctional pathways that lead to one type of hereditary form of the CRC; namely familial adenomatous polyposis (FAP)...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28331548/discovering-feature-relevancy-and-dependency-by-kernel-guided-probabilistic-model-building-evolution
#15
Nestor Rodriguez, Sergio Rojas-Galeano
BACKGROUND: Discovering relevant features (biomarkers) that discriminate etiologies of a disease is useful to provide biomedical researchers with candidate targets for further laboratory experimentation while saving costs; dependencies among biomarkers may suggest additional valuable information, for example, to characterize complex epistatic relationships from genetic data. The use of classifiers to guide the search for biomarkers (the so-called wrapper approach) has been widely studied...
2017: BioData Mining
https://www.readbyqxmd.com/read/28331401/dna-barcoding-and-species-delimitation-of-chaitophorinae-hemiptera-aphididae
#16
Xi-Chao Zhu, Jing Chen, Rui Chen, Li-Yun Jiang, Ge-Xia Qiao
Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process)...
2017: ZooKeys
https://www.readbyqxmd.com/read/28331352/skin-disorders-in-parkinson-s-disease-potential-biomarkers-and-risk-factors
#17
REVIEW
Astrid-Helene Ravn, Jacob P Thyssen, Alexander Egeberg
Parkinson's disease (PD) is one of the most common neurodegenerative disorders, characterized by a symptom triad comprising resting tremor, rigidity, and akinesia. In addition, non-motor symptoms of PD are well recognized and often precede the overt motor manifestations. Cutaneous manifestations as markers of PD have long been discussed, and cumulative evidence shows an increased prevalence of certain dermatological disorders in PD. Seborrheic dermatitis is considered to occur as a premotor feature of PD referable to dysregulation of the autonomic nervous system...
2017: Clinical, Cosmetic and Investigational Dermatology
https://www.readbyqxmd.com/read/28331344/adverse-prognostic-impact-of-tgfb1-t869c-polymorphism-in-non-small-cell-lung-cancer
#18
Yulan Sang, Xin Bi, Yan Liu, Wei Zhang, Dongjie Wang
Previously, several polymorphisms in TGFB1 have been identified in non-small-cell lung cancer (NSCLC), and the variants, C-509T, T869C, and G915C, have been demonstrated to associate with higher circulating levels of TGF-β1. However, little is known about the prognostic value of TGF-β1 polymorphisms in cancers. In this study, by genotyping the TGF-β1 T869C polymorphism in a total of 261 patients with NSCLC using DNA from blood lymphocytes, we first found that NSCLC patients, especially those with allele C carriers, had significantly higher serum TGF-β1 levels than healthy individuals...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28331182/construction-of-a-high-density-genetic-map-and-quantitative-trait-locus-mapping-in-the-manila-clam-ruditapes-philippinarum
#19
Hongtao Nie, Xiwu Yan, Zhongming Huo, Liwen Jiang, Peng Chen, Hui Liu, Jianfeng Ding, Feng Yang
Genetic linkage maps are indispensable tools in a wide range of genetic and genomic research. With the advancement of genotyping-by-sequencing (GBS) methods, the construction of a high-density linkage maps has become achievable in marine organisms lacking sufficient genomic resources, such as mollusks. In this study, high-density linkage map was constructed for an ecologically and commercially important clam species, Ruditapes philippinarum. For the consensus linkage map, a total of 9658 markers spanning 1926...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28330873/amp-activated-protein-kinase-%C3%AE-1-promotes-atherogenesis-by-increasing-monocyte-to-macrophage-differentiation
#20
Miao Zhang, Huaiping Zhu, Ye Ding, Zhaoyu Liu, Zhejun Cai, Ming-Hui Zou
Monocyte-to-macrophage differentiation, which can be initiated by physiological or atherogenic factors, is a pivotal process in atherogenesis, a disorder in which monocytes adhere to endothelial cells and subsequently migrate into the sub-endothelial spaces, where they differentiate into macrophages and macrophage-derived foam cells and cause atherosclerotic lesions. However, the monocyte-differentiation signaling pathways that are activated by atherogenic factors are poorly defined. Here we report that the AMP- activated protein kinase (AMPK) α1 in monocytes promotes atherosclerosis by increasing monocyte differentiation and survival...
March 22, 2017: Journal of Biological Chemistry
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