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Genomic medicine

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https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#1
Yonghong Du, Joshua S Martin, John McGee, Yuchen Yang, Eric Yi Liu, Yingrui Sun, Matthias Geihs, Xuejun Kong, Eric Lingfeng Zhou, Yun Li, Jie Huang
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade...
2017: PloS One
https://www.readbyqxmd.com/read/28925997/precision-annotation-of-digital-samples-in-ncbi-s-gene-expression-omnibus
#2
Dexter Hadley, James Pan, Osama El-Sayed, Jihad Aljabban, Imad Aljabban, Tej D Azad, Mohamad O Hadied, Shuaib Raza, Benjamin Abhishek Rayikanti, Bin Chen, Hyojung Paik, Dvir Aran, Jordan Spatz, Daniel Himmelstein, Maryam Panahiazar, Sanchita Bhattacharya, Marina Sirota, Mark A Musen, Atul J Butte
The Gene Expression Omnibus (GEO) contains more than two million digital samples from functional genomics experiments amassed over almost two decades. However, individual sample meta-data remains poorly described by unstructured free text attributes preventing its largescale reanalysis. We introduce the Search Tag Analyze Resource for GEO as a web application (http://STARGEO.org) to curate better annotations of sample phenotypes uniformly across different studies, and to use these sample annotations to define robust genomic signatures of disease pathology by meta-analysis...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28924942/exploring-the-anti-proliferative-activity-of-pelargonium-sidoides-dc-with-in-silico-target-identification-and-network-pharmacology
#3
A S P Pereira, M J Bester, Z Apostolides
Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated...
September 18, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28923015/transcriptome-analysis-of-pseudostellaria-heterophylla-in-response-to-the-infection-of-pathogenic-fusarium-oxysporum
#4
Xianjin Qin, Hongmiao Wu, Jun Chen, Linkun Wu, Sheng Lin, Muhammad Umar Khan, Mohammad Reza Boorboori, Wenxiong Lin
BACKGROUND: Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Our previous study found that consecutive monoculture of Pseudostellaria heterophylla could lead to the deterioration of the rhizosphere microenvironment. The specialized forms of pathogenic fungus Fusarium oxysporum f...
September 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28922794/genome-wide-variation-patterns-uncover-the-origin-and-selection-in-cultivated-ginseng-panax-ginseng-meyer
#5
Ming-Rui Li, Feng-Xue Shi, Ya-Ling Li, Peng Jiang, Lili Jiao, Bao Liu, Lin-Feng Li
Chinese ginseng (Panax ginseng Meyer) is a medicinally important herb and plays crucial roles in traditional Chinese medicine. Pharmacological analyses identified diverse bioactive components from Chinese ginseng. However, basic biological attributes including domestication and selection of the ginseng plant remain under-investigated. Here, we presented a genome-wide view of the domestication and selection of cultivated ginseng based on the whole genome data. A total of 8,660 protein-coding genes were selected for genome-wide scanning of the 30 wild and cultivated ginseng accessions...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28921651/somatic-mutation-analysis-of-human-cancers-challenges-in-clinical-practice
#6
Gregory J Tsongalis, William B Coleman
Somatic mutation analysis of human cancers has become the standard of practice. Whether screening for single gene variants or sequencing hundreds of cancer-related genes, this genomic information is the basis for precision medicine initiatives in oncology. Genomic profiling results in information that allows oncologists to make a more educated selection of appropriate therapeutic strategies that more often combine traditional cytotoxic chemotherapy and radiation with novel targeted therapies. Here we discuss the nuances of implementing somatic mutation testing in a clinical setting...
October 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28921531/a-naive-bayes-algorithm-for-tissue-origin-diagnosis-tod-bayes-of-synchronous-multifocal-tumors-in-the-hepatobiliary-and-pancreatic-system
#7
Weiqin Jiang, Yifei Shen, Yongfeng Ding, Chuyu Ye, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Linfu Zhou, Shuo Sun, Xingchen Zhang, Lisong Teng, Michael P Timko, Longjiang Fan, Weijia Fang
Synchronous multifocal tumors are common in the hepatobiliary and pancreatic system but because of similarities in their histological features, oncologists have difficulty in identifying their precise tissue clonal origin through routine histopathological methods. To address this problem and assist in more precise diagnosis, we developed a computational approach for tissue origin diagnosis based on naive Bayes algorithm (TOD-Bayes) using ubiquitous RNA-Seq data. Massive tissue-specific RNA-Seq data sets were first obtained from The Cancer Genome Atlas (TCGA) and ∼1,000 feature genes were used to train and validate the TOD-Bayes algorithm...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28920829/allobranchiibius-huperziae-gen-nov-sp-nov-a-member-of-dermacoccaceae-isolated-from-the-root-of-a-medicinal-plant-huperzia-serrata-thunb
#8
Meng-Jie Ai, Ye Sun, Hong-Min Sun, Hong-Yu Liu, Li-Yan Yu, Yu-Qin Zhang
A Gram-stain-positive, non-spore-forming actinobacterial strain, designated CPCC 204077T, was isolated from the surface-sterilized root of a medicinal plant Huperzia serrata (Thunb.) collected from Sichuan Province, south-west China. The peptidoglycan type of strain CPCC 204077T was detected as A4α with an l-Lys-l-Ser-d-Asp interpeptide bridge. Galactose, glucose, rhamnose and ribose were the sugar compositions in the whole-cell hydrolysates. MK-8(H4) was the only menaquinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified phospholipid and one unidentified glycolipid...
September 18, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28918520/derivation-of-human-induced-pluripotent-stem-cell-ipsc-lines-and-mechanism-of-pluripotency-historical-perspective-and-recent-advances
#9
REVIEW
Arvind Chhabra
Derivation of human embryonic stem cell (hES) lines in 1998 was not only a major technological breakthrough in the field of regenerative medicine; it also triggered a passionate debate about the ethical issues associated with the utilization of human embryos for derivation of hESC lines. Successful derivation of induced pluripotent stem cell (iPS) lines from human somatic cells with defined reprogramming factors by Shinya Yamanaka`s group in 2007 was another breakthrough that generated enormous excitement and hope for the development of donor-specific personalized cell replacement therapies (CRT) without the ethical dilemma associated with it...
September 16, 2017: Stem Cell Reviews
https://www.readbyqxmd.com/read/28916934/cohort-research-in-omics-and-preventive-medicine
#10
Yi Shen, Sheng Zhang, Jie Zhou, Jiajia Chen
Cohort studies are observational studies in which the investigator determines the exposure status of subjects and then follows them for subsequent outcomes. The incidence of outcomes is observed in the exposed group and compared with that in a nonexposed group. Recently, new epidemiologic strategies have encouraged cohort research information exchange and cooperation to improve the cognition of disease etiology, such as case-cohort design and nested case-control study, which is available for "omics" data. Meanwhile, large-scale cohort studies using a prospective multiple design and long follow-ups have explored some of the challenges in preventive medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916928/newborn-screening-in-the-era-of-precision-medicine
#11
Lan Yang, Jiajia Chen, Bairong Shen
As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916782/predicting-clinical-outcomes-from-large-scale-cancer-genomic-profiles-with-deep-survival-models
#12
Safoora Yousefi, Fatemeh Amrollahi, Mohamed Amgad, Chengliang Dong, Joshua E Lewis, Congzheng Song, David A Gutman, Sameer H Halani, Jose Enrique Velazquez Vega, Daniel J Brat, Lee A D Cooper
Translating the vast data generated by genomic platforms into accurate predictions of clinical outcomes is a fundamental challenge in genomic medicine. Many prediction methods face limitations in learning from the high-dimensional profiles generated by these platforms, and rely on experts to hand-select a small number of features for training prediction models. In this paper, we demonstrate how deep learning and Bayesian optimization methods that have been remarkably successful in general high-dimensional prediction tasks can be adapted to the problem of predicting cancer outcomes...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28915716/implementation-and-utilization-of-the-molecular-tumor-board-to-guide-precision-medicine
#13
REVIEW
Shuko Harada, Rebecca Arend, Qian Dai, Jessica A Levesque, Thomas S Winokur, Rongjun Guo, Martin J Heslin, Lisle Nabell, L Burt Nabors, Nita A Limdi, Kevin A Roth, Edward E Partridge, Gene P Siegal, Eddy S Yang
BACKGROUND: With rapid advances in genomic medicine, the complexity of delivering precision medicine to oncology patients across a university health system demanded the creation of a Molecular Tumor Board (MTB) for patient selection and assessment of treatment options. The objective of this report is to analyze our progress to date and discuss the importance of the MTB in the implementation of personalized medicine. MATERIALS AND METHODS: Patients were reviewed in the MTB for appropriateness for comprehensive next generation sequencing (NGS) cancer gene set testing based on set criteria that were in place...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28914974/mucocutaneous-inflammation-in-the-ikaros-family-zinc-finger-1-ikzf1-keratin-5-specifc-transgenic-mice
#14
Mayumi Ueta, Junji Hamuro, Hiromi Nishigaki, Naomi Nakamura, Katsuhiko Shinomiya, Katsura Mizushima, Yuki Hitomi, Risa Tamagawa-Mineoka, Norihiko Yokoi, Yuji Naito, Katsushi Tokunaga, Norito Katoh, Chie Sotozono, Shigeru Kinoshita
BACKGROUND: Our genome-wide association study documented an association between cold medicine related Stevens-Johnson syndrome / toxic epidermal necrolysis (CM-SJS/TEN) and Ikaros Family Zinc Finger 1 (IKZF1). Few studies examined biological and pathological functions of IKZF1 in mucosal immunity. We hypothesized that IKZF1 contributes to the mucocutaneous inflammation. METHODS: Human skin and conjunctival tissues were obtained for immunohistological studies. Primary human conjunctival epithelial cells (PHCjECs) and adult human epidermal keratinocytes (HEKa) also used for gene expression analysis...
September 15, 2017: Allergy
https://www.readbyqxmd.com/read/28914759/isoform-sequencing-provides-a-more-comprehensive-view-of-the-panax-ginseng-transcriptome
#15
Ick-Hyun Jo, Jinsu Lee, Chi Eun Hong, Dong Jin Lee, Wonsil Bae, Sin-Gi Park, Yong Ju Ahn, Young Chang Kim, Jang Uk Kim, Jung Woo Lee, Dong Yun Hyun, Sung-Keun Rhee, Chang Pyo Hong, Kyong Hwan Bang, Hojin Ryu
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness...
September 15, 2017: Genes
https://www.readbyqxmd.com/read/28914268/impact-of-hipaa-s-minimum-necessary-standard-on-genomic-data-sharing
#16
Barbara J Evans, Gail P Jarvik
This article provides a brief introduction to the Health Insurance Portability and Accountability Act of 1996 (HIPAA) Privacy Rule's minimum necessary standard, which applies to sharing of genomic data, particularly clinical data, following 2013 Privacy Rule revisions. This research used the Thomson Reuters Westlaw database and law library resources in its legal analysis of the HIPAA privacy tiers and the impact of the minimum necessary standard on genomic data sharing. We considered relevant example cases of genomic data-sharing needs...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914267/developing-a-common-framework-for-evaluating-the-implementation-of-genomic-medicine-interventions-in-clinical-care-the-ignite-network-s-common-measures-working-group
#17
Lori A Orlando, Nina R Sperber, Corrine Voils, Marshall Nichols, Rachel A Myers, R Ryanne Wu, Tejinder Rakhra-Burris, Kenneth D Levy, Mia Levy, Toni I Pollin, Yue Guan, Carol R Horowitz, Michelle Ramos, Stephen E Kimmel, Caitrin W McDonough, Ebony B Madden, Laura J Damschroder
PurposeImplementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing Genomics in Practice (IGNITE) Network's efforts to promote (i) a broader understanding of genomic medicine implementation research and (ii) the sharing of knowledge generated in the network.MethodsTo facilitate this goal, the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide its approach to identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross-network analyses...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#18
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28912773/hirsutine-an-indole-alkaloid-of-uncaria-rhynchophylla-inhibits-late-step-in-dengue-virus-lifecycle
#19
Takayuki Hishiki, Fumihiro Kato, Shigeru Tajima, Kazufumi Toume, Masahito Umezaki, Tomohiko Takasaki, Tomoyuki Miura
Dengue virus (DENV) is transmitted to humans by Aedes mosquitoes and is a public health issue worldwide. No antiviral drugs specific for treating dengue infection are currently available. To identify novel DENV inhibitors, we analyzed a library of 95 compounds and 120 extracts derived from crude drugs (herbal medicines). In the primary screening, A549 cells infected with DENV-1 were cultured in the presence of each compound and extract at a final concentration of 10 μM (compound) and 100 μg/mL (extract), and reduction of viral focus formation was assessed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28911628/antifungal-activity-of-momordica-charantia-seed-extracts-toward-the-pathogenic-fungus-fusarium-solani-l
#20
Shuzhen Wang, Yongliang Zheng, Fu Xiang, Shiming Li, Guliang Yang
Momordica charantia L., a vegetable crop with high nutritional value, has been used as an antimutagenic, antihelminthic, anticancer, antifertility, and antidiabetic agent in traditional folk medicine. In this study, the antifungal activity of M. charantia seed extract toward Fusarium solani L. was evaluated. Results showed that M. charantia seed extract effectively inhibited the mycelial growth of F. solani, with a 50% inhibitory rate (IC50) value of 108.934 μg/mL. Further analysis with optical microscopy and fluorescence microscopy revealed that the seed extract led to deformation of cells with irregular budding, loss of integrity of cell wall, as well as disruption of the fungal cell membrane...
October 2016: Journal of Food and Drug Analysis
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