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Genomics Medicine

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https://www.readbyqxmd.com/read/29782246/precision-medicine-and-radiogenomics-in-breast-cancer-new-approaches-toward-diagnosis-and-treatment
#1
Katja Pinker, Joanne Chin, Amy N Melsaether, Elizabeth A Morris, Linda Moy
Precision medicine is medicine optimized to the genotypic and phenotypic characteristics of an individual and, when present, his or her disease. It has a host of targets, including genes and their transcripts, proteins, and metabolites. Studying precision medicine involves a systems biology approach that integrates mathematical modeling and biology genomics, transcriptomics, proteomics, and metabolomics. Moreover, precision medicine must consider not only the relatively static genetic codes of individuals, but also the dynamic and heterogeneous genetic codes of cancers...
June 2018: Radiology
https://www.readbyqxmd.com/read/29780747/precision-medicine-in-hormone-receptor-positive-breast-cancer
#2
REVIEW
Azadeh Nasrazadani, Roby A Thomas, Steffi Oesterreich, Adrian V Lee
In recent decades, breast cancer has become largely manageable due to successes with hormone receptor targeting. Hormone receptor-positive tumors have favorable outcomes in comparison to estrogen receptor (ESR1, ER)/progesterone receptor-negative tumors given the targetable nature of these tumors, as well as their inherently less aggressive character. Nonetheless, treatment resistance is frequently encountered due to a variety of mechanisms, including ESR1 mutations and loss of ER expression. A new era of precision medicine utilizes a range of methodologies to allow real-time analysis of individual genomic signatures in metastases and liquid biopsies with the goal of finding clinically actionable targets...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29780001/automated-typing-of-red-blood-cell-and-platelet-antigens-a-whole-genome-sequencing-study
#3
William J Lane, Connie M Westhoff, Nicholas S Gleadall, Maria Aguad, Robin Smeland-Wagman, Sunitha Vege, Daimon P Simmons, Helen H Mah, Matthew S Lebo, Klaudia Walter, Nicole Soranzo, Emanuele Di Angelantonio, John Danesh, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Richard M Kaufman, Heidi L Rehm, Leslie E Silberstein, Robert C Green
BACKGROUND: There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone...
May 17, 2018: Lancet Haematology
https://www.readbyqxmd.com/read/29779898/oncostatin-m-and-kit-ligand-control-hematopoietic-stem-cell-fate-during-zebrafish-embryogenesis
#4
Christopher B Mahony, Corentin Pasche, Julien Y Bertrand
Understanding the molecular pathways controlling hematopoietic stem cell specification and expansion is a necessary milestone to perform regenerative medicine. Here, we used the zebrafish model to study the role of the ckit signaling pathway in this process. We show the importance of kitb/kitlgb signaling in the specification and expansion of hematopoietic stem cells (HSCs), in the hemogenic endothelium and caudal hematopoietic tissue (CHT), respectively. Moreover, we identified the zebrafish ortholog of Oncostatin M (osm) in the zebrafish genome...
May 10, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29779563/association-of-polygenic-risk-scores-for-multiple-cancers-in-a-phenome-wide-study-results-from-the-michigan-genomics-initiative
#5
Lars G Fritsche, Stephen B Gruber, Zhenke Wu, Ellen M Schmidt, Matthew Zawistowski, Stephanie E Moser, Victoria M Blanc, Chad M Brummett, Sachin Kheterpal, Gonçalo R Abecasis, Bhramar Mukherjee
Health systems are stewards of patient electronic health record (EHR) data with extraordinarily rich depth and breadth, reflecting thousands of diagnoses and exposures. Measures of genomic variation integrated with EHRs offer a potential strategy to accurately stratify patients for risk profiling and discover new relationships between diagnoses and genomes. The objective of this study was to evaluate whether polygenic risk scores (PRS) for common cancers are associated with multiple phenotypes in a phenome-wide association study (PheWAS) conducted in 28,260 unrelated, genotyped patients of recent European ancestry who consented to participate in the Michigan Genomics Initiative, a longitudinal biorepository effort within Michigan Medicine...
May 17, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29777097/gwas-on-family-history-of-alzheimer-s-disease
#6
Riccardo E Marioni, Sarah E Harris, Qian Zhang, Allan F McRae, Saskia P Hagenaars, W David Hill, Gail Davies, Craig W Ritchie, Catharine R Gale, John M Starr, Alison M Goate, David J Porteous, Jian Yang, Kathryn L Evans, Ian J Deary, Naomi R Wray, Peter M Visscher
Alzheimer's disease (AD) is a public health priority for the 21st century. Risk reduction currently revolves around lifestyle changes with much research trying to elucidate the biological underpinnings. We show that self-report of parental history of Alzheimer's dementia for case ascertainment in a genome-wide association study of 314,278 participants from UK Biobank (27,696 maternal cases, 14,338 paternal cases) is a valid proxy for an AD genetic study. After meta-analysing with published consortium data (n = 74,046 with 25,580 cases across the discovery and replication analyses), three new AD-associated loci (P < 5 × 10-8 ) are identified...
May 18, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29774075/plectin-targeted-liposomes-enhance-the-therapeutic-efficacy-of-a-parp-inhibitor-in-the-treatment-of-ovarian-cancer
#7
Siva Sai Krishna Dasa, Galina Diakova, Ryo Suzuki, Anne M Mills, Michael F Gutknecht, Alexander L Klibanov, Jill K Slack-Davis, Kimberly A Kelly
Advances in genomics and proteomics drive precision medicine by providing actionable genetic alterations and molecularly targeted therapies, respectively. While genomic analysis and medicinal chemistry have advanced patient stratification with treatments tailored to the genetic profile of a patient's tumor, proteomic targeting has the potential to enhance the therapeutic index of drugs like poly(ADP-ribose) polymerase (PARP) inhibitors. PARP inhibitors in breast and ovarian cancer patients with BRCA1/2 mutations have shown promise...
2018: Theranostics
https://www.readbyqxmd.com/read/29773584/mechanisms-in-endocrinology-cell-cycle-regulation-in-adrenocortical-carcinoma
#8
Sofia Pereira, Mariana P Monteiro, Isabelle Bourdeau, Andre Lacroix, Duarte Pignatelli
Adrenocortical carcinomas are rather rare endocrine tumors that often have a poor prognosis. The reduced survival rate associated with these tumors is due to their aggressive biological behavior, combined with the scarcity of effective treatment options that are currently available. The recent identification of the genomic alterations present in ACC have provided further molecular mechanisms to develop consistent strategies for the diagnosis, prevention of progression and treatment of advanced ACCs. Taken together, molecular and genomic advances could be leading the way to develop personalized medicine in ACCs similarly to similar developments in lung or breast cancers...
May 17, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29773007/cell-proliferation-and-dna-repair-ability-of-ganoderma-neo-japonicum-agaricomycetes-an-indigenous-medicinal-mushroom-from-malaysia
#9
Wee Cheat Tan, Umah Rani Kuppusamy, Chia Wei Phan, Vikineswary Sabaratnam
Ganoderma neo-japonicum is an annual polypore that grows on decaying bamboo in the forests of Malaysia. The indigenous Temuan tribe uses this species as a medicinal mushroom to cure fever and epilepsy and to improve body strength. The potential use of G. neo-japonicum in genoprotection and DNA repair was established using a single-cell gel electrophoresis (comet) assay. The effects of the ethanol and hot aqueous extracts from wild and cultivated basidiocarps, solid substrate-fermented (SSF) wheat grains, and mycelia via submerged culture on H2O2-damaged murine RAW264...
2018: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/29771541/plasmodial-kinase-inhibitors-license-to-cure
#10
Diego Gonzalez Cabrera, André Horatscheck, Colin Rylott Wilson, Gregory S Basarab, Charles J Eyermann, Kelly Chibale
Advances in the genetics, function and stage-specificity of Plasmodium kinases has driven robust efforts to identify targets for the design of antimalarial therapies. Reverse genomics following phenotypic screening against Plasmodia or related parasites has uncovered vulnerable kinase targets including PI4K, PKG and GSK-3, an approach bolstered by access to human disease-directed kinase libraries. Alternatively, screening compound libraries against Plasmodium kinases has successfully led to inhibitors with antiplasmodial activity...
May 17, 2018: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29770269/ten-years-of-progress-and-promise-of-induced-pluripotent-stem-cells-historical-origins-characteristics-mechanisms-limitations-and-potential-applications
#11
Adekunle Ebenezer Omole, Adegbenro Omotuyi John Fakoya
The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy...
2018: PeerJ
https://www.readbyqxmd.com/read/29769805/genome-wide-sequencing-technologies-a-primer-for-paediatricians
#12
Robin Z Hayeems, Kym M Boycott
Genetic testing has been a routine part of paediatic medicine for decades. Over time, the number of genetic tests available for children presenting with features thought to be explained by an underlying genetic aetiology has expanded considerably. Genome-wide sequencing approaches (e.g., whole-exome sequencing, whole-genome sequencing) are now emerging as the most comprehensive approaches to genetic diagnosis that we have seen to date; multiple serial tests that were once required for a child under diagnostic investigation can now be accomplished in a single assay...
May 2018: Paediatrics & Child Health
https://www.readbyqxmd.com/read/29769331/temporal-transcriptional-logic-of-dynamic-regulatory-networks-underlying-nitrogen-signaling-and-use-in-plants
#13
Kranthi Varala, Amy Marshall-Colón, Jacopo Cirrone, Matthew D Brooks, Angelo V Pasquino, Sophie Léran, Shipra Mittal, Tara M Rock, Molly B Edwards, Grace J Kim, Sandrine Ruffel, W Richard McCombie, Dennis Shasha, Gloria M Coruzzi
This study exploits time, the relatively unexplored fourth dimension of gene regulatory networks (GRNs), to learn the temporal transcriptional logic underlying dynamic nitrogen (N) signaling in plants. Our "just-in-time" analysis of time-series transcriptome data uncovered a temporal cascade of cis elements underlying dynamic N signaling. To infer transcription factor (TF)-target edges in a GRN, we applied a time-based machine learning method to 2,174 dynamic N-responsive genes. We experimentally determined a network precision cutoff, using TF-regulated genome-wide targets of three TF hubs (CRF4, SNZ, and CDF1), used to "prune" the network to 155 TFs and 608 targets...
May 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29768213/mirnas-that-induce-human-cardiomyocyte-proliferation-converge-on-the-hippo-pathway
#14
Marta Diez-Cuñado, Ke Wei, Paul J Bushway, Mano R Maurya, Ranjan Perera, Shankar Subramaniam, Pilar Ruiz-Lozano, Mark Mercola
Understanding the mechanisms that control human cardiomyocyte proliferation might be applicable to regenerative medicine. We screened a whole genome collection of human miRNAs, identifying 96 to be capable of increasing proliferation (DNA synthesis and cytokinesis) of human iPSC-derived cardiomyocytes. Chemical screening and computational approaches indicated that most of these miRNAs (67) target different components of the Hippo pathway and that their activity depends on the nuclear translocation of the Hippo transcriptional effector YAP...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29765977/systems-pharmacology-based-approach-of-connecting-disease-genes-in-genome-wide-association-studies-with-traditional-chinese-medicine
#15
Jihye Kim, Minjae Yoo, Jimin Shin, Hyunmin Kim, Jaewoo Kang, Aik Choon Tan
Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29765667/a-novel-non-sequencing-approach-for-rapid-authentication-of-testudinis-carapax-et-plastrum-and-trionycis-carapax-by-species-specific-primers
#16
Huan Yang, Pingtian Yu, Yi Lu, Zhaoqun Jiao, Liqun Chen, Ying Zhou, Yuping Shen, Xiaobin Jia
A novel non-sequencing approach was developed to detect short DNA fragments ( ca 100 bp) for rapid authentication of two natural products, namely Testudinis Carapax et Plastrum and Trionycis Carapax, based on the difference in mitochondrial genome. Five specifically designed primer reactions were established to target species for reliable identification of their commercial products. They were confirmed to have a high level of inter-species-specificity and good intra-species stability. The limit of detection was estimated to be 1 ng of genomes for all of five assays...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29765380/the-complete-plastome-sequences-of-seven-species-in-gentiana-sect-kudoa-gentianaceae-insights-into-plastid-gene-loss-and-molecular-evolution
#17
Shan-Shan Sun, Peng-Cheng Fu, Xiao-Jun Zhou, Yan-Wei Cheng, Fa-Qi Zhang, Shi-Long Chen, Qing-Bo Gao
The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa , to represent its three serious: ser...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29764369/vareporter-variant-reporter-for-cancer-research-of-massive-parallel-sequencing
#18
Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu, Petrus Tang
BACKGROUND: High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29761524/the-24th-annual-prostate-cancer-foundation-scientific-retreat-report
#19
REVIEW
Andrea K Miyahira, Howard R Soule
INTRODUCTION: The 24th Annual Prostate Cancer Foundation (PCF) Scientific Retreat was held from October 5-7, 2017, at the Omni Shoreham Hotel in Washington, DC. METHODS: The PCF Scientific Retreat is a scientific conference that specifically focuses on cutting edge research deemed to have significant promise for accelerating advances in prostate cancer biology and treatment. RESULTS: Themes highlighted at this year's meeting included: (i) new understandings in prostate cancer biology and disease progression; (ii) new mechanisms and treatment targets in advanced prostate cancer; (iii) advances in precision medicine genomics, germline genetics, and selection of targeted therapies; (iv) PSMA-targeted agents for PET imaging and radionuclide therapy; (v) approaches for improving the efficacy of immunotherapy in prostate cancer; (vi) applications of 3D Genomics in prostate cancer research; and (vii) potential applications of artificial intelligence in prostate cancer...
May 15, 2018: Prostate
https://www.readbyqxmd.com/read/29759018/accelerating-pediatric-cancer-drug-development-challenges-and-opportunities-for-pediatric-master-protocols
#20
Tahira Khan, Mark Stewart, Samuel Blackman, Raphaël Rousseau, Martha Donoghue, Kenneth Cohen, Nita Seibel, Mark Fleury, Bouchra Benettaib, Raleigh Malik, Gilles Vassal, Gregory Reaman
Although outcomes for children with cancer have significantly improved over the past 40 years, there has been little progress in the treatment of some pediatric cancers, particularly when advanced. Additionally, clinical trial options and availability are often insufficient. Improved genomic and immunologic understanding of pediatric cancers, combined with innovative clinical trial designs, may provide an enhanced opportunity to study childhood cancers. Master protocols, which incorporate the use of precision medicine approaches, coupled with the ability to quickly assess the safety and effectiveness of new therapies, have the potential to accelerate early-phase clinical testing of novel therapeutics and which may result in more rapid approval of new drugs for children with cancer...
January 1, 2018: Therapeutic Innovation & Regulatory Science
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