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Genetics, genomics, translational medicine

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https://www.readbyqxmd.com/read/29220507/assessing-the-heterogeneity-of-in-silico-plasmid-predictions-based-on-whole-genome-sequenced-clinical-isolates
#1
Cedric C Laczny, Valentina Galata, Achim Plum, Andreas E Posch, Andreas Keller
High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data...
December 5, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29215763/breast-cancer-the-translation-of-big-genomic-data-to-cancer-precision-medicine
#2
REVIEW
Siew-Kee Low, Hitoshi Zembutsu, Yusuke Nakamura
Cancer is a complex genetic disease that consequence from the accumulation of genomic alterations, in which germline variations predispose individuals to cancer and somatic alterations initiate and trigger the progression of cancer. For the past two decades, genomic research has advanced remarkably, evolving from single-gene to whole-genome screening by using genome-wide association study (GWAS) and next generation sequencing (NGS) that contributing to big genomic data. International collaborative efforts have contributed in curating these data to identify clinically significant alterations that could be used in the clinical settings...
December 7, 2017: Cancer Science
https://www.readbyqxmd.com/read/29182607/the-current-state-of-funded-nih-grants-in-implementation-science-in-genomic-medicine-a-portfolio-analysis
#3
Megan C Roberts, Mindy Clyne, Amy E Kennedy, David A Chambers, Muin J Khoury
PurposeImplementation science offers methods to evaluate the translation of genomic medicine research into practice. The extent to which the National Institutes of Health (NIH) human genomics grant portfolio includes implementation science is unknown. This brief report's objective is to describe recently funded implementation science studies in genomic medicine in the NIH grant portfolio, and identify remaining gaps.MethodsWe identified investigator-initiated NIH research grants on implementation science in genomic medicine (funding initiated 2012-2016)...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29168653/utilizing-biomarkers-in-colorectal-cancer-an-interview-with-ajay-goel
#4
Ajay Goel
Ajay Goel, PhD, is a Professor and Director, Center for Gastrointestinal Research, and Director, Center for Translational Genomics and Oncology, at the Baylor Scott & White Research Institute, Baylor University Medical Center in Dallas, Texas. Dr Goel has spent more than 20 years researching cancer and has been the lead author or contributor to over 240 scientific articles published in peer-reviewed international journals and several book chapters. He is also a primary inventor on more than 15 international patents aimed at developing various biomarkers for the diagnosis, prognosis and prediction of gastrointestinal cancers...
November 23, 2017: Future Oncology
https://www.readbyqxmd.com/read/29164808/a-universal-approach-to-correct-various-hbb-gene-mutations-in-human-stem-cells-for-gene-therapy-of-beta-thalassemia-and-sickle-cell-disease
#5
Liuhong Cai, Hao Bai, Vasiliki Mahairaki, Yongxing Gao, Chaoxia He, Yanfei Wen, You-Chuan Jin, You Wang, Rachel L Pan, Armaan Qasba, Zhaohui Ye, Linzhao Cheng
Beta-thalassemia is one of the most common recessive genetic diseases, caused by mutations in the HBB gene. Over 200 different types of mutations in the HBB gene containing three exons have been identified in patients with β-thalassemia (β-thal) whereas a homozygous mutation in exon 1 causes sickle cell disease (SCD). Novel therapeutic strategies to permanently correct the HBB mutation in stem cells that are able to expand and differentiate into erythrocytes producing corrected HBB proteins are highly desirable...
November 21, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29154141/novel-genes-associated-with-amyotrophic-lateral-sclerosis-diagnostic-and-clinical-implications
#6
REVIEW
Ruth Chia, Adriano Chiò, Bryan J Traynor
BACKGROUND: The disease course of amyotrophic lateral sclerosis (ALS) is rapid and, because its pathophysiology is unclear, few effective treatments are available. Genetic research aims to understand the underlying mechanisms of ALS and identify potential therapeutic targets. The first gene associated with ALS was SOD1, identified in 1993 and, by early 2014, more than 20 genes had been identified as causative of, or highly associated with, ALS. These genetic discoveries have identified key disease pathways that are therapeutically testable and could potentially lead to the development of better treatments for people with ALS...
November 16, 2017: Lancet Neurology
https://www.readbyqxmd.com/read/29132412/prospects-for-using-risk-scores-in-polygenic-medicine
#7
Cathryn M Lewis, Evangelos Vassos
Genome-wide association studies have made strides in identifying common variation associated with disease. The modest effect sizes preclude risk prediction based on single genetic variants, but polygenic risk scores that combine thousands of variants show some predictive ability across a range of complex traits and diseases, including neuropsychiatric disorders. Here, we consider the potential for translation to clinical use.
November 13, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29122391/genetics-and-epigenetics-of-nafld-and-nash-clinical-impact
#8
REVIEW
Mohammed Eslam, Luca Valenti, Stefano Romeo
Non-alcoholic fatty liver disease (NAFLD) is now recognised as the most common liver disease worldwide. It encompasses a broad spectrum of conditions, from simple steatosis, through non-alcoholic steatohepatitis, to fibrosis and ultimately cirrhosis and hepatocellular carcinoma. A hallmark of NAFLD is the substantial inter-patient variation in disease progression. NAFLD is considered a complex disease trait such that interactions between the environment and a susceptible polygenic host background determine disease phenotype and influence progression...
November 2, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/29118424/methods-for-scarless-selection-free-generation-of-human-cells-and-allele-specific-functional-analysis-of-disease-associated-snps-and-variants-of-uncertain-significance
#9
Nicole B Coggins, Jacob Stultz, Henriette O'Geen, Luis G Carvajal-Carmona, David J Segal
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29080249/concise-review-epigenetic-regulation-of-hematopoiesis-biological-insights-and-therapeutic-applications
#10
REVIEW
Chiara Antoniani, Oriana Romano, Annarita Miccio
Hematopoiesis is the process of blood cell formation starting from hematopoietic stem/progenitor cells (HSPCs). The understanding of regulatory networks involved in hematopoiesis and their impact on gene expression is crucial to decipher the molecular mechanisms that control hematopoietic development in physiological and pathological conditions, and to develop novel therapeutic strategies. An increasing number of epigenetic studies aim at defining, on a genome-wide scale, the cis-regulatory sequences (e.g., promoters and enhancers) used by human HSPCs and their lineage-restricted progeny at different stages of development...
October 28, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/29079728/plato-software-provides-analytic-framework-for-investigating-complexity-beyond-genome-wide-association-studies
#11
Molly A Hall, John Wallace, Anastasia Lucas, Dokyoon Kim, Anna O Basile, Shefali S Verma, Cathy A McCarty, Murray H Brilliant, Peggy L Peissig, Terrie E Kitchner, Anurag Verma, Sarah A Pendergrass, Scott M Dudek, Jason H Moore, Marylyn D Ritchie
Genome-wide, imputed, sequence, and structural data are now available for exceedingly large sample sizes. The needs for data management, handling population structure and related samples, and performing associations have largely been met. However, the infrastructure to support analyses involving complexity beyond genome-wide association studies is not standardized or centralized. We provide the PLatform for the Analysis, Translation, and Organization of large-scale data (PLATO), a software tool equipped to handle multi-omic data for hundreds of thousands of samples to explore complexity using genetic interactions, environment-wide association studies and gene-environment interactions, phenome-wide association studies, as well as copy number and rare variant analyses...
October 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/29069341/epigenetics-and-precision-medicine-in-cardiovascular-patients-from-basic-concepts-to-the-clinical-arena
#12
Sarah Costantino, Peter Libby, Raj Kishore, Jean-Claude Tardif, Assam El-Osta, Francesco Paneni
Cardiovascular diseases (CVDs) remain the leading cause of mortality worldwide and also inflict major burdens on morbidity, quality of life, and societal costs. Considering that CVD preventive medications improve vascular outcomes in less than half of patients (often relative risk reductions range from 12% to 20% compared with placebo), precision medicine offers an attractive approach to refine the targeting of CVD medications to responsive individuals in a population and thus allocate resources more wisely and effectively...
October 23, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29068566/scaffold-based-microrna-therapies-in-regenerative-medicine-and-cancer
#13
REVIEW
Caroline M Curtin, Irene Mencía Castaño, Fergal J O'Brien
microRNA-based therapies are an advantageous strategy with applications in both regenerative medicine (RM) and cancer treatments. microRNAs (miRNAs) are an evolutionary conserved class of small RNA molecules that modulate up to one third of the human nonprotein coding genome. Thus, synthetic miRNA activators and inhibitors hold immense potential to finely balance gene expression and reestablish tissue health. Ongoing industry-sponsored clinical trials inspire a new miRNA therapeutics era, but progress largely relies on the development of safe and efficient delivery systems...
October 25, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29068423/comprehensive-analysis-of-cancer-proteogenome-to-identify-biomarkers-for-the-early-diagnosis-and-prognosis-of-cancer
#14
REVIEW
Hem D Shukla
During the past century, our understanding of cancer diagnosis and treatment has been based on a monogenic approach, and as a consequence our knowledge of the clinical genetic underpinnings of cancer is incomplete. Since the completion of the human genome in 2003, it has steered us into therapeutic target discovery, enabling us to mine the genome using cutting edge proteogenomics tools. A number of novel and promising cancer targets have emerged from the genome project for diagnostics, therapeutics, and prognostic markers, which are being used to monitor response to cancer treatment...
October 25, 2017: Proteomes
https://www.readbyqxmd.com/read/29019032/nanotechnology-as-a-delivery-tool-for-precision-cancer-therapies
#15
Bhawna Sharma, Rachael M Crist, Pavan P Adiseshaiah
Genomic analyses from patients with cancer have improved the understanding of the genetic elements that drive the disease, provided new targets for treating this relentless disease, and offered criteria for stratifying patient populations that will benefit most from treatments. In the last decade, several new targeted therapies have been approved by the FDA based on these omics findings, leading to significantly improved survival and quality of life for select patient populations. However, many of these precision medicines, e...
November 2017: AAPS Journal
https://www.readbyqxmd.com/read/28987179/genetics-of-neurodegenerative-diseases-an-overview
#16
Lasse Pihlstrøm, Sarah Wiethoff, Henry Houlden
Genetic factors are central to the etiology of neurodegeneration, both as monogenic causes of heritable disease and as modifiers of susceptibility to complex, sporadic disorders. Over the last two decades, the identification of disease genes and risk loci has led to some of the greatest advances in medicine and invaluable insights into pathogenic mechanisms and disease pathways. Large-scale research efforts, novel study designs, and advances in methodology are rapidly expanding our understanding of the genome and the genetic architecture of neurodegenerative disease...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/28982267/institutional-profile-translational-pharmacogenomics-at-the-icahn-school-of-medicine-at-mount-sinai
#17
Stuart A Scott, Aniwaa Owusu Obeng, Mariana R Botton, Yao Yang, Erick R Scott, Stephen B Ellis, Richard Wallsten, Tom Kaszemacher, Xiang Zhou, Rong Chen, Paola Nicoletti, Hetanshi Naik, Eimear E Kenny, Aida Vega, Eva Waite, George A Diaz, Joel Dudley, Jonathan L Halperin, Lisa Edelmann, Andrew Kasarskis, Jean-Sébastien Hulot, Inga Peter, Erwin P Bottinger, Kurt Hirschhorn, Pamela Sklar, Judy H Cho, Robert J Desnick, Eric E Schadt
For almost 50 years, the Icahn School of Medicine at Mount Sinai has continually invested in genetics and genomics, facilitating a healthy ecosystem that provides widespread support for the ongoing programs in translational pharmacogenomics. These programs can be broadly cataloged into discovery, education, clinical implementation and testing, which are collaboratively accomplished by multiple departments, institutes, laboratories, companies and colleagues. Focus areas have included drug response association studies and allele discovery, multiethnic pharmacogenomics, personalized genotyping and survey-based education programs, pre-emptive clinical testing implementation and novel assay development...
October 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/28945736/rapid-functional-analysis-of-computationally-complex-rare-human-irf6-gene-variants-using-a-novel-zebrafish-model
#18
Edward B Li, Dawn Truong, Shawn A Hallett, Kusumika Mukherjee, Brian C Schutte, Eric C Liao
Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations. However, the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions. Interferon Regulatory Factor 6 (IRF6) gene variants are significant genetic contributors to orofacial clefts. Although approximately three hundred IRF6 gene variants have been documented, their effects on protein functions remain difficult to interpret. Here, we demonstrate the protein functions of human IRF6 missense gene variants could be rapidly assessed in detail by their abilities to rescue the irf6 -/- phenotype in zebrafish through variant mRNA microinjections at the one-cell stage...
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28944295/towards-precision-medicine-in-alzheimer-s-disease-deciphering-genetic-data-to-establish-informative-biomarkers
#19
Ornit Chiba-Falek, Michael W Lutz
INTRODUCTION: Developing biomarker tools for identification of individuals at high-risk for late-onset Alzheimer's disease (LOAD) is important for prognosis and early treatment. This review focuses on genetic factors and their potential role for precision medicine in LOAD. AREAS COVERED: APOEe4 is the strongest genetic risk factor for non-Mendelian LOAD, and the APOE-linkage disequilibrium (LD) region has produced the most significant association signal in multi-center genome-wide-association-studies (GWAS)...
2017: Expert Review of Precision Medicine and Drug Development
https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#20
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
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