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Personal genomics

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https://www.readbyqxmd.com/read/27921197/counselees-perspectives-of-genomic-counseling-following-online-receipt-of-multiple-actionable-complex-disease-and-pharmacogenomic-results-a-qualitative-research-study
#1
Kevin Sweet, Shelly Hovick, Amy C Sturm, Tara Schmidlen, Erynn Gordon, Barbara Bernhardt, Lisa Wawak, Karen Wernke, Joseph McElroy, Laura Scheinfeldt, Amanda E Toland, J S Roberts, Michael Christman
Genomic applications raise multiple challenges including the optimization of genomic counseling (GC) services as part of the results delivery process. More information on patients' motivations, preferences, and informational needs are essential to guide the development of new, more efficient practice delivery models that capitalize on the existing strengths of a limited genetic counseling workforce. Semi-structured telephone interviews were conducted with a subset of counselees from the Coriell Personalized Medicine Collaborative following online receipt of multiple personalized genomic test reports...
December 5, 2016: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/27920271/the-need-for-a-privacy-standard-for-medical-devices-that-transmit-protected-health-information-used-in-the-precision-medicine-initiative-for-diabetes-and-other-diseases
#2
David C Klonoff, W Nicholson Price
Privacy is an important concern for the Precision Medicine Initiative (PMI) because success of this initiative will require the public to be willing to participate by contributing large amounts of genetic/genomic information and sensor data. This sensitive personal information is intended to be used only for specified research purposes. Public willingness to participate will depend on the public's level of trust that their information will be protected and kept private. Medical devices may constantly provide information...
December 4, 2016: Journal of Diabetes Science and Technology
https://www.readbyqxmd.com/read/27918536/genome-wide-analyses-for-personality-traits-identify-six-genomic-loci-and-show-correlations-with-psychiatric-disorders
#3
Min-Tzu Lo, David A Hinds, Joyce Y Tung, Carol Franz, Chun-Chieh Fan, Yunpeng Wang, Olav B Smeland, Andrew Schork, Dominic Holland, Karolina Kauppi, Nilotpal Sanyal, Valentina Escott-Price, Daniel J Smith, Michael O'Donovan, Hreinn Stefansson, Gyda Bjornsdottir, Thorgeir E Thorgeirsson, Kari Stefansson, Linda K McEvoy, Anders M Dale, Ole A Andreassen, Chi-Hua Chen
Personality is influenced by genetic and environmental factors and associated with mental health. However, the underlying genetic determinants are largely unknown. We identified six genetic loci, including five novel loci, significantly associated with personality traits in a meta-analysis of genome-wide association studies (N = 123,132-260,861). Of these genome-wide significant loci, extraversion was associated with variants in WSCD2 and near PCDH15, and neuroticism with variants on chromosome 8p23.1 and in L3MBTL2...
December 5, 2016: Nature Genetics
https://www.readbyqxmd.com/read/27917384/genetic-alterations-in-intervertebral-disc-disease
#4
REVIEW
Nikolay L Martirosyan, Arpan A Patel, Alessandro Carotenuto, M Yashar S Kalani, Evgenii Belykh, Corey T Walker, Mark C Preul, Nicholas Theodore
BACKGROUND: Intervertebral disc degeneration (IVDD) is considered a multifactorial disease that is influenced by both environmental and genetic factors. The last two decades of research strongly demonstrate that genetic factors contribute about 75% of the IVDD etiology. Recent total genome sequencing studies have shed light on the various single-nucleotide polymorphisms (SNPs) that are associated with IVDD. AIM: This review presents comprehensive and updated information about the diversity of genetic factors in the inflammatory, degradative, homeostatic, and structural systems involved in the IVDD...
2016: Frontiers in Surgery
https://www.readbyqxmd.com/read/27915479/trends-in-next-generation-sequencing-and-a-new-era-for-whole-genome-sequencing
#5
REVIEW
Sang Tae Park, Jayoung Kim
This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields...
November 2016: International Neurourology Journal
https://www.readbyqxmd.com/read/27915106/insights-gained-from-ancient-biomolecules-into-past-and-present-tuberculosis-a-personal-perspective
#6
REVIEW
Helen D Donoghue
Ancient and historical tuberculosis (TB) can be recognized by its typical paleopathology in human remains. Using paleomicrobiology, it is possible to detect many more individuals infected with TB but with no visible lesions. Due to advances in molecular analysis over the past two decades, it is clear that TB was widespread in humans from the Neolithic period until the present day. Past human populations were associated with different lineages of the Mycobacterium tuberculosis (MTB) complex, thereby elucidating early human migrations...
November 30, 2016: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/27914918/epigenetic-game-theory-how-to-compute-the-epigenetic-control-of-maternal-to-zygotic-transition
#7
REVIEW
Qian Wang, Kirk Gosik, Sujuan Xing, Libo Jiang, Lidan Sun, Vernon M Chinchilli, Rongling Wu
Epigenetic reprogramming is thought to play a critical role in maintaining the normal development of embryos. How the methylation state of paternal and maternal genomes regulates embryogenesis depends on the interaction and coordination of the gametes of two sexes. While there is abundant research in exploring the epigenetic interactions of sperms and oocytes, a knowledge gap exists in the mechanistic quantitation of these interactions and their impact on embryo development. This review aims at formulating a modeling framework to address this gap through the integration and synthesis of evolutionary game theory and the latest discoveries of the epigenetic control of embryo development by next-generation sequencing...
November 9, 2016: Physics of Life Reviews
https://www.readbyqxmd.com/read/27913501/mutations-in-aml-prognostic-and-therapeutic-implications
#8
Courtney D DiNardo, Jorge E Cortes
Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy characterized by the proliferation and aberrant differentiation of immature clonal myeloid cells. The prognosis of AML is variable, based on clinical features such as patient age, performance status, and comorbidities, as well as leukemia-specific genetic features including cytogenetics and molecular classification. The modern application of next-generation sequencing technology has uncovered marked heterogeneity and genomic complexity within AML, based on the presence or absence of cooperating mutations within functional categories such as epigenetic regulators, cell signaling and proliferation pathways, and master hematopoietic transcription factors...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27910030/recurrent-cytogenetic-abnormalities-in-non-hodgkin-s-lymphoma-and-chronic-lymphocytic-leukemia
#9
Edmond S K Ma
Characteristic chromosomal translocations are found to be associated with subtypes of B-cell non-Hodgkin lymphoma (NHL), for example t(8;14)(q24;q32) and Burkitt lymphoma, t(14;18)(q32;q21) and follicular lymphoma, and t(11;14)(q13;q32) in mantle cell lymphoma. Only few recurrent cytogenetic aberrations have been identified in the T-cell NHL and the best known is the ALK gene translocation t(2;5)(p23;q35) in anaplastic large cell lymphoma. Since lymph node or other tissue is seldom submitted for conventional cytogenetics study, alternative approaches for translocation detection are polymerase chain reaction (PCR) or fluorescence in situ hybridization (FISH)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27910009/cancer-cytogenetics-an-introduction
#10
Thomas S K Wan
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909533/patient-specific-induced-pluripotent-stem-cell-derived-cardiomyocytes-for-drug-development-and-screening-in-catecholaminergic-polymorphic-ventricular-tachycardia
#11
REVIEW
Ben Jehuda Ronen, Barad Lili
Catecholaminergic polymorphic ventricular tachycardia (CPVT), an inherited arrhythmia often leading to sudden cardiac death in children and young adults, is characterized by polymorphic/bidirectional ventricular tachycardia induced by adrenergic stimulation associated with emotionally stress or physical exercise. There are two forms of CPVT: 1. CPVT1 is caused by mutations in the RYR2 gene, encoding for ryanodine receptor type 2. CPVT1 is the most common form of CPVT in the population, and is inherited by a dominant mechanism...
August 2016: Journal of Atrial Fibrillation
https://www.readbyqxmd.com/read/27908614/a-critical-discussion-on-diet-genomic-mutations-and-repair-mechanisms-in-colon-carcinogenesis
#12
Juliana Yumi Sakita, Bianca Gasparotto, Sergio Britto Garcia, Sergio Akira Uyemura, Vinicius Kannen
Colon cancer is one of the most common malignancies and its etiology closely tied to dietary habits. Recent epidemiological data shows that colon cancer incidence is shifting to a much younger population. In this regard, some dietary components from a regular human meal might have various DNA-damaging compounds. Given that not every person endure cancer, the colonic malignancy develops throughout decades, and persistent DNA damage promotes cancer when induced at the proper intensity, a critical discussion of possible novel mechanisms by which carcinogens promote these tumors is urgently needed...
November 28, 2016: Toxicology Letters
https://www.readbyqxmd.com/read/27907810/prediction-of-autosomal-str-typing-success-in-ancient-and-second-world-war-bone-samples
#13
Irena Zupanič Pajnič, Tomaž Zupanc, Jože Balažic, Živa Miriam Geršak, Oliver Stojković, Ivan Skadrić, Matija Črešnar
Human-specific quantitative PCR (qPCR) has been developed for forensic use in the last 10 years and is the preferred DNA quantification technique since it is very accurate, sensitive, objective, time-effective and automatable. The amount of information that can be gleaned from a single quantification reaction using commercially available quantification kits has increased from the quantity of nuclear DNA to the amount of male DNA, presence of inhibitors and, most recently, to the degree of DNA degradation. In skeletal remains samples from disaster victims, missing persons and war conflict victims, the DNA is usually degraded...
November 19, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27903906/eupathdb-the-eukaryotic-pathogen-genomics-database-resource
#14
Cristina Aurrecoechea, Ana Barreto, Evelina Y Basenko, John Brestelli, Brian P Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S Harb, Mark Heiges, Christiane Hertz-Fowler, Sufen Hu, John Iodice, Jessica C Kissinger, Cris Lawrence, Wei Li, Deborah F Pinney, Jane A Pulman, David S Roos, Achchuthan Shanmugasundram, Fatima Silva-Franco, Sascha Steinbiss, Christian J Stoeckert, Drew Spruill, Haiming Wang, Susanne Warrenfeltz, Jie Zheng
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902343/the-frequency-and-significance-of-the-parvovirus-b19-infection-in-patients-with-rheumatoid-arthritis
#15
Milda Naciute, Diana Mieliauskaite, Rita Rugiene, Rita Nikitenkiene, Ligita Jancoriene, Mykolas Mauricas, Zaiga Nora-Krukle, Modra Murovska, Irute Girkontaite
The present study aims to clarify the possible involvement of parvovirus B19 (B19V) infection in rheumatoid arthritis (RA) pathogenesis by investigating the presence of B19V infection markers (genomic sequences and virus-specific antibodies) in association with the level of cytokines and RA clinical activity and aggressiveness. 118 RA patients and 49 age and sex matched healthy volunteers were enrolled in the study. Nested PCR was used to detect B19V sequences in whole blood and cell free plasma DNA, ELISA to detect virus-specific antibodies and cytokine levels in plasma, and recomLine dot blot assay for antibodies to separate B19V antigens...
October 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901097/sequencing-based-breast-cancer-diagnostics-as-an-alternative-to-routine-biomarkers
#16
Mattias Rantalainen, Daniel Klevebring, Johan Lindberg, Emma Ivansson, Gustaf Rosin, Lorand Kis, Fuat Celebioglu, Irma Fredriksson, Kamila Czene, Jan Frisell, Johan Hartman, Jonas Bergh, Henrik Grönberg
Sequencing-based breast cancer diagnostics have the potential to replace routine biomarkers and provide molecular characterization that enable personalized precision medicine. Here we investigate the concordance between sequencing-based and routine diagnostic biomarkers and to what extent tumor sequencing contributes clinically actionable information. We applied DNA- and RNA-sequencing to characterize tumors from 307 breast cancer patients with replication in up to 739 patients. We developed models to predict status of routine biomarkers (ER, HER2,Ki-67, histological grade) from sequencing data...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#17
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27900402/effects-of-ugt1a9-genetic-polymorphisms-on-monohydroxylated-derivative-of-oxcarbazepine-concentrations-and-oxcarbazepine-monotherapeutic-efficacy-in-chinese-patients-with-epilepsy
#18
Yao Lu, Youxin Fang, Xunyi Wu, Chunlai Ma, Yue Wang, Lan Xu
AIM: The human UDP-glucuronosyltransferase which is genetically polymorphic catalyzes glucuronidations of various drugs. The interactions among UGT1A4, UGT1A6, UGT1A9, and UGT2B15 genetic polymorphisms, monohydroxylated derivative (MHD) of oxcarbazepine (OXC) plasma concentrations, and OXC monotherapeutic efficacy were explored in 124 Chinese patients with epilepsy receiving OXC monotherapy. METHOD: MHD is the major active metabolite of OXC, and its plasma concentration was measured using high-performance liquid chromatography when patients reached their maintenance dose of OXC...
November 29, 2016: European Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27899914/how-useful-are-monogenic-rodent-models-for-the-study-of-human-non-alcoholic-fatty-liver-disease
#19
REVIEW
Jake P Mann, Robert K Semple, Matthew J Armstrong
Improving understanding of the genetic basis of human non-alcoholic fatty liver disease (NAFLD) has the potential to facilitate risk stratification of affected patients, permit personalized treatment, and inform development of new therapeutic strategies. Animal models have been widely used to interrogate the pathophysiology of, and genetic predisposition to, NAFLD. Nevertheless, considerable interspecies differences in intermediary metabolism potentially limit the extent to which results can be extrapolated to humans...
2016: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/27899773/-a-novel-treatment-strategy-for-pancreatic-cancer-based-on-gene-profiles
#20
Hideyuki Hayashi, Hiroshi Nishihara
Pancreatic cancer has one of the highest rates of mortality among malignancies and the development of promising future therapies is strongly required. Recently, the utility of gene aberrations as biomarkers for determining therapeutic strategies has been demonstrated in several types of cancer. The detection of druggable mutations that aid in the selection of effective molecular targeting drugs is feasible in clinical settings for certain cancers. On the other hand, personalized therapy for pancreatic cancer guided by genomic biomarkers has not yet been realized and suitable molecular targets for the disease have been unclear until now...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
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