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Personal genomics

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https://www.readbyqxmd.com/read/28220018/germline-variants-in-familial-pituitary-tumour-syndrome-genes-are-common-in-young-patients-and-families-with-additional-endocrine-tumours
#1
Sunita Mc De Sousa, Mark J McCabe, Kathy Wu, Tony Roscioli, Velimir Gayevskiy, Katelyn Brook, Lesley Rawlings, Hamish S Scott, Tanya J Thompson, Peter Earls, Anthony J Gill, Mark J Cowley, Marcel E Dinger, Ann I McCormack
Objective: Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design: We undertook a nation-wide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes...
February 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28219893/toxin-positive-clostridium-difficile-latently-infect-mouse-colonies-and-protect-against-highly-pathogenic-c-difficile
#2
Lucie Etienne-Mesmin, Benoit Chassaing, Oluwaseyi Adekunle, Lisa M Mattei, Frederic D Bushman, Andrew T Gewirtz
OBJECTIVE: Clostridium difficile is a toxin-producing bacterium and a leading cause of antibiotic-associated disease. The ability of C. difficile to form spores and infect antibiotic-treated persons at low multiplicity of infection (MOI) underlies its large disease burden. However, C. difficile-induced disease might also result from long-harboured C. difficile that blooms in individuals administered antibiotics. DESIGN: Mice purchased from multiple vendors and repeatedly testing negative for this pathogen by quantitative PCR bloomed C...
February 20, 2017: Gut
https://www.readbyqxmd.com/read/28218387/defining-personal-utility-in-genomics-a-delphi-study
#3
J Kohler, E Turbitt, K L Lewis, B S Wilfond, L Jamal, H L Peay, L G Biesecker, B B Biesecker
Individual genome sequencing results are valued by patients in ways distinct from clinical utility. Such outcomes have been described as components of "personal utility," a concept that broadly encompasses patient-endorsed benefits, that is operationally defined as non-clinical outcomes. No empirical delineation of these outcomes has been reported. To address this gap, we administered a Delphi survey to adult participants in a NIH clinical exome study to extract the most highly endorsed outcomes constituting personal utility...
February 20, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28216574/an-in-silico-identification-of-common-putative-vaccine-candidates-against-treponema-pallidum-a-reverse-vaccinology-and-subtractive-genomics-based-approach
#4
Arun Kumar Jaiswal, Sandeep Tiwari, Syed Babar Jamal, Debmalya Barh, Vasco Azevedo, Siomar C Soares
Sexually transmitted infections (STIs) are caused by a wide variety of bacteria, viruses, and parasites that are transmitted from one person to another primarily by vaginal, anal, or oral sexual contact. Syphilis is a serious disease caused by a sexually transmitted infection. Syphilis is caused by the bacterium Treponema pallidum subspecies pallidum. Treponema pallidum (T. pallidum) is a motile, gram-negative spirochete, which can be transmitted both sexually and from mother to child, and can invade virtually any organ or structure in the human body...
February 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28213763/the-lactobacillus-rhamnosus-and-lactobacillus-fermentum-strains-from-human-biotopes-characterized-with-mlst-and-toxin-antitoxin-gene-polymorphism
#5
E U Poluektova, R A Yunes, M V Epiphanova, V S Orlova, V N Danilenko
The diversity of Lb. rhamnosus and Lb. fermentum strains isolated from feces, saliva, and the vaginal cavity of 18-22-year-old healthy women residing in central regions of the Russian Federation has been characterized. The results obtained using multilocus sequence typing were identical to those obtained with the analysis of genetic and genomic polymorphism in TA systems. Different as well as identical Lb. rhamnosus and Lb. fermentum sequence types (ST) were isolated from various parts of the body of the same person...
February 17, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/28213088/personalized-medicine-genetic-risk-prediction-of-drug-response
#6
REVIEW
Ge Zhang, Daniel W Nebert
Pharmacogenomics (PGx), a substantial component of "personalized medicine", seeks to understand each individual's genetic composition to optimize drug therapy -- maximizing beneficial drug response, while minimizing adverse drug reactions (ADRs). Drug responses are highly variable because innumerable factors contribute to ultimate phenotypic outcomes. Recent genome-wide PGx studies have provided some insight into genetic basis of variability in drug response. These can be grouped into three categories. [a] Monogenic (Mendelian) traits include early examples mostly of inherited disorders, and some severe (idiosyncratic) ADRs typically influenced by single rare coding variants...
February 14, 2017: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/28212966/estimating-preferences-for-complex-health-technologies-lessons-learned-and-implications-for-personalized-medicine
#7
Deborah A Marshall, Juan Marcos Gonzalez, Karen V MacDonald, F Reed Johnson
We examine key study design challenges of using stated-preference methods to estimate the value of whole-genome sequencing (WGS) as a specific example of genomic testing. Assessing the value of WGS is complex because WGS provides multiple findings, some of which can be incidental in nature and unrelated to the specific health concerns that motivated the test. In addition, WGS results can include actionable findings (variants considered to be clinically useful and can be acted on), findings for which evidence for best clinical action is not available (variants considered clinically valid but do not meet as high of a standard for clinical usefulness), and findings of unknown significance...
January 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/28212290/defining-clinical-response-criteria-and-early-response-criteria-for-precision-oncology-current-state-of-the-art-and-future-perspectives
#8
Vivek Subbiah, Hubert H Chuang, Dhiraj Gambhire, Kalevi Kairemo
In this era of precision oncology, there has been an exponential growth in the armamentarium of genomically targeted therapies and immunotherapies. Evaluating early responses to precision therapy is essential for "go" versus "no go" decisions for these molecularly targeted drugs and agents that arm the immune system. Many different response assessment criteria exist for use in solid tumors and lymphomas. We reviewed the literature using the Medline/PubMed database for keywords "response assessment" and various known response assessment criteria published up to 2016...
February 15, 2017: Diagnostics
https://www.readbyqxmd.com/read/28211800/upregulated-mir-483-5p-expression-as-a-prognostic-biomarker-for-esophageal-squamous-cell-carcinoma
#9
Liying Xue, Jinglong Nan, Li Dong, Cuiying Zhang, Hui Li, Rentura Na, Huijie He, Yadi Wang
BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is one of the most common cause of cancer-associated mortality. Uncovering novel molecular biomarkers that can predict ESCC development will improve personalized therapy. OBJECTIVE: The goal of the current study was to investigate the expression pattern of miR-483-5p and determine its prognostic value in ESCC. METHODS: We first analyzed miRNA-seq data obtained from the Cancer Genome Atlas (TCGA) cohort to evaluate the prognostic value of miR-483-5p in ESCC...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28211229/serum-micrornas-as-predictors-for-liver-fibrosis-staging-in-hepatitis-c-virus-associated-chronic-liver-disease-patients
#10
Olfat G Shaker, Mahmoud A Senousy
Accurate staging of liver fibrosis is important for clinical decision making and personalized management. Liver fibrosis is influenced by patients' genomics, including IFNL3 genotype and microRNA expression. However, incorporating microRNAs into fibrosis prediction algorithms has not been investigated. We examined the potential of 8 selected serum microRNAs; miR-122, miR-126, miR-129, miR-199a, miR-155, miR-203a, miR-221, and miR-223 as non-invasive biomarkers to stage liver fibrosis in HCV-associated chronic liver disease (HCV-CLD)...
February 17, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28207930/elevation-of-glycosaminoglycans-in-the-amniotic-fluid-of-a-fetus-with-mucopolysaccharidosis-vii
#11
Francyne Kubaski, Ana Carolina Brusius-Facchin, Robert W Mason, Pravin Patel, Maira G Burin, Kristiane Michelin-Tirelli, Rejane Gus Kessler, Fernanda Bender, Sandra Leistner-Segal, Carolina A Moreno, Denise P Cavalcanti, Roberto Giugliani, Shunji Tomatsu
OBJECTIVE: The aim of this study was to quantify GAGs in amniotic fluid (AF) from an MPS VII fetus compared with age-matched fetuses obtained from normal pregnancies. METHOD: Disaccharides were measured by liquid chromatography tandem mass spectrometry (LC/MS/MS), compared to age-matched controls. Enzyme assay was performed in AF supernatant or cultured amniocytes. GUSB was analyzed by next generation sequencing using Ion Torrent Personal Genome Machine with a customized panel...
February 16, 2017: Prenatal Diagnosis
https://www.readbyqxmd.com/read/28207198/integrated-precision-medicine-the-role-of-electronic-health-records-in-delivering-personalized-treatment
#12
REVIEW
Amy Sitapati, Hyeoneui Kim, Barbara Berkovich, Rebecca Marmor, Siddharth Singh, Robert El-Kareh, Brian Clay, Lucila Ohno-Machado
Precision Medicine involves the delivery of a targeted, personalized treatment for a given patient. By harnessing the power of electronic health records (EHRs), we are increasingly able to practice precision medicine to improve patient outcomes. In this article, we introduce the scientific community at large to important building blocks for personalized treatment, such as terminology standards that are the foundation of the EHR and allow for exchange of health information across systems. We briefly review different types of clinical decision support (CDS) and present the current state of CDS, which is already improving the care patients receive with genetic profile-based tailored recommendations regarding diagnostic and treatment plans...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28206814/biomarkers-in-tumor-microenvironment-upregulation-of-fibroblast-activation-protein-%C3%AE-correlates-with-gastric-cancer-progression-and-poor-prognosis
#13
Mengmou Hu, Chengjia Qian, Ziwei Hu, Bojian Fei, Haibo Zhou
Gastric cancer is the third leading cause of cancer-related mortality worldwide. Recent evidence points to importance of cross talk between cancer cells and the surrounding stroma on gastric cancer progression. Tumor microenvironment biomarkers thus represent a new opportunity for diagnostics innovation. Reactive stromal fibroblasts selectively express the fibroblast activation protein alpha (FAP-α), a homodimeric integral membrane gelatinase that belongs to the serine protease family. We report here that FAP-α expression is significantly elevated in gastric cancer samples by more than fivefold (p < 0...
January 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28205045/characteristics-of-brca1-2-mutations-carriers-including-large-genomic-rearrangements-in-high-risk-breast-cancer-patients
#14
Boyoung Park, Ji Yeon Sohn, Kyong-Ah Yoon, Keun Seok Lee, Eun Hae Cho, Myong Cheol Lim, Moon Jung Yang, Soo Jin Park, Moo Hyun Lee, See Youn Lee, Yoon Jung Chang, Dong Ock Lee, Sun-Young Kong, Eun Sook Lee
PURPOSE: We investigated the prevalence of BRCA1/2 small mutations and large genomic rearrangements in high risk breast cancer patients who attended a genetic counseling clinic. METHODS: In total 478 patients were assessed for BRCA1/2 mutations by direct sequencing, of whom, 306 were identified as non-carriers of BRCA1/2 mutation and assessed for large rearrangement mutations by multiplex ligation-dependent probe amplification. Family history and clinicopathological characteristics of patients were evaluated...
February 15, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28202223/filtration-based-enrichment-of-circulating-tumor-cells-from-all-prostate-cancer-risk-groups
#15
Julius Adebayo Awe, Jeff Saranchuk, Darrel Drachenberg, Sabine Mai
OBJECTIVE: To combine circulating tumor cell (CTC) isolation by filtration and immunohistochemistry to investigate the presence of CTCs in low, intermediate, and high-risk prostate cancer (PCa). CTCs isolated from these risk groups stained positive for both cytokeratin and androgen receptors, but negative for CD45. PATIENTS AND METHODS: Blood samples from 41 biopsy confirmed patients with PCa at different clinical stages such as low, intermediate, and high risk were analyzed...
February 12, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28199202/racial-disparity-in-metabolic-regulation-of-cancer
#16
Kuldeep S Attri, Divya Murthy, Pankaj K Singh
Genetic mutations and metabolic reprogramming are two key hallmarks of cancer, required for proliferation, invasion, and metastasis of the disease. While genetic mutations, whether inherited or acquired, are critical for the initiation of tumor development, metabolic reprogramming is an effector mechanism imperative for adaptational transition during the progression of cancer. Recent findings in the literature emphasize the significance of molecular cross-talk between these two cellular processes in regulating signaling and differentiation of cancer cells...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28199197/childhood-cancers-and-systems-medicine
#17
William L Stone, Kathryn J Klopfenstein, M J Hajianpour, Marcela I Popescu, Cathleen M Cook, Koymangalath Krishnan
Despite major advances in treatment, pediatric cancers in the 5-16 age group remain the most common cause of disease death, and one out of eight children with cancer will not survive. Among children that do survive, some 60% suffer from late effects such as cancer recurrence and increased risk of obesity. This paper will provide a broad overview of pediatric oncology in the context of systems medicine. Systems medicine utilizes an integrative approach that relies on patient information gained from omics technology...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198009/endoscopic-ultrasound-guided-fine-needle-aspirate-derived-preclinical-pancreatic-cancer-models-reveal-panitumumab-sensitivity-in-kras-wild-type-tumours
#18
William Berry, Elizabeth Algar, Beena Kumar, Christopher Desmond, Michael Swan, Brendan J Jenkins, Daniel Croagh
Pancreatic cancer (PC) is largely refractory to existing therapies used in unselected patient trials, thus emphasizing the pressing need for new approaches for patient selection in personalized medicine. KRAS mutations occur in 90% of PC patients and confer resistance to epidermal growth factor receptor (EGFR) inhibitors (e.g. panitumumab), suggesting that KRAS wild-type PC patients may benefit from targeted panitumumab therapy. Here we use tumour tissue procured by endoscopic ultrasound-guided fine-needle aspirate (EUS-FNA) to compare the in vivo sensitivity in patient derived xenografts (PDXs) of KRAS wild-type and mutant PC tumours to panitumumab, and to profile the molecular signature of these tumours in patients with metastatic or localized disease...
February 15, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28194769/precision-medicine-nobody-is-average
#19
EDITORIAL
A A Vinks
Medicine gets personal and tailor-made treatments are underway. Hospitals have started to advertise their advanced genomic testing capabilities and even their disruptive technologies to help foster a culture of innovation. The prediction in the lay press is that in decades from now we may look back and see 2017 as the year precision medicine blossomed. It is all part of the Precision Medicine Initiative that takes into account individual differences in people's genes, environments, and lifestyles.
March 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28194004/genetic-contributions-to-self-reported-tiredness
#20
V Deary, S P Hagenaars, S E Harris, W D Hill, G Davies, D C M Liewald, A M McIntosh, C R Gale, I J Deary
Self-reported tiredness and low energy, often called fatigue, are associated with poorer physical and mental health. Twin studies have indicated that this has a heritability between 6 and 50%. In the UK Biobank sample (N=108 976), we carried out a genome-wide association study (GWAS) of responses to the question, 'Over the last two weeks, how often have you felt tired or had little energy?' Univariate GCTA-GREML found that the proportion of variance explained by all common single-nucleotide polymorphisms for this tiredness question was 8...
February 14, 2017: Molecular Psychiatry
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