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Personal genomics

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https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#1
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28326544/personalized-genetics-of-the-cholinergic-blockade-of-neuroinflammation
#2
REVIEW
Alon Simchovitz, Michael T Heneka, Hermona Soreq
Acetylcholine signaling is essential for cognitive functioning and blocks inflammation. To maintain homeostasis, cholinergic signaling is subjected to multi-leveled and bidirectional regulation by both proteins and non-coding microRNAs ('CholinomiRs'). CholinomiRs coordinate the cognitive and inflammatory aspects of cholinergic signaling by targeting major cholinergic transcripts including the acetylcholine hydrolyzing enzyme acetylcholinesterase (AChE). Notably, AChE inhibitors are the only currently approved line of treatment for Alzheimer's disease patients...
March 21, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28324009/whole-exome-sequencing-for-diagnosis-of-turner-syndrome-towards-next-generation-sequencing-and-newborn-screening
#3
David R Murdock, Frank X Donovan, Settara C Chandrasekharappa, Nicole Banks, Carolyn Bondy, Maximilian Muenke, Paul Kruszka
Context, Objectives: Turner syndrome (TS) is due to a complete or partial loss of an X chromosome in females and is not currently part of newborn screening. Diagnosis is often delayed resulting in missed crucial diagnostic and therapeutic opportunities. This study sought to determine if whole-exome sequencing (WES) as part of a potential newborn screening program could be used to diagnose TS. Design, Setting, Patients: Karyotype, chromosomal microarray, and WES were performed on women with TS (n=27) enrolled in the Personalized Genomic Research study at the National Institutes of Health...
January 24, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323658/changing-face-of-metastatic-prostate-cancer-the-law-of-diminishing-returns-holds-true
#4
Ulka N Vaishampayan
PURPOSE OF REVIEW: Prostate cancer presents with a multitude of faces. It ranges from localized cancers staying quiescent for many years during active surveillance to the raging diffuse liver metastases causing terminal disease. The incidence of metastatic disease is increasing. This review will highlight some of the recent developments as well as ongoing challenges of managing advanced prostate cancer. RECENT FINDINGS: Significant strides are being made in managing metastatic prostate cancer...
March 18, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/28321632/metastatic-melanoma-moves-on-translational-science-in-the-era-of-personalized-medicine
#5
Mitchell P Levesque, Phil F Cheng, Marieke I G Raaijmakers, Annalisa Saltari, Reinhard Dummer
Progress in understanding and treating metastatic melanoma is the result of decades of basic and translational research as well as the development of better in vitro tools for modeling the disease. Here, we review the latest therapeutic options for metastatic melanoma and the known genetic and non-genetic mechanisms of resistance to these therapies, as well as the in vitro toolbox that has provided the greatest insights into melanoma progression. These include next-generation sequencing technologies and more complex 2D and 3D cell culture models to functionally test the data generated by genomics approaches...
March 20, 2017: Cancer Metastasis Reviews
https://www.readbyqxmd.com/read/28319896/a-dynamic-sandwich-assay-on-magnetic-beads-for-selective-detection-of-single-nucleotide-mutations-at-room-temperature
#6
Junxiu Wang, Guoliang Xiong, Liang Ma, Shihui Wang, Xu Zhou, Lei Wang, Lehui Xiao, Xin Su, Changyuan Yu
Single-nucleotide mutation (SNM) has proven to be associated with a variety of human diseases. Development of reliable methods for the detection of SNM is crucial for molecular diagnosis and personalized medicine. The sandwich assays are widely used tools for detecting nucleic acid biomarkers due to their low cost and rapid signaling. However, the poor hybridization specificity of signal probe at room temperature hampers the discrimination of mutant and wild type. Here, we demonstrate a dynamic sandwich assay on magnetic beads for SNM detection based on the transient binding between signal probe and target...
March 12, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28317403/intrahepatic-cholangiocarcinoma-current-management-and-emerging-therapies
#7
Amir A Rahnemai-Azar, Allison B Weisbrod, Mary Dillhoff, Carl Schmidt, Timothy M Pawlik
Intrahepatic cholangiocarcinoma (iCCA) is a malignancy with an increasing incidence and a high-case fatality. While surgery offers the best hope at long-term survival, only one-third of tumors are amenable to surgical resection at the time of the diagnosis. Unfortunately, conventional chemotherapy offers limited survival benefit in the management of unresectable or metastatic disease. Recent advances in understanding the molecular pathogenesis of iCCA and the use of next-generation sequencing techniques have provided a chance to identify "target-able" molecular aberrations...
March 20, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28317033/returning-genome-sequences-to-research-participants-policy-and-practice
#8
Caroline F Wright, Anna Middleton, Jeffrey C Barrett, Helen V Firth, David R FitzPatrick, Matthew E Hurles, Michael Parker
Despite advances in genomic science stimulating an explosion of literature around returning health-related findings, the possibility of returning entire genome sequences to individual research participants has not been widely considered. Through direct involvement in large-scale translational genomics studies, we have identified a number of logistical challenges that would need to be overcome prior to returning individual genome sequence data, including verifying that the data belong to the requestor and providing appropriate informatics support...
February 24, 2017: Wellcome Open Res
https://www.readbyqxmd.com/read/28316112/molecular-ecology-studies-of-species-radiations-current-research-gaps-opportunities-and-challenges
#9
Marylaure de la Harpe, Margot Paris, Dirk N Karger, Jonathan Rolland, Michael Kessler, Nicolas Salamin, Christian Lexer
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and re-visit recent high-profile examples of evolutionary genomic research on radiations...
March 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28314689/dna-methylation-based-classification-and-grading-system-for-meningioma-a-multicentre-retrospective-analysis
#10
Felix Sahm, Daniel Schrimpf, Damian Stichel, David T W Jones, Thomas Hielscher, Sebastian Schefzyk, Konstantin Okonechnikov, Christian Koelsche, David E Reuss, David Capper, Dominik Sturm, Hans-Georg Wirsching, Anna Sophie Berghoff, Peter Baumgarten, Annekathrin Kratz, Kristin Huang, Annika K Wefers, Volker Hovestadt, Martin Sill, Hayley P Ellis, Kathreena M Kurian, Ali Fuat Okuducu, Christine Jungk, Katharina Drueschler, Matthias Schick, Melanie Bewerunge-Hudler, Christian Mawrin, Marcel Seiz-Rosenhagen, Ralf Ketter, Matthias Simon, Manfred Westphal, Katrin Lamszus, Albert Becker, Arend Koch, Jens Schittenhelm, Elisabeth J Rushing, V Peter Collins, Stefanie Brehmer, Lukas Chavez, Michael Platten, Daniel Hänggi, Andreas Unterberg, Werner Paulus, Wolfgang Wick, Stefan M Pfister, Michel Mittelbronn, Matthias Preusser, Christel Herold-Mende, Michael Weller, Andreas von Deimling
BACKGROUND: The WHO classification of brain tumours describes 15 subtypes of meningioma. Nine of these subtypes are allotted to WHO grade I, and three each to grade II and grade III. Grading is based solely on histology, with an absence of molecular markers. Although the existing classification and grading approach is of prognostic value, it harbours shortcomings such as ill-defined parameters for subtypes and grading criteria prone to arbitrary judgment. In this study, we aimed for a comprehensive characterisation of the entire molecular genetic landscape of meningioma to identify biologically and clinically relevant subgroups...
March 14, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28303388/the-impact-of-antibiotic-stewardship-programs-in-combating-quinolone-resistance-a-systematic-review-and-recommendations-for-more-efficient-interventions
#11
REVIEW
Vasiliki Pitiriga, Georgia Vrioni, George Saroglou, Athanasios Tsakris
Quinolones are among the most commonly prescribed antibiotics worldwide. A clear relationship has been demonstrated between excessive quinolone use and the steady increase in the incidence of quinolone-resistant bacterial pathogens, both in hospital and community sites. In addition, exposure to quinolones has been associated with colonization and infection with healthcare-associated pathogens such as methicillin-resistant Staphylococcus aureus and Clostridium difficile in hospitalized patients. Therefore, the management of quinolone prescribing in hospitals through antibiotic stewardship programs is considered crucial...
March 16, 2017: Advances in Therapy
https://www.readbyqxmd.com/read/28302711/precision-and-prognostic-value-of-clone-specific-minimal-residual-disease-in-acute-myeloid-leukemia
#12
Pierre Hirsch, Ruoping Tang, Nassera Abermil, Pascale Flandrin, Hannah Moatti, Fabrizia Favale, Ludovic Suner, Florence Lorre, Christophe Marzac, Fanny Fava, Anne-Claire Mamez, Simona Lapusan, Françoise Isnard, Mohamad Mohty, Ollivier Legrand, Luc Douay, Chrystele Bilhou-Nabera, François Delhommeau
The genetic landscape of adult acute myeloid leukemias has been recently unraveled. However, due to their genetic heterogeneity, only a handful of markers are currently used for the evaluation of minimal residual disease. Recent studies using multi-target strategies indicate that detection of residual mutations in less than 5% of cells in complete remission is associated with a better survival. Here, in a series of 69 acute myeloid leukemias with known clonal architecture, we design a clone-specific strategy based on fluorescent in situ hybridization and high-sensitivity next generation sequencing to detect chromosomal aberrations and mutations, respectively, in follow-up samples...
March 16, 2017: Haematologica
https://www.readbyqxmd.com/read/28302680/genomic-and-epigenomic-heterogeneity-of-hepatocellular-carcinoma
#13
De-Chen Lin, Anand Mayakonda, Huy Q Dinh, Pinbo Huang, Lehang Lin, Xiaoping Liu, Ling-Wen Ding, Jie Wang, Benjamin Berman, Erwei Song, Dong Yin, H Phillip Koeffler
Understanding the intratumoral heterogeneity of hepatocellular carcinoma (HCC) is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 HCC cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions i...
February 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28302551/role-of-structural-bioinformatics-in-drug-discovery-by-computational-snp-analysis-a-proposed-protocol-for-analyzing-variation-at-the-protein-level
#14
REVIEW
David K Brown, Özlem Tastan Bishop
With the completion of the human genome project at the beginning of the 21st century, the biological sciences entered an unprecedented age of data generation, and made its first steps toward an era of personalized medicine. This abundance of sequence data has led to the proliferation of numerous sequence-based techniques for associating variation with disease, such as genome-wide association studies and candidate gene association studies. However, these statistical methods do not provide an understanding of the functional effects of variation...
March 13, 2017: Global Heart
https://www.readbyqxmd.com/read/28302057/clinically-proven-mtdna-mutations-are-not-common-in-those-with-chronic-fatigue-syndrome
#15
Elizna M Schoeman, Francois H Van Der Westhuizen, Elardus Erasmus, Etresia van Dyk, Charlotte V Y Knowles, Shereen Al-Ali, Wan-Fai Ng, Robert W Taylor, Julia L Newton, Joanna L Elson
BACKGROUND: Chronic Fatigue Syndrome (CFS) is a prevalent debilitating condition that affects approximately 250,000 people in the UK. There is growing interest in the role of mitochondrial function and mitochondrial DNA (mtDNA) variation in CFS. It is now known that fatigue is common and often severe in patients with mitochondrial disease irrespective of their age, gender or mtDNA genotype. More recently, it has been suggested that some CFS patients harbour clinically proven mtDNA mutations...
March 16, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28301737/the-clinic-is-my-laboratory-life-as-a-clinical-geneticist
#16
Judith G Hall
Clinical genetics is the application of advances in genetics and medicine to real human families. It involves diagnosis, care, and counseling concerning options available to affected individuals and their family members. Advances in medicine and genetics have led to dramatic changes in the scope and responsibilities of clinical genetics. This reflection on the last 50+ years of clinical genetics comes from personal experience, with an emphasis on the important contributions that clinical geneticists have made to the understanding of disease/disorder processes and mechanisms...
March 6, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28301457/exploring-the-feasibility-of-delivering-standardized-genomic-care-using-ophthalmology-as-an-example
#17
Niall Davison, Katherine Payne, Martin Eden, Marion McAllister, Stephen A Roberts, Stuart Ingram, Graeme C M Black, Georgina Hall
PURPOSE: Broadening access to genomic testing and counseling will be necessary to realize the benefits of personalized health care. This study aimed to assess the feasibility of delivering a standardized genomic care model for inherited retinal dystrophy (IRD) and of using selected measures to quantify its impact on patients. METHODS: A pre-/post- prospective cohort study recruited 98 patients affected by IRD to receive standardized multidisciplinary care. A checklist was used to assess the fidelity of the care process...
March 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28299357/integrating-functional-genomics-to-accelerate-mechanistic-personalized-medicine
#18
Jeffrey W Tyner
The advent of deep sequencing technologies has resulted in the deciphering of tremendous amounts of genetic information. These data have led to major discoveries, and many anecdotes now exist of individual patients whose clinical outcomes have benefited from novel, genetically guided therapeutic strategies. However, the majority of genetic events in cancer are currently undrugged, leading to a biological gap between understanding of tumor genetic etiology and translation to improved clinical approaches. Functional screening has made tremendous strides in recent years with the development of new experimental approaches to studying ex vivo and in vivo drug sensitivity...
March 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28298902/global-distribution-and-evolutionary-history-of-enterovirus-d68-with-emphasis-on-the-2014-outbreak-in-ontario-canada
#19
Alireza Eshaghi, Venkata R Duvvuri, Sandra Isabel, Philip Banh, Aimin Li, Adriana Peci, Samir N Patel, Jonathan B Gubbay
Despite its first appearance in 1962, human enterovirus D68 (EV-D68) has been recognized as an emerging respiratory pathogen in the last decade when it caused outbreaks and clusters in several countries including Japan, the Philippines, and the Netherlands. The most recent and largest outbreak of EV-D68 associated with severe respiratory illness took place in North America between August 2014 and January 2015. Between September 1 and October 31 2014, EV-D68 infection was laboratory confirmed among 153/907 (16...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28298424/richer-data-with-personalized-gems
#20
Miles A Miller
Personalized genome-scale metabolic models augment clinical hepatic steatosis data and motivate treatment based on glutathione repletion.
March 15, 2017: Science Translational Medicine
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