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https://www.readbyqxmd.com/read/27814364/deep-learning-automates-the-quantitative-analysis-of-individual-cells-in-live-cell-imaging-experiments
#1
David A Van Valen, Takamasa Kudo, Keara M Lane, Derek N Macklin, Nicolas T Quach, Mialy M DeFelice, Inbal Maayan, Yu Tanouchi, Euan A Ashley, Markus W Covert
Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic, living systems. A major critical challenge for this class of experiments is the problem of image segmentation, or determining which parts of a microscope image correspond to which individual cells. Current approaches require many hours of manual curation and depend on approaches that are difficult to share between labs. They are also unable to robustly segment the cytoplasms of mammalian cells. Here, we show that deep convolutional neural networks, a supervised machine learning method, can solve this challenge for multiple cell types across the domains of life...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27681629/early-somatic-mosaicism-is-a-rare-cause-of-long-qt-syndrome
#2
James Rush Priest, Charles Gawad, Kristopher M Kahlig, Joseph K Yu, Thomas O'Hara, Patrick M Boyle, Sridharan Rajamani, Michael J Clark, Sarah T K Garcia, Scott Ceresnak, Jason Harris, Sean Boyle, Frederick E Dewey, Lindsey Malloy-Walton, Kyla Dunn, Megan Grove, Marco V Perez, Norma F Neff, Richard Chen, Katsuhide Maeda, Anne Dubin, Luiz Belardinelli, John West, Christian Antolik, Daniela Macaya, Thomas Quertermous, Natalia A Trayanova, Stephen R Quake, Euan A Ashley
Somatic mosaicism, the occurrence and propagation of genetic variation in cell lineages after fertilization, is increasingly recognized to play a causal role in a variety of human diseases. We investigated the case of life-threatening arrhythmia in a 10-day-old infant with long QT syndrome (LQTS). Rapid genome sequencing suggested a variant in the sodium channel NaV1.5 encoded by SCN5A, NM_000335:c.5284G > T predicting p.(V1762L), but read depth was insufficient to be diagnostic. Exome sequencing of the trio confirmed read ratios inconsistent with Mendelian inheritance only in the proband...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27582424/in-vivo-post-cardiac-arrest-myocardial-dysfunction-is-supported-by-ca2-calmodulin-dependent-protein-kinase-ii-mediated-calcium-long-term-potentiation-and-mitigated-by-alda-1-an-agonist-of-aldehyde-dehydrogenase-type-2
#3
Christopher E Woods, Ching Shang, Fouad Taghavi, Peter Downey, Adrian Zalewski, Gabriel R Rubio, Jing Liu, Julian R Homburger, Zachary Grunwald, Wei Qi, Christian Bollensdorff, Porama Thanaporn, Ayyaz Ali, R Kirk Riemer, Peter Kohl, Daria Mochly-Rosen, Edward Gerstenfeld, Stephen Large, Ziad A Ali, Euan A Ashley
BACKGROUND: Survival after sudden cardiac arrest is limited by postarrest myocardial dysfunction, but understanding of this phenomenon is constrained by a lack of data from a physiological model of disease. In this study, we established an in vivo model of cardiac arrest and resuscitation, characterized the biology of the associated myocardial dysfunction, and tested novel therapeutic strategies. METHODS: We developed rodent models of in vivo postarrest myocardial dysfunction using extracorporeal membrane oxygenation resuscitation followed by invasive hemodynamics measurement...
September 27, 2016: Circulation
https://www.readbyqxmd.com/read/27528417/towards-precision-medicine
#4
Euan A Ashley
There is great potential for genome sequencing to enhance patient care through improved diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential, genomics strategies that have been developed for genetic discovery - including DNA-sequencing technologies and analysis algorithms - need to be adapted to fit clinical needs. This will require the optimization of alignment algorithms, attention to quality-coverage metrics, tailored solutions for paralogous or low-complexity areas of the genome, and the adoption of consensus standards for variant calling and interpretation...
August 16, 2016: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/27373587/alterations-in-cardiac-mechanics-following-ultra-endurance-exercise-insights-from-left-and-right-ventricular-area-deformation-loops
#5
Rachel Lord, Keith George, John Somauroo, Mike Stembridge, Nikhil Jain, Martin D Hoffman, Rob Shave, Francois Haddad, Euan Ashley, Helen Jones, David Oxborough
BACKGROUND: The aim of this study was to use novel area-deformation (ε) loops to interrogate the interaction between the right ventricular (RV) and left ventricular (LV) mechanics following a 100-mile endurance run. METHODS: Fifteen participants (mean body mass, 70.1 ± 8.8 kg; mean age, 40 ± 8 years) were recruited for the study. Echocardiography was performed before the race, after the race, and 6 hours into recovery. RV and LV area and longitudinal ε were assessed using standard and speckle-tracking echocardiography...
September 2016: Journal of the American Society of Echocardiography
https://www.readbyqxmd.com/read/27324065/taming-the-genome-towards-better-genetic-test-interpretation
#6
Colleen Caleshu, Euan A Ashley
Advances in sequencing technology have taught us much about the human genome, including how difficult it is to interpret rare variation. Improvements in genetic test interpretation are likely to come through data sharing, international collaborative efforts to develop disease-gene specific guidelines, and computational analyses using big data.
2016: Genome Medicine
https://www.readbyqxmd.com/read/27256036/interdisciplinary-psychosocial-care-for-families-with-inherited-cardiovascular-diseases
#7
REVIEW
Colleen Caleshu, Nadine A Kasparian, Katharine S Edwards, Laura Yeates, Christopher Semsarian, Marco Perez, Euan Ashley, Christian J Turner, Joshua W Knowles, Jodie Ingles
Inherited cardiovascular diseases pose unique and complex psychosocial challenges for families, including coming to terms with life-long cardiac disease, risk of sudden death, grief related to the sudden death of a loved one, activity restrictions, and inheritance risk to other family members. Psychosocial factors impact not only mental health but also physical health and cooperation with clinical recommendations. We describe an interdisciplinary approach to the care of families with inherited cardiovascular disease, in which psychological care provided by specialized cardiac genetic counselors, nurses, and psychologists is embedded within the cardiovascular care team...
October 2016: Trends in Cardiovascular Medicine
https://www.readbyqxmd.com/read/27247418/multidimensional-structure-function-relationships-in-human-%C3%AE-cardiac-myosin-from-population-scale-genetic-variation
#8
Julian R Homburger, Eric M Green, Colleen Caleshu, Margaret S Sunitha, Rebecca E Taylor, Kathleen M Ruppel, Raghu Prasad Rao Metpally, Steven D Colan, Michelle Michels, Sharlene M Day, Iacopo Olivotto, Carlos D Bustamante, Frederick E Dewey, Carolyn Y Ho, James A Spudich, Euan A Ashley
Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin...
June 14, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27099173/a-research-roadmap-for-next-generation-sequencing-informatics
#9
REVIEW
Russ B Altman, Snehit Prabhu, Arend Sidow, Justin M Zook, Rachel Goldfeder, David Litwack, Euan Ashley, George Asimenos, Carlos D Bustamante, Katherine Donigan, Kathleen M Giacomini, Elaine Johansen, Natalia Khuri, Eunice Lee, Xueying Sharon Liang, Marc Salit, Omar Serang, Zivana Tezak, Dennis P Wall, Elizabeth Mansfield, Taha Kass-Hout
Next-generation sequencing technologies are fueling a wave of new diagnostic tests. Progress on a key set of nine research challenge areas will help generate the knowledge required to advance effectively these diagnostics to the clinic.
April 20, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/27058611/de-novo-and-rare-variants-at-multiple-loci-support-the-oligogenic-origins-of-atrioventricular-septal-heart-defects
#10
James R Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra Kundu, Kathleen Schultz, Edward J Lammer, Santhosh Girirajan, Todd Scheetz, Daryl Waggott, Francois Haddad, Sushma Reddy, Daniel Bernstein, Trudy Burns, Jeffrey D Steimle, Xinan H Yang, Ivan P Moskowitz, Matthew Hurles, Richard P Lifton, Debbie Nickerson, Michael Bamshad, Evan E Eichler, Seema Mital, Val Sheffield, Thomas Quertermous, Bruce D Gelb, Michael Portman, Euan A Ashley
Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD)...
April 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27027796/exploratory-insights-from-the-right-sided-electrocardiogram-following-prolonged-endurance-exercise
#11
Rachel Lord, Keith George, John Somauroo, Nikhil Jain, Kristin Reese, Martin D Hoffman, Francois Haddad, Euan Ashley, Helen Jones, David Oxborough
BACKGROUND: Prolonged strenuous exercise has a profound effect on cardiac function. The right heart may be more susceptible to this imposition; yet, right-sided chest leads have not been utilised in this setting. METHODS: Thirty highly trained athletes at the 2014 Western States 100-mile Endurance Run from Squaw Valley to Auburn, California (body mass 68 ± 12 kg, age 45 ± 10 years, 57 ± 15 miles per week) were recruited for the study. Pre- and post-race, a right-sided 12-lead ECG was obtained and data were extracted for P, R and S waves, J point, ST segment and T wave amplitude...
November 2016: European Journal of Sport Science
https://www.readbyqxmd.com/read/26966283/effect-of-lossy-compression-of-quality-scores-on-variant-calling
#12
Idoia Ochoa, Mikel Hernaez, Rachel Goldfeder, Tsachy Weissman, Euan Ashley
Recent advancements in sequencing technology have led to a drastic reduction in genome sequencing costs. This development has generated an unprecedented amount of data that must be stored, processed, and communicated. To facilitate this effort, compression of genomic files has been proposed. Specifically, lossy compression of quality scores is emerging as a natural candidate for reducing the growing costs of storage. A main goal of performing DNA sequencing in population studies and clinical settings is to identify genetic variation...
March 10, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/26932475/medical-implications-of-technical-accuracy-in-genome-sequencing
#13
Rachel L Goldfeder, James R Priest, Justin M Zook, Megan E Grove, Daryl Waggott, Matthew T Wheeler, Marc Salit, Euan A Ashley
BACKGROUND: As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome. METHODS: We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease...
2016: Genome Medicine
https://www.readbyqxmd.com/read/26926154/impact-of-septal-reduction-on-left-atrial-size-and-diastole-in-hypertrophic-cardiomyopathy
#14
Gherardo Finocchiaro, Francois Haddad, Yukari Kobayashi, David Lee, Aleksandra Pavlovic, Ingela Schnittger, Gianfranco Sinagra, Emma Magavern, Jonathan Myers, Victor Froelicher, Joshua W Knowles, Euan Ashley
BACKGROUND AND AIMS: Both myectomy and alcohol septal ablation (ASA) can substantially reduce left ventricular (LV) outflow obstruction, relieve symptoms, and improve outcomes in hypertrophic cardiomyopathy (HCM). It is unclear whether septal reduction decreases left atrial (LA) size and improves diastolic function. The aim of this study was to analyze the consequences of septal reduction on LA size and diastolic function in a cohort of patients with HCM. METHODS: Forty patients (mean age: 50 ± 14, male sex 64%) with HCM who underwent septal reduction (myectomy or alcohol septal ablation) were studied...
May 2016: Echocardiography
https://www.readbyqxmd.com/read/26800575/hypertrophic-cardiomyopathy-as-a-cause-of%C3%A2-sudden-cardiac-death-in-the-young-a-meta-analysis
#15
Aditya J Ullal, Ramy S Abdelfattah, Euan A Ashley, Victor F Froelicher
BACKGROUND: Sudden cardiac death is often linked with hypertrophic cardiomyopathy in young athletes, but with a divergence of study results. We performed a meta-analysis to compare the prevalence of sudden cardiac deaths associated with hypertrophic cardiomyopathy vs sudden cardiac deaths associated with structurally normal hearts. METHODS: A structured search of MEDLINE was conducted for studies published from 1990 through 2014. Retrospective cohort studies, patient registries, and autopsy series examining sudden cardiac death etiology in young individuals (age ≤35 years) were included...
May 2016: American Journal of Medicine
https://www.readbyqxmd.com/read/26757801/sports-genetics-moving-forward-lessons-learned-from-medical-research
#16
REVIEW
C Mikael Mattsson, Matthew T Wheeler, Daryl Waggott, Colleen Caleshu, Euan A Ashley
Sports genetics can take advantage of lessons learned from human disease genetics. By righting past mistakes and increasing scientific rigor, we can magnify the breadth and depth of knowledge in the field. We present an outline of challenges facing sports genetics in the light of experiences from medical research. Sports performance is complex, resulting from a combination of a wide variety of different traits and attributes. Improving sports genetics will foremost require analyses based on detailed phenotyping...
March 2016: Physiological Genomics
https://www.readbyqxmd.com/read/26715623/athlome-project-consortium-a-concerted-effort-to-discover-genomic-and-other-omic-markers-of-athletic-performance
#17
REVIEW
Yannis P Pitsiladis, Masashi Tanaka, Nir Eynon, Claude Bouchard, Kathryn N North, Alun G Williams, Malcolm Collins, Colin N Moran, Steven L Britton, Noriyuki Fuku, Euan A Ashley, Vassilis Klissouras, Alejandro Lucia, Ildus I Ahmetov, Eco de Geus, Mohammed Alsayrafi
Despite numerous attempts to discover genetic variants associated with elite athletic performance, injury predisposition, and elite/world-class athletic status, there has been limited progress to date. Past reliance on candidate gene studies predominantly focusing on genotyping a limited number of single nucleotide polymorphisms or the insertion/deletion variants in small, often heterogeneous cohorts (i.e., made up of athletes of quite different sport specialties) have not generated the kind of results that could offer solid opportunities to bridge the gap between basic research in exercise sciences and deliverables in biomedicine...
March 2016: Physiological Genomics
https://www.readbyqxmd.com/read/26653627/systems-genomics-identifies-a-key-role-for-hypocretin-orexin-receptor-2-in-human-heart-failure
#18
Marco V Perez, Aleksandra Pavlovic, Ching Shang, Matthew T Wheeler, Clint L Miller, Jing Liu, Frederick E Dewey, Stephen Pan, Porama K Thanaporn, Devin Absher, Jeffrey Brandimarto, Heidi Salisbury, Khin Chan, Rupak Mukherjee, Roda P Konadhode, Richard M Myers, Daniel Sedehi, Thomas E Scammell, Thomas Quertermous, Thomas Cappola, Euan A Ashley
BACKGROUND: The genetic determinants of heart failure (HF) and response to medical therapy remain unknown. We hypothesized that identifying genetic variants of HF that associate with response to medical therapy would elucidate the genetic basis of cardiac function. OBJECTIVES: This study sought to identify genetic variations associated with response to HF therapy. METHODS: This study compared extremes of response to medical therapy in 866 HF patients using a genome-wide approach that informed the systems-based design of a customized single nucleotide variant array...
December 8, 2015: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/26582191/direct-to-consumer-genetic-testing-for-predicting-sports-performance-and-talent-identification-consensus-statement
#19
Nick Webborn, Alun Williams, Mike McNamee, Claude Bouchard, Yannis Pitsiladis, Ildus Ahmetov, Euan Ashley, Nuala Byrne, Silvia Camporesi, Malcolm Collins, Paul Dijkstra, Nir Eynon, Noriyuki Fuku, Fleur C Garton, Nils Hoppe, Søren Holm, Jane Kaye, Vassilis Klissouras, Alejandro Lucia, Kamiel Maase, Colin Moran, Kathryn N North, Fabio Pigozzi, Guan Wang
The general consensus among sport and exercise genetics researchers is that genetic tests have no role to play in talent identification or the individualised prescription of training to maximise performance. Despite the lack of evidence, recent years have witnessed the rise of an emerging market of direct-to-consumer marketing (DTC) tests that claim to be able to identify children's athletic talents. Targeted consumers include mainly coaches and parents. There is concern among the scientific community that the current level of knowledge is being misrepresented for commercial purposes...
December 2015: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/26578468/comparison-of-left-ventricular-manual-versus-automated-derived-longitudinal-strain-implications-for-clinical-practice-and-research
#20
Yukari Kobayashi, Miyuki Ariyama, Yuhei Kobayashi, Genevieve Giraldeau, Dominik Fleischman, Mirta Kozelj, Bojan Vrtovec, Euan Ashley, Tatiana Kuznetsova, Ingela Schnittger, David Liang, Francois Haddad
Systolic global longitudinal strain (GLS) is emerging as a useful metric of ventricular function in heart failure and usually assessed using post-processing software. The purpose of this study was to investigate whether longitudinal strain (LS) derived using manual-tracings of ventricular lengths (manual-LS) can be reliable and time efficient when compared to LS obtained by post-processing software (software-LS). Apical 4-chamber view images were retrospectively examined in 50 healthy controls, 100 patients with dilated cardiomyopathy (DCM), and 100 with hypertrophic cardiomyopathy (HCM)...
March 2016: International Journal of Cardiovascular Imaging
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