keyword
https://read.qxmd.com/read/38538605/advancing-access-to-genome-sequencing-for-rare-genetic-disorders-recent-progress-and-call-to-action
#1
JOURNAL ARTICLE
Vaidehi Jobanputra, Brock Schroeder, Heidi L Rehm, Wei Shen, Elizabeth Spiteri, Ghunwa Nakouzi, Stacie Taylor, Christian R Marshall, Linyan Meng, Stephen F Kingsmore, Katarzyna Ellsworth, Euan Ashley, Ryan J Taft
No abstract text is available yet for this article.
March 27, 2024: NPJ Genomic Medicine
https://read.qxmd.com/read/38506054/regional-variation-in-cardiovascular-genes-enables-a-tractable-genome-editing-strategy
#2
JOURNAL ARTICLE
Vikki A Krysov, Rachel H Wilson, Nicholas S Ten, Nathan Youlton, Hannah N De Jong, Shirley Sutton, Yong Huang, Chloe M Reuter, Megan E Grove, Matthew T Wheeler, Euan A Ashley, Victoria N Parikh
BACKGROUND: To realize the potential of genome engineering therapeutics, tractable strategies must be identified that balance personalized therapy with the need for off-the-shelf availability. We hypothesized that regional clustering of pathogenic variants can inform the design of rational prime editing therapeutics to treat the majority of genetic cardiovascular diseases with a limited number of reagents. METHODS: We collated 2435 high-confidence pathogenic/likely pathogenic (P/LP) variants in 82 cardiovascular disease genes from ClinVar...
March 20, 2024: Circulation. Genomic and Precision Medicine
https://read.qxmd.com/read/38503537/deep-learning-to-detect-left-ventricular-structural-abnormalities-in-chest-x-rays
#3
JOURNAL ARTICLE
Shreyas Bhave, Victor Rodriguez, Timothy Poterucha, Simukayi Mutasa, Dwight Aberle, Kathleen M Capaccione, Yibo Chen, Belinda Dsouza, Shifali Dumeer, Jonathan Goldstein, Aaron Hodes, Jay Leb, Matthew Lungren, Mitchell Miller, David Monoky, Benjamin Navot, Kapil Wattamwar, Anoop Wattamwar, Kevin Clerkin, David Ouyang, Euan Ashley, Veli K Topkara, Mathew Maurer, Andrew J Einstein, Nir Uriel, Shunichi Homma, Allan Schwartz, Diego Jaramillo, Adler J Perotte, Pierre Elias
BACKGROUND AND AIMS: Early identification of cardiac structural abnormalities indicative of heart failure is crucial to improving patient outcomes. Chest X-rays (CXRs) are routinely conducted on a broad population of patients, presenting an opportunity to build scalable screening tools for structural abnormalities indicative of Stage B or worse heart failure with deep learning methods. In this study, a model was developed to identify severe left ventricular hypertrophy (SLVH) and dilated left ventricle (DLV) using CXRs...
March 20, 2024: European Heart Journal
https://read.qxmd.com/read/38475989/quantifying-assumptions-underlying-peak-oxygen-consumption-equations-across-the-body-mass-spectrum
#4
JOURNAL ARTICLE
Vincent Busque, Jeffrey W Christle, Kegan J Moneghetti, Nicholas Cauwenberghs, Tatiana Kouznetsova, Yair Blumberg, Matthew T Wheeler, Euan Ashley, Francois Haddad, Jonathan Myers
The goal of this study is to quantify the assumptions associated with the Wasserman-Hansen (WH) and Fitness Registry and the Importance of Exercise: A National Database (FRIEND) predictive peak oxygen consumption (pVO2 ) equations across body mass index (BMI). Assumptions in pVO2 for both equations were first determined using a simulation and then evaluated using exercise data from the Stanford Exercise Testing registry. We calculated percent-predicted VO2 (ppVO2 ) values for both equations and compared them using the Bland-Altman method...
March 12, 2024: Clinical Obesity
https://read.qxmd.com/read/38421234/knowledge-and-attitudes-on-implementing-cardiovascular-pharmacogenomic-testing
#5
JOURNAL ARTICLE
Callan Russell, MaryAnn Campion, Megan E Grove, Kelly Matsuda, Teri E Klein, Euan Ashley, Hetanshi Naik, Matthew T Wheeler, Stuart A Scott
Pharmacogenomics has the potential to inform drug dosing and selection, reduce adverse events, and improve medication efficacy; however, provider knowledge of pharmacogenomic testing varies across provider types and specialties. Given that many actionable pharmacogenomic genes are implicated in cardiovascular medication response variability, this study aimed to evaluate cardiology providers' knowledge and attitudes on implementing clinical pharmacogenomic testing. Sixty-one providers responded to an online survey, including pharmacists (46%), physicians (31%), genetic counselors (15%), and nurses (8%)...
March 2024: Clinical and Translational Science
https://read.qxmd.com/read/38343631/almanac-retrieval-augmented-language-models-for-clinical-medicine
#6
JOURNAL ARTICLE
Cyril Zakka, Rohan Shad, Akash Chaurasia, Alex R Dalal, Jennifer L Kim, Michael Moor, Robyn Fong, Curran Phillips, Kevin Alexander, Euan Ashley, Jack Boyd, Kathleen Boyd, Karen Hirsch, Curt Langlotz, Rita Lee, Joanna Melia, Joanna Nelson, Karim Sallam, Stacey Tullis, Melissa Ann Vogelsong, John Patrick Cunningham, William Hiesinger
BACKGROUND: Large language models (LLMs) have recently shown impressive zero-shot capabilities, whereby they can use auxiliary data, without the availability of task-specific training examples, to complete a variety of natural language tasks, such as summarization, dialogue generation, and question answering. However, despite many promising applications of LLMs in clinical medicine, adoption of these models has been limited by their tendency to generate incorrect and sometimes even harmful statements...
February 2024: NEJM AI
https://read.qxmd.com/read/38301753/improving-reporting-of-exercise-capacity-across-age-ranges-using-novel-workload-reference-equations
#7
JOURNAL ARTICLE
Everton J Santana, Jeffrey W Christle, Nicholas Cauwenberghs, James E Peterman, Vincent Busque, Bruna Gomes, Shadi P Bagherzadeh, Kegan Moneghetti, Tatiana Kuznetsova, Matthew Wheeler, Euan Ashley, Matthew P Harber, Ross Arena, Leonard A Kaminsky, Jonathan Myers, Francois Haddad
Exercise capacity (EC) is an important predictor of survival in the general population and in subjects with cardiopulmonary disease. Despite its relevance, considering the percent-predicted workload (%pWL) given by current equations may overestimate EC in older adults. Therefore, to improve the reporting of EC in clinical practice, our main objective was to develop workload reference equations (pWL) that better reflect the relation between workload and age. Using the Fitness Registry and the Importance of Exercise National Database (FRIEND), we analyzed a reference group of 6,966 apparently healthy participants and 1,060 participants with heart failure who underwent graded treadmill cardiopulmonary exercise testing...
January 30, 2024: American Journal of Cardiology
https://read.qxmd.com/read/38301647/apoe-loss-of-function-variants-compatible-with-longevity-and-associated-with-resistance-to-alzheimer-s-disease-pathology
#8
JOURNAL ARTICLE
Augustine Chemparathy, Yann Le Guen, Sunny Chen, Eun-Gyung Lee, Lesley Leong, John E Gorzynski, Tanner D Jensen, Alexis Ferrasse, Guangxue Xu, Hong Xiang, Michael E Belloy, Nandita Kasireddy, Andrés Peña-Tauber, Kennedy Williams, Ilaria Stewart, Lia Talozzi, Thomas S Wingo, James J Lah, Suman Jayadev, Chadwick M Hales, Elaine Peskind, Daniel D Child, Sigrun Roeber, C Dirk Keene, Le Cong, Euan A Ashley, Chang-En Yu, Michael D Greicius
The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years...
January 29, 2024: Neuron
https://read.qxmd.com/read/38135699/unsupervised-machine-learning-to-investigate-trajectory-patterns-of-covid-19-symptoms-and-physical-activity-measured-via-the-myheart-counts-app-and-smart-devices
#9
JOURNAL ARTICLE
Varsha Gupta, Sokratis Kariotis, Mohammed D Rajab, Niamh Errington, Elham Alhathli, Emmanuel Jammeh, Martin Brook, Naomi Meardon, Paul Collini, Joby Cole, Jim M Wild, Steven Hershman, Ali Javed, A A Roger Thompson, Thushan de Silva, Euan A Ashley, Dennis Wang, Allan Lawrie
Previous studies have associated COVID-19 symptoms severity with levels of physical activity. We therefore investigated longitudinal trajectories of COVID-19 symptoms in a cohort of healthcare workers (HCWs) with non-hospitalised COVID-19 and their real-world physical activity. 121 HCWs with a history of COVID-19 infection who had symptoms monitored through at least two research clinic visits, and via smartphone were examined. HCWs with a compatible smartphone were provided with an Apple Watch Series 4 and were asked to install the MyHeart Counts Study App to collect COVID-19 symptom data and multiple physical activity parameters...
December 22, 2023: NPJ Digital Medicine
https://read.qxmd.com/read/38126168/race-sex-and-age-disparities-in-the-performance-of-ecg-deep-learning-models-predicting-heart-failure
#10
JOURNAL ARTICLE
Dhamanpreet Kaur, J Weston Hughes, Albert J Rogers, Guson Kang, Sanjiv M Narayan, Euan A Ashley, Marco V Perez
BACKGROUND: Deep learning models may combat widening racial disparities in heart failure outcomes through early identification of individuals at high risk. However, demographic biases in the performance of these models have not been well-studied. METHODS: This retrospective analysis used 12-lead ECGs taken between 2008 and 2018 from 326 518 patient encounters referred for standard clinical indications to Stanford Hospital. The primary model was a convolutional neural network model trained to predict incident heart failure within 5 years...
December 21, 2023: Circulation. Heart Failure
https://read.qxmd.com/read/38082205/genetic-architecture-of-cardiac-dynamic-flow-volumes
#11
JOURNAL ARTICLE
Bruna Gomes, Aditya Singh, Jack W O'Sullivan, Theresia M Schnurr, Pagé C Goddard, Shaun Loong, David Amar, J Weston Hughes, Mykhailo Kostur, Francois Haddad, Michael Salerno, Roger Foo, Stephen B Montgomery, Victoria N Parikh, Benjamin Meder, Euan A Ashley
Cardiac blood flow is a critical determinant of human health. However, the definition of its genetic architecture is limited by the technical challenge of capturing dynamic flow volumes from cardiac imaging at scale. We present DeepFlow, a deep-learning system to extract cardiac flow and volumes from phase-contrast cardiac magnetic resonance imaging. A mixed-linear model applied to 37,653 individuals from the UK Biobank reveals genome-wide significant associations across cardiac dynamic flow volumes spanning from aortic forward velocity to aortic regurgitation fraction...
December 11, 2023: Nature Genetics
https://read.qxmd.com/read/38045390/epistasis-regulates-genetic-control-of-cardiac-hypertrophy
#12
Qianru Wang, Tiffany Tang, Nathan Youlton, Chad Weldy, Ana Kenney, Omer Ronen, John Hughes, Elizabeth Chin, Shirley Sutton, Abhineet Agarwal, Xiao Li, Merle Behr, Karl Kumbier, Christine Moravec, W H Wilson Tang, Kenneth Margulies, Thomas Cappola, Atul Butte, Rima Arnaout, James Brown, James Priest, Victoria Parikh, Bin Yu, Euan Ashley
The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141 , IGF1R , TTN , and TNKS ...
November 20, 2023: Research Square
https://read.qxmd.com/read/37987017/epistasis-regulates-genetic-control-of-cardiac-hypertrophy
#13
Qianru Wang, Tiffany M Tang, Nathan Youlton, Chad S Weldy, Ana M Kenney, Omer Ronen, J Weston Hughes, Elizabeth T Chin, Shirley C Sutton, Abhineet Agarwal, Xiao Li, Merle Behr, Karl Kumbier, Christine S Moravec, W H Wilson Tang, Kenneth B Margulies, Thomas P Cappola, Atul J Butte, Rima Arnaout, James B Brown, James R Priest, Victoria N Parikh, Bin Yu, Euan A Ashley
The combinatorial effect of genetic variants is often assumed to be additive. Although genetic variation can clearly interact non-additively, methods to uncover epistatic relationships remain in their infancy. We develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy. We derive deep learning-based estimates of left ventricular mass from the cardiac MRI scans of 29,661 individuals enrolled in the UK Biobank. We report epistatic genetic variation including variants close to CCDC141 , IGF1R , TTN , and TNKS...
November 8, 2023: medRxiv
https://read.qxmd.com/read/37883018/two-epilepsy-associated-variants-in-kcna2-k-v-1-2-at-position-h310-oppositely-affect-channel-functional-expression
#14
JOURNAL ARTICLE
Teresa Mínguez-Viñas, Varsha Prakash, Kaiqian Wang, Sarah H Lindström, Serena Pozzi, Stuart A Scott, Elizabeth Spiteri, David A Stevenson, Euan A Ashley, Cecilia Gunnarsson, Antonios Pantazis
Two KCNA2 variants (p.H310Y and p.H310R) were discovered in paediatric patients with epilepsy and developmental delay. KCNA2 encodes KV 1.2-channel subunits, which regulate neuronal excitability. Both gain and loss of KV 1.2 function cause epilepsy, precluding the prediction of variant effects; and while H310 is conserved throughout the KV -channel superfamily, it is largely understudied. We investigated both variants in heterologously expressed, human KV 1.2 channels by immunocytochemistry, electrophysiology and voltage-clamp fluorometry...
October 26, 2023: Journal of Physiology
https://read.qxmd.com/read/37850394/improved-cardiac-performance-and-decreased-arrhythmia-in-hypertrophic-cardiomyopathy-with-non-%C3%AE-blocking-r-enantiomer-carvedilol
#15
JOURNAL ARTICLE
Kinya Seo, Yuta Yamamoto, Anna Kirillova, Masataka Kawana, Sunil Yadav, Yong Huang, Qianru Wang, Kerry V Lane, Beth L Pruitt, Marco V Perez, Daniel Bernstein, Joseph C Wu, Matthew T Wheeler, Victoria N Parikh, Euan A Ashley
BACKGROUND: Hypercontractility and arrhythmia are key pathophysiologic features of hypertrophic cardiomyopathy (HCM), the most common inherited heart disease. β-Adrenergic receptor antagonists (β-blockers) are the first-line therapy for HCM. However, β-blockers commonly selected for this disease are often poorly tolerated in patients, where heart-rate reduction and noncardiac effects can lead to reduced cardiac output and fatigue. Mavacamten, myosin ATPase inhibitor recently approved by the US Food and Drug Administration, has demonstrated the ability to ameliorate hypercontractility without lowering heart rate, but its benefits are so far limited to patients with left ventricular (LV) outflow tract obstruction, and its effect on arrhythmia is unknown...
October 18, 2023: Circulation
https://read.qxmd.com/read/37813962/author-correction-cosmos-a-platform-for-real-time-morphology-based-label-free-cell-sorting-using-deep-learning
#16
Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B Jacobs, Chassidy Johnson, Vivian Lu, Esther J Lee, Christina Chang, Phuc Nguyen, Jeanette Mei, Krishna P Pant, Amy Y Wong-Thai, Quillan F Smith, Stephanie Huang, Ryan Chow, Janifer Cruz, Jeff Walker, Bryan Chan, Thomas J Musci, Euan A Ashley, Maddison Mahdokht Masaeli
No abstract text is available yet for this article.
October 9, 2023: Communications Biology
https://read.qxmd.com/read/37794870/personalized-digital-behaviour-interventions-increase-short-term-physical-activity-a-randomized-control-crossover-trial-substudy-of-the-myheart-counts-cardiovascular-health-study
#17
JOURNAL ARTICLE
Ali Javed, Daniel Seung Kim, Steven G Hershman, Anna Shcherbina, Anders Johnson, Alexander Tolas, Jack W O'Sullivan, Michael V McConnell, Laura Lazzeroni, Abby C King, Jeffrey W Christle, Marily Oppezzo, C Mikael Mattsson, Robert A Harrington, Matthew T Wheeler, Euan A Ashley
AIMS: Physical activity is associated with decreased incidence of the chronic diseases associated with aging. We previously demonstrated that digital interventions delivered through a smartphone app can increase short-term physical activity. METHODS AND RESULTS: We offered enrolment to community-living iPhone-using adults aged ≥18 years in the USA, UK, and Hong Kong who downloaded the MyHeart Counts app. After completion of a 1-week baseline period, e-consented participants were randomized to four 7-day interventions...
October 2023: European heart journal. Digital health
https://read.qxmd.com/read/37794183/rare-variant-associations-with-plasma-protein-levels-in-the-uk-biobank
#18
JOURNAL ARTICLE
Ryan S Dhindsa, Oliver S Burren, Benjamin B Sun, Bram P Prins, Dorota Matelska, Eleanor Wheeler, Jonathan Mitchell, Erin Oerton, Ventzislava A Hristova, Katherine R Smith, Keren Carss, Sebastian Wasilewski, Andrew R Harper, Dirk S Paul, Margarete A Fabre, Heiko Runz, Coralie Viollet, Benjamin Challis, Adam Platt, Dimitrios Vitsios, Euan A Ashley, Christopher D Whelan, Menelas N Pangalos, Quanli Wang, Slavé Petrovski
Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4 . Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5 ...
October 2023: Nature
https://read.qxmd.com/read/37745389/local-read-haplotagging-enables-accurate-long-read-small-variant-calling
#19
Alexey Kolesnikov, Daniel Cook, Maria Nattestad, Brandy McNulty, John Gorzynski, Sneha Goenka, Euan A Ashley, Miten Jain, Karen H Miga, Benedict Paten, Pi-Chuan Chang, Andrew Carroll, Kishwar Shafin
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced...
September 12, 2023: bioRxiv
https://read.qxmd.com/read/37740030/cosmos-a-platform-for-real-time-morphology-based-label-free-cell-sorting-using-deep-learning
#20
JOURNAL ARTICLE
Mahyar Salek, Nianzhen Li, Hou-Pu Chou, Kiran Saini, Andreja Jovic, Kevin B Jacobs, Chassidy Johnson, Vivian Lu, Esther J Lee, Christina Chang, Phuc Nguyen, Jeanette Mei, Krishna P Pant, Amy Y Wong-Thai, Quillan F Smith, Stephanie Huang, Ryan Chow, Janifer Cruz, Jeff Walker, Bryan Chan, Thomas J Musci, Euan A Ashley, Maddison Mahdokht Masaeli
Cells are the singular building blocks of life, and a comprehensive understanding of morphology, among other properties, is crucial to the assessment of underlying heterogeneity. We developed Computational Sorting and Mapping of Single Cells (COSMOS), a platform based on Artificial Intelligence (AI) and microfluidics to characterize and sort single cells based on real-time deep learning interpretation of high-resolution brightfield images. Supervised deep learning models were applied to characterize and sort cell lines and dissociated primary tissue based on high-dimensional embedding vectors of morphology without the need for biomarker labels and stains/dyes...
September 22, 2023: Communications Biology
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