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Jason H Moore

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https://www.readbyqxmd.com/read/29044470/analysis-of-gene-gene-interactions
#1
Brian S Cole, Molly A Hall, Ryan J Urbanowicz, Diane Gilbert-Diamond, Jason H Moore
The goal of this unit is to introduce epistasis, or gene-gene interactions, as a significant contributor to the genetic architecture of complex traits, including disease susceptibility. This unit begins with an historical overview of the concept of epistasis and the challenges inherent in the identification of potential gene-gene interactions. Then, it reviews statistical and machine learning methods for discovering epistasis in the context of genetic studies of quantitative and categorical traits. This unit concludes with a discussion of meta-analysis, replication, and other topics of active research...
October 18, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/29023970/phenotype-validation-in-electronic-health-records-based-genetic-association-studies
#2
Lu Wang, Scott M Damrauer, Hong Zhang, Alan X Zhang, Rui Xiao, Jason H Moore, Jinbo Chen
The linkage between electronic health records (EHRs) and genotype data makes it plausible to study the genetic susceptibility of a wide range of disease phenotypes. Despite that EHR-derived phenotype data are subjected to misclassification, it has been shown useful for discovering susceptible genes, particularly in the setting of phenome-wide association studies (PheWAS). It is essential to characterize discovered associations using gold standard phenotype data by chart review. In this work, we propose a genotype stratified case-control sampling strategy to select subjects for phenotype validation...
October 11, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28978191/incorporation-of-biological-knowledge-into-the-study-of-gene-environment-interactions
#3
Marylyn D Ritchie, Joe R Davis, Hugues Aschard, Alexis Battle, David Conti, Mengmeng Du, Eleazar Eskin, M Daniele Fallin, Li Hsu, Peter Kraft, Jason H Moore, Brandon L Pierce, Stephanie A Bien, Duncan C Thomas, Peng Wei, Stephen B Montgomery
A growing knowledge base of genetic and environmental information has greatly enabled the study of disease risk factors. However, the computational complexity and statistical burden of testing all variants by all environments has required novel study designs and hypothesis-driven approaches. We discuss how incorporating biological knowledge from model organisms, functional genomics, and integrative approaches can empower the discovery of novel gene-environment interactions and discuss specific methodological considerations with each approach...
October 1, 2017: American Journal of Epidemiology
https://www.readbyqxmd.com/read/28957327/up-for-a-challenge-u4c-stimulating-innovation-in-breast-cancer-genetic-epidemiology
#4
EDITORIAL
Leah E Mechanic, Sara Lindström, Kenneth M Daily, Solveig K Sieberts, Christopher I Amos, Huann-Sheng Chen, Nancy J Cox, Marina Dathe, Eric J Feuer, Michael J Guertin, Joshua Hoffman, Yunxian Liu, Jason H Moore, Chad L Myers, Marylyn D Ritchie, Joellen Schildkraut, Fredrick Schumacher, John S Witte, Wen Wang, Scott M Williams, Elizabeth M Gillanders
No abstract text is available yet for this article.
September 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28944497/evolutionarily-derived-networks-to-inform-disease-pathways
#5
Britney E Graham, Christian Darabos, Minjun Huang, Louis J Muglia, Jason H Moore, Scott M Williams
Methods to identify genes or pathways associated with complex diseases are often inadequate to elucidate most risk because they make implicit and oversimplified assumptions about underlying models of disease etiology. These can lead to incomplete or inadequate conclusions. To address this, we previously developed human phenotype networks (HPN), linking phenotypes based on shared biology. However, such visualization alone is often uninterpretable, and requires additional filtering. Here, we expand the HPN to include another method, evolutionary triangulation (ET)...
September 25, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28770004/discovery-and-replication-of-snp-snp-interactions-for-quantitative-lipid-traits-in-over-60-000-individuals
#6
Emily R Holzinger, Shefali S Verma, Carrie B Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E Furlong, Tom R Gaunt, Daniel Seung Kim, Helene Riess, Suthesh Sivapalaratnam, Vinicius Tragante, Erik P A van Iperen, Ariel Brautbar, David S Carrell, David R Crosslin, Gail P Jarvik, Helena Kuivaniemi, Iftikhar J Kullo, Eric B Larson, Laura J Rasmussen-Torvik, Gerard Tromp, Jens Baumert, Karen J Cruickshanks, Martin Farrall, Aroon D Hingorani, G K Hovingh, Marcus E Kleber, Barbara E Klein, Ronald Klein, Wolfgang Koenig, Leslie A Lange, Winfried Mӓrz, Kari E North, N Charlotte Onland-Moret, Alex P Reiner, Philippa J Talmud, Yvonne T van der Schouw, James G Wilson, Mika Kivimaki, Meena Kumari, Jason H Moore, Fotios Drenos, Folkert W Asselbergs, Brendan J Keating, Marylyn D Ritchie
BACKGROUND: The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits: low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), total cholesterol (TC), and triglycerides (TG). RESULTS: Our analysis consisted of a discovery phase using a merged dataset of five different cohorts (n = 12,853 to n = 16,849 depending on lipid phenotype) and a replication phase with ten independent cohorts totaling up to 36,938 additional samples...
2017: BioData Mining
https://www.readbyqxmd.com/read/28628665/a-chromosome-5q31-1-locus-associates-with-tuberculin-skin-test-reactivity-in-hiv-positive-individuals-from-tuberculosis-hyper-endemic-regions-in-east-africa
#7
Rafal S Sobota, Catherine M Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P Igo, Albert Magohe, LaShaunda L Malone, Keith Chervenak, Noemi B Hall, Mecky Matee, Harriet Mayanja-Kizza, Moses Joloba, Jason H Moore, William K Scott, Timothy Lahey, W Henry Boom, C Fordham von Reyn, Scott M Williams, Giorgio Sirugo
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28617599/effects-of-the-adulteration-technique-on-the-near-infrared-detection-of-melamine-in-milk-powder
#8
COMPARATIVE STUDY
Peter F Scholl, Marti Mamula Bergana, Betsy Jean Yakes, Zhuohong Xie, Steven Zbylut, Gerard Downey, Magdi Mossoba, Joseph Jablonski, Robert Magaletta, Stephen E Holroyd, Martin Buehler, Jianwei Qin, William Hurst, Joseph H LaPointe, Dean Roberts, Carol Zrybko, Andrew Mackey, Jason D Holton, Greg A Israelson, Anitra Payne, Moon S Kim, Kuanglin Chao, Jeffrey C Moore
The United States Pharmacopeial Convention has led an international collaborative project to develop a toolbox of screening methods and reference standards for the detection of milk powder adulteration. During the development of adulterated milk powder reference standards, blending methods used to combine melamine and milk had unanticipated strong effects on the near-infrared (NIR) spectrum of melamine. The prominent absorbance band at 1468 nm of melamine was retained when it was dry-blended with skim milk powder but disappeared in wet-blended mixtures, where spray-dried milk powder samples were prepared from solution...
July 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28612213/influence-of-substance-use-disorders-on-2-year-hiv-care-retention-in-the-united-states
#9
Bryan Hartzler, Julia C Dombrowski, Jason R Williams, Heidi M Crane, Joseph J Eron, Elvin H Geng, Christopher Mathews, Kenneth H Mayer, Richard D Moore, Michael J Mugavero, Sonia Napravnik, Benigno Rodriguez, Dennis M Donovan
Substance use disorders (SUDs) are thought to predict care discontinuity, though magnitude and substance-specific variance of effects are unclear. This report of analytic work undertaken with a multi-regional American cohort of 9153 care enrollees addresses these gaps. Care retention was computed from 24-month post-linkage clinic visit documentation, with SUD cases identified from patient-report screening instruments. Two generalized estimating equations tested binary and hierarchial SUD predictors of retention, and potential effect modification by patient age-group, sex, and care site...
June 13, 2017: AIDS and Behavior
https://www.readbyqxmd.com/read/28575147/tissue-specific-network-based-genome-wide-study-of-amygdala-imaging-phenotypes-to-identify-functional-interaction-modules
#10
Xiaohui Yao, Jingwen Yan, Kefei Liu, Sungeun Kim, Kwangsik Nho, Shannon L Risacher, Casey S Greene, Jason H Moore, Andrew J Saykin, Li Shen
Motivation: Network-based genome-wide association studies (GWAS) aim to identify functional modules from biological networks that are enriched by top GWAS findings. Although gene functions are relevant to tissue context, most existing methods analyze tissue-free networks without reflecting phenotypic specificity. Results: We propose a novel module identification framework for imaging genetic studies using the tissue-specific functional interaction network. Our method includes three steps: 1) re-prioritize imaging GWAS findings by applying machine learning methods to incorporate network topological information and enhance the connectivity among top genes; 2) detect densely connected modules based on interactions among top re-prioritized genes; and 3) identify phenotype-relevant modules enriched by top GWAS findings...
May 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28572842/grid-based-stochastic-search-for-hierarchical-gene-gene-interactions-in-population-based-genetic-studies-of-common-human-diseases
#11
Jason H Moore, Peter C Andrews, Randal S Olson, Sarah E Carlson, Curt R Larock, Mario J Bulhoes, James P O'Connor, Ellen M Greytak, Steven L Armentrout
BACKGROUND: Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had some success, but much of the genetic architecture of common disease remains unexplained. Attention is now turning to detecting SNPs that impact disease susceptibility in the context of other genetic factors and environmental exposures. These context-dependent genetic effects can manifest themselves as non-additive interactions, which are more challenging to model using parametric statistical approaches...
2017: BioData Mining
https://www.readbyqxmd.com/read/28559929/gene-set-enrichment-analyses-lessons-learned-from-the-heart-failure-phenotype
#12
Vinicius Tragante, Johannes M I H Gho, Janine F Felix, Ramachandran S Vasan, Nicholas L Smith, Benjamin F Voight, Colin Palmer, Pim van der Harst, Jason H Moore, Folkert W Asselbergs
BACKGROUND: Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. RESULTS: Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions...
2017: BioData Mining
https://www.readbyqxmd.com/read/28538102/effects-of-wet-blending-on-detection-of-melamine-in-spray-dried-lactose
#13
Betsy Jean Yakes, Marti M Bergana, Peter F Scholl, Magdi M Mossoba, Sanjeewa R Karunathilaka, Luke K Ackerman, Jason D Holton, Boyan Gao, Jeffrey C Moore
During the development of rapid screening methods to detect economic adulteration, spray-dried milk powders prepared by dissolving melamine in liquid milk exhibited an unexpected loss of characteristic melamine features in the near-infrared (NIR) and Raman spectra. To further characterize this "wet-blending" phenomenon, spray-dried melamine and lactose samples were produced as a simplified model and investigated by NIR spectroscopy, Raman spectroscopy, proton nuclear magnetic resonance ((1)H NMR), and direct analysis in real time Fourier transform mass spectrometry (DART-FTMS)...
July 19, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28520685/pelvic-fracture-pattern-predicts-the-need-for-hemorrhage-control-intervention-results-of-an-aast-multi-institutional-study
#14
MULTICENTER STUDY
Todd W Costantini, Raul Coimbra, John B Holcomb, Jeanette M Podbielski, Richard D Catalano, Allie Blackburn, Thomas M Scalea, Deborah M Stein, Lashonda Williams, Joseph Conflitti, Scott Keeney, Christy Hoey, Tianhua Zhou, Jason Sperry, Dimitra Skiada, Kenji Inaba, Brian H Williams, Joseph P Minei, Alicia Privette, Robert C Mackersie, Brenton R Robinson, Forrest O Moore
BACKGROUND: Early identification of patients with pelvic fractures at risk of severe bleeding requiring intervention is critical. We performed a multi-institutional study to test our hypothesis that pelvic fracture patterns predict the need for a pelvic hemorrhage control intervention. METHODS: This prospective, observational, multicenter study enrolled patients with pelvic fracture due to blunt trauma. Inclusion criteria included shock on admission (systolic blood pressure <90 mm Hg or heart rate >120 beats/min and base deficit >5, and the ability to review pelvic imaging)...
June 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28450890/multi-class-computational-evolution-development-benchmark-evaluation-and-application-to-rna-seq-biomarker-discovery
#15
Nathaniel M Crabtree, Jason H Moore, John F Bowyer, Nysia I George
BACKGROUND: A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model complexity when evolving classifiers. Using Pareto optimization, a CES is able to identify a very small number of features while maintaining high classification accuracy. A CES can be designed for various types of data, and the user can exploit expert knowledge about the classification problem in order to improve discrimination between classes...
2017: BioData Mining
https://www.readbyqxmd.com/read/28445112/tracking-the-evolution-of-non-small-cell-lung-cancer
#16
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal, Max Salm, Stuart Horswell, Mickael Escudero, Nik Matthews, Andrew Rowan, Tim Chambers, David A Moore, Samra Turajlic, Hang Xu, Siow-Ming Lee, Martin D Forster, Tanya Ahmad, Crispin T Hiley, Christopher Abbosh, Mary Falzon, Elaine Borg, Teresa Marafioti, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Rajesh Shah, Leena Joseph, Anne M Quinn, Phil A Crosbie, Babu Naidu, Gary Middleton, Gerald Langman, Simon Trotter, Marianne Nicolson, Hardy Remmen, Keith Kerr, Mahendran Chetty, Lesley Gomersall, Dean A Fennell, Apostolos Nakas, Sridhar Rathinam, Girija Anand, Sajid Khan, Peter Russell, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Jason F Lester, Malgorzata Kornaszewska, Richard Attanoos, Haydn Adams, Helen Davies, Stefan Dentro, Philippe Taniere, Brendan O'Sullivan, Helen L Lowe, John A Hartley, Natasha Iles, Harriet Bell, Yenting Ngai, Jacqui A Shaw, Javier Herrero, Zoltan Szallasi, Roland F Schwarz, Aengus Stewart, Sergio A Quezada, John Le Quesne, Peter Van Loo, Caroline Dive, Allan Hackshaw, Charles Swanton
BACKGROUND: Among patients with non-small-cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early-stage NSCLC. METHODS: In this prospective cohort study, we performed multiregion whole-exome sequencing on 100 early-stage NSCLC tumors that had been resected before systemic therapy...
June 1, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28414475/cognitive-functioning-of-adolescent-and-young-adult-cannabis-users-in-the-philadelphia-neurodevelopmental-cohort
#17
J Cobb Scott, Daniel H Wolf, Monica E Calkins, Emily C Bach, Jennifer Weidner, Kosha Ruparel, Tyler M Moore, Jason D Jones, Chad T Jackson, Raquel E Gur, Ruben C Gur
Cannabis use in youth is rising and has been linked to deficits in cognitive functioning. However, cognitive findings have primarily been based on small samples of users seeking treatment, and few studies have evaluated cognition in occasional cannabis users. Here, we examined 4,568 adolescents and young adults (ages 14-21 years) drawn from the Philadelphia Neurodevelopmental Cohort, a prospective, population-based study. Participants were classified as cannabis Non-Users (n = 3,401), Occasional Users (twice per week or less; n = 940), or Frequent Users (>3 times per week; n = 227)...
June 2017: Psychology of Addictive Behaviors: Journal of the Society of Psychologists in Addictive Behaviors
https://www.readbyqxmd.com/read/28408189/genetic-effects-on-the-correlation-structure-of%C3%A2-cvd-risk-factors-exome-wide-data-from-a-ghanaian-population
#18
REVIEW
Nuri Kodaman, Rafal S Sobota, Folkert W Asselbergs, Matthew T Oetjens, Jason H Moore, Nancy J Brown, Melinda C Aldrich, Scott M Williams
Plasma concentration of plasminogen activator inhibitor-1 (PAI-1) is highly correlated with several cardiovascular disease (CVD) risk factors. It also plays a direct role in CVD, including myocardial infarction and stroke, by impeding the dissolution of thrombi in the blood. Insofar as PAI-1 links CVD's risk factors to its endpoints, genetic variants modulating the relationship between PAI-1 and risk factors may be of particular clinical and biological interest. The high heritability of PAI-1, which has not been explained by genetic association studies, may also, in large part, be due to this relationship with CVD risk factors...
June 2017: Global Heart
https://www.readbyqxmd.com/read/28338600/pelvic-fracture-pattern-predicts-the-need-for-hemorrhage-control-intervention-results-of-a-aast-multi-institutional-study
#19
Todd W Costantini, Raul Coimbra, John B Holcomb, Jeanette M Podbielski, Richard Catalano, Allie Blackburn, Thomas M Scalea, Deborah M Stein, Lashonda Williams, Joseph Conflitti, Scott Keeney, Christy Hoey, Tianhua Zhou, Jason Sperry, Dimitra Skiada, Kenji Inaba, Brian H Williams, Joseph P Minei, Alicia Privette, Robert C Mackersie, Brenton R Robinson, Forrest O Moore
BACKGROUND: Early identification of patients with pelvic fractures at risk for severe bleeding requiring intervention is critical. We performed a multi-institutional study to test our hypothesis that pelvic fracture patterns predict the need for a pelvic hemorrhage control intervention. METHODS: This prospective, observational multi-center study enrolled patients with pelvic fracture due to blunt trauma. Inclusion criteria included shock on admission (SBP<90 or HR>120 and base deficit > 5, and the ability to review pelvic imaging...
March 23, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28271566/minimum-lymph-node-yield-in-elective-level-i-iii-neck-dissection
#20
Jason D Pou, Blair M Barton, Claire M Lawlor, Christopher H Frederick, Brian A Moore, Christian P Hasney
OBJECTIVES/HYPOTHESIS: Unlike lymphadenectomy at other sites, there is no discrete lymph node count defining an adequate neck dissection. The purpose of this study was to determine the minimum lymph node yield (LNY) of an elective level I-III neck dissection required to reliably capture any positive nodes present in these nodal basins. STUDY DESIGN: Retrospective single-institution analysis. METHODS: All patients with the diagnosis of head and neck squamous cell carcinoma who underwent elective level I-III neck dissection between 2004 and 2015 at our institution were analyzed...
September 2017: Laryngoscope
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