Review
Biochemistry & Molecular Biology
Clara de Jorge Martinez, Gull Rukh, Michael J. Williams, Santino Gaudio, Samantha Brooks, Helgi B. Schioth
Summary: Anorexia nervosa is a complex disorder with strong genetic components, and it often overlaps with other disorders. Recent advances in genetics have provided insights into the molecular pathways and potential origins of the disease.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Computer Science, Interdisciplinary Applications
Xinyue Wang, Xiaoqian Jiang, Jaideep Vaidya
Summary: The paper proposes two algorithms for generating synthetic SNPs that are indistinguishable from real SNPs. Through game theoretic analysis, it demonstrates the possibility of incentivizing honest behavior by the server. Extensive experiments show that the proposed method can ensure efficient and trustworthy outsourcing of logistic regression for GWAS.
JOURNAL OF BIOMEDICAL INFORMATICS
(2021)
Article
Multidisciplinary Sciences
Xiaoyu Liang, Xuewei Cao, Qiuying Sha, Shuanglin Zhang
Summary: The article introduces a novel multivariate method for phenome-wide association studies (PheWAS) and demonstrates its superiority through extensive simulation studies and real-life application. The proposed method involves hierarchical clustering, clustering linear combination, and false discovery rate control steps.
Review
Plant Sciences
Laura Tibbs Cortes, Zhiwu Zhang, Jianming Yu
Summary: Genome-wide association studies (GWAS) have become a powerful tool for investigating complex traits, with the development of the mixed model framework reducing false positives. Advances in technology have led to the development of methods to increase computational speed or improve statistical power in GWAS.
Article
Multidisciplinary Sciences
Ludivine Obry, Cyril Dalmasso
Summary: In this study, we evaluated recent weighted multiple testing procedures for genome wide association studies (GWAS) through a simulation study. We also introduced a new efficient procedure called wBHa, which prioritizes the detection of genetic variants with low minor allel frequencies while maximizing overall detection power. Our results demonstrated that wBHa outperformed other procedures in detecting rare variants while maintaining good overall power.
Review
Biochemistry & Molecular Biology
Imane Lalami, Carole Abo, Bruno Borghese, Charles Chapron, Daniel Vaiman
Summary: This review discusses the genetics of endometriosis, a common feminine disease with a genetic heritability estimated at around 50%. Large GWAS studies have identified some genes and loci associated with the disease, but a significant portion of the heritability remains unexplained. Additional efforts such as exome sequencing may be needed to fully elucidate the genetic factors of endometriosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Editorial Material
Medicine, General & Internal
Lisa Bastarache, Joshua C. Denny, Dan M. Roden
Summary: This article discusses the concept and methodology of phenome-wide association studies, which aim to identify associations between genetic variations and phenotypic traits using a dataset.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2022)
Article
Multidisciplinary Sciences
Abbas Saad Alatrany, Wasiq Khan, Abir Hussain, Dhiya Al-Jumeily
Summary: The increasing incidence of Alzheimer's disease (AD) poses socioeconomic challenges. In this study, a hybrid feature selection approach and neural network models are used to predict AD. The approach outperformed existing methods with 99% accuracy and f1-score, providing impactful outcomes for other chronic diseases.
Article
Multidisciplinary Sciences
Jack W. O'Sullivan, John P. A. Ioannidis
Summary: This study compared SNVs from earlier and later GWAS and found a replication rate of 85.0% in subsequent studies, with a lower replication rate for binary phenotypes compared to quantitative phenotypes. The study also identified a decrease in SNV effect size for binary phenotypes, but an increase for quantitative phenotypes, and developed a model that could predict SNV replication effectively.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Matteo Sesia, Stephen Bates, Emmanuel Candes, Jonathan Marchini, Chiara Sabatti
Summary: The study introduces a comprehensive statistical framework for analyzing data from genome-wide association studies of polygenic traits, demonstrating validity and effectiveness through simulations and applications to the UK Biobank data. The method outperforms state-of-the-art alternatives and is supported by comparisons with other studies, offering researchers fast software for analyzing Biobank-scale datasets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Adrian I. Campos, Shinichi Namba, Shu-Chin Lin, Kisung Nam, Julia Sidorenko, Huanwei Wang, Yoichiro Kamatani, Ling-Hua Wang, Seunggeun Lee, Yen-Feng Lin, Yen-Chen Anne Feng, Yukinori Okada, Peter M. Visscher, Loic Yengo
Summary: Simulations and applications to real data show that adjustment of genome-wide association analyses for polygenic scores increases the statistical power for discovery across all ancestries, suggesting an analytical strategy for future studies in underrepresented populations.
Article
Biochemical Research Methods
Itziar Irigoien, Bru Cormand, Maria Soler-Artigas, Cristina Sanchez-Mora, Josep-Antoni Ramos-Quiroga, Concepcion Arenas
Summary: With the rise of GWAS, the analysis of large-scale SNP data has become crucial in biomedical research. This paper proposes a new method based on genetic distances between individuals to identify disease-related SNPs in case-control studies. By considering population substructure and avoiding multiple testing issues, the method provides ordered lists of SNPs and serves as a useful tool for researchers to focus their attention in the initial stage.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Review
Multidisciplinary Sciences
David O. Enoma, Janet Bishung, Theresa Abiodun, Olubanke Ogunlana, Victor Chukwudi Osamor
Summary: This article discusses the applications and future trends of machine learning algorithms in genome-wide association studies (GWAS) to better understand the effects of population genetic variants. The study found that algorithms such as classification, regression, ensemble, and neural networks have been applied to GWAS and their application areas are comprehensively discussed.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2022)
Article
Cell Biology
Yingjie Guo, Chenxi Wu, Zhian Yuan, Yansu Wang, Zhen Liang, Yang Wang, Yi Zhang, Lei Xu
Summary: This article introduces a gene-based method to detect gene-gene interactions by adding additive constraints to the model, and experimental results show that this method outperforms previous experiments in detecting gene-gene interactions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Boghuma K. Titanji, Marta Gwinn, Vincent C. Marconi, Yan Sun
Summary: This review summarizes the current state of epigenetic epidemiologic studies of people with HIV, identifies the main challenges of this approach, and highlights future directions for the field. Emerging epigenetic epidemiologic studies can expand our understanding of HIV infection and health outcomes, improve scientific validity through collaboration and replication, and increase the research coverage of diverse populations affected by the global HIV pandemic.
CLINICAL EPIGENETICS
(2022)
Article
Nutrition & Dietetics
Eugene Kobyliansky, Dmitry Torchinsky, Leonid Kalichman, David Karasik
AMERICAN JOURNAL OF CLINICAL NUTRITION
(2016)
Article
Endocrinology & Metabolism
M. Raygorodskaya, Y. Gabet, C. Shochat, E. Kobyliansky, A. Torchinsky, D. Karasik
Article
Biochemistry & Molecular Biology
Yi-Hsiang Hsu, Guo Li, Ching-Ti Liu, Jennifer A. Brody, David Karasik, Wen-Chi Chou, Serkalem Demissie, Kannabiran Nandakumar, Yanhua Zhou, Chia-Ho Cheng, Richard Gill, Richard A. Gibbs, Donna Muzny, Jireh Santibanez, Karol Estrada, Fernando Rivadeneira, Tamara Harris, Vilmundur Gudnason, Andre Uitterlinden, Bruce M. Psaty, John A. Robbins, L. Adrienne Cupples, Douglas P. Kiel
HUMAN MOLECULAR GENETICS
(2016)
Article
Endocrinology & Metabolism
David Karasik, Serkalem Demissie, Yanhua Zhou, Darlene Lu, Kerry E. Broe, Mary L. Bouxsein, L. Adrienne Cupples, Douglas P. Kiel
JOURNAL OF BONE AND MINERAL RESEARCH
(2017)
Article
Endocrinology & Metabolism
Carrie M. Nielson, Ching-Ti Liu, Albert V. Smith, Cheryl L. Ackert-Bicknell, Sjur Reppe, Johanna Jakobsdottir, Christina Wassel, Thomas C. Register, Ling Oei, Nerea Alonso, Edwin H. Oei, Neeta Parimi, Elizabeth J. Samelson, Mike A. Nalls, Joseph Zmuda, Thomas Lang, Mary Bouxsein, Jeanne Latourelle, Melina Claussnitzer, Kristin Siggeirsdottir, Priya Srikanth, Erik Lorentzen, Liesbeth Vandenput, Carl Langefeld, Laura Raffield, Greg Terry, Amanda J. Cox, Matthew A. Allison, Michael H. Criqui, Don Bowden, M. Arfan Ikram, Dan Mellstrom, Magnus K. Karlsson, John Carr, Matthew Budoff, Caroline Phillips, L. Adrienne Cupples, Wen-Chi Chou, Richard H. Myers, Stuart H. Ralston, Kaare M. Gautvik, Peggy M. Cawthon, Steven Cummings, David Karasik, Fernando Rivadeneira, Vilmundur Gudnason, Eric S. Orwoll, Tamara B. Harris, Claes Ohlsson, Douglas P. Kiel, Yi-Hsiang Hsu
JOURNAL OF BONE AND MINERAL RESEARCH
(2016)
Article
Endocrinology & Metabolism
Michelle S. Yau, Serkalem Demissie, Yanhua Zhou, Dennis E. Anderson, Amanda L. Lorbergs, Douglas P. Kiel, Brett T. Allaire, Laiji Yang, L. Adrienne Cupples, Thomas G. Travison, Mary L. Bouxsein, David Karasik, Elizabeth J. Samelson
JOURNAL OF BONE AND MINERAL RESEARCH
(2016)
Article
Clinical Neurology
Kazuko Shem, Darlene Karasik, Paul Carufel, Ming-Chih Kao, Patricia Zheng
JOURNAL OF SPINAL CORD MEDICINE
(2016)
Article
Biochemistry & Molecular Biology
A. Hinney, M. Kesselmeier, S. Jall, A-L Volckmar, M. Foecker, J. Antel, I. M. Heid, T. W. Winkler, S. F. A. Grant, Y. Guo, A. W. Bergen, W. Kaye, W. Berrettini, H. Hakonarson, B. Herpertz-Dahlmann, M. de Zwaan, W. Herzog, S. Ehrlich, S. Zipfel, K. M. Egberts, R. Adan, M. Brandys, A. van Elburg, V. Boraska Perica, C. S. Franklin, M. H. Tschoep, E. Zeggini, C. M. Bulik, D. Collier, A. Scherag, T. D. Mueller, J. Hebebrand
MOLECULAR PSYCHIATRY
(2017)
Review
Rheumatology
David Karasik, Fernando Rivadeneira, Mark L. Johnson
NATURE REVIEWS RHEUMATOLOGY
(2016)
Article
Cell Biology
L. C. Pilling, R. Joehanes, T. Kacprowski, M. Peters, R. Jansen, D. Karasik, D. P. Kiel, L. W. Harries, A. Teumer, J. Powell, D. Levy, H. Lin, K. Lunetta, P. Munson, S. Bandinelli, W. Henley, D. Hernandez, A. Singleton, T. Tanaka, G. van Grootheest, A. Hofman, A. G. Uitterlinden, R. Biffar, S. Glaeser, G. Homuth, C. Malsch, U. Voelker, B. Penninx, J. B. J. van Meurs, L. Ferrucci, T. Kocher, J. Murabito, D. Melzer
PHYSIOLOGICAL GENOMICS
(2016)
Article
Cell Biology
Miri Cohen-Zinder, Aviv Asher, Ehud Lipkin, Roi Feingersch, Rotem Agmon, David Karasik, Arieh Brosh, Ariel Shabtay
PHYSIOLOGICAL GENOMICS
(2016)
Article
Materials Science, Biomaterials
Deepak Kumar Khajuria, Ramakrishna Vasireddi, Martin Trebbin, David Karasik, Rema Razdan
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS
(2017)
Review
Genetics & Heredity
Erika Kague, David Karasik
Summary: The advancement of human genomics has revolutionized our understanding of genetic architecture in skeletal diseases. Interpreting results from association studies remains a challenge due to non-coding index variants. Animal models, such as zebrafish, offer a systematic functional investigation to bridge this gap and help identify causal mechanisms.
Article
Nutrition & Dietetics
Lihi Grinberg, Fadwa Dabbah Assadi, Gideon Baum, Romy Zemel, Ran Tur-Kaspa, Chen Shochat, David Karasik, Marcela V. V. Karpuj
Summary: Non-alcoholic fatty liver disease (NAFLD) is a major cause of chronic liver disease, cirrhosis, and hepatocellular carcinoma, resulting from excessive liver fat accumulation. Vitamin D (VitD) plays multiple important roles in diverse physiological processes. This study explores the role of VitD in NAFLD pathogenesis and its potential therapeutic role in NAFLD treatment through the induction of NAFLD in zebrafish and the monitoring of VitD supplementation effects.
Article
Cell Biology
Dan Ben-Avraham, David Karasik, Joe Verghese, Kathryn L. Lunetta, Jennifer A. Smith, John D. Eicher, Rotem Vered, Joris Deelen, Alice M. Arnold, Aron S. Buchman, Toshiko Tanaka, Jessica D. Faul, Maria Nethander, Myriam Fornage, Hieab H. Adams, Amy M. Matteini, Michele L. Callisaya, Albert V. Smith, Lei Yu, Philip L. De Jager, Denis A. Evans, Vilmundur Gudnason, Albert Hofman, Alison Pattie, Janie Corley, Lenore J. Launer, Davis S. Knopman, Neeta Parimi, Stephen T. Turner, Stefania Bandinelli, Marian Beekman, Danielle Gutman, Lital Sharvit, Simon P. Mooijaart, David C. Liewald, Jeanine J. Houwing-Duistermaat, Claes Ohlsson, Matthijs Moed, Vincent J. Verlinden, Dan Mellstrom, Jos N. van der Geest, Magnus Karlsson, Dena Hernandez, Rebekah McWhirter, Yongmei Liu, Russell Thomson, Gregory J. Tranah, Andre G. Uitterlinden, David R. Weir, Wei Zhao, John M. Starr, Andrew D. Johnson, M. Arfan Ikram, David A. Bennett, Steven R. Cummings, Ian J. Deary, Tamara B. Harris, Sharon L. R. Kardia, Thomas H. Mosley, Velandai K. Srikanth, Beverly G. Windham, Ann B. Newman, Jeremy D. Walston, Gail Davies, Daniel S. Evans, Eline P. Slagboom, Luigi Ferrucci, Douglas P. Kiel, Joanne M. Murabito, Gil Atzmon