Article
Genetics & Heredity
Merve Kasap, Donard S. Dwyer
Summary: Schizophrenia is a highly heritable polygenic psychiatric disorder. Characterization of its genetic architecture may help understand the burden of risk variants and their impact on susceptibility. Using a mathematical model, this study found that schizophrenia risk genes have higher interactions with other genes, potentially amplifying the effects of risk variants. The model also suggests that the number of risk alleles required to reach susceptibility threshold is influenced by multiple factors.
Article
Plant Sciences
Mita Khatun, Md Mamun Monir, Xiangyang Lou, Jun Zhu, Haiming Xu
Summary: This study analyzed four ear traits associated with corn production and identified significant genetic factors and environmental effects that contribute to the phenotypic variations of these traits. The results also suggested that different genotype combinations in different geographical regions may be more effective and hybrid-line variety breeding could have a greater potential to improve ear traits.
Article
Multidisciplinary Sciences
Md Tauhidul Islam, Lei Xing
Summary: The authors develop a cartography strategy based on gene-gene interactions to transform high-dimensional gene expression data into a spatially configured genomap, enabling accurate deep pattern discovery. This approach presents significant challenges and opportunities in the field of single cell genomics for biomedical research. The unique cartography method captures gene interactions in the spatial configuration of genomaps, allowing for the extraction of deep genomic interaction features and the discovery of discriminative patterns in the data.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Manon A. Morin, Anneliese J. Morrison, Michael J. Harms, Rachel J. Dutton
Summary: Non-pairwise interactions, or higher-order interactions (HOIs), have been identified as significant drivers of emergent features in microbial communities. This study investigated the re-organization of microbial interactions between pairwise cultures and larger communities in a simple microbiome. The results showed a deep reorganization of interaction-associated mutants and the emergence of multiple HOIs. Furthermore, quantitative genetics analysis revealed that 82% of conserved interactions followed an additive pattern.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Katarzyna Toch, Mateusz Buczek, Marta K. Labocha
Summary: Epistasis plays an important role in evolutionary processes, but our understanding of genetic interactions in multicellular organisms is limited. By studying Caenorhabditis elegans, we found that epistasis can vary depending on environmental conditions, and most interactions are specific to a particular environment.
Article
Cell Biology
Serena Dato, Francesco De Rango, Paolina Crocco, Stefano Pallotti, Michael E. Belloy, Yann Le Guen, Michael D. Greicius, Giuseppe Passarino, Giuseppina Rose, Valerio Napolioni
Summary: Advanced age is the biggest risk factor for late-onset Alzheimer's disease (LOAD), with shared genetic signatures between LOAD and longevity. Gene-gene interactions in pathways related to insulin/IGF1 signaling, DNA repair, and oxidative stress were found to affect LOAD. These findings suggest that risk factor interactions may drive different trajectories of cognitive aging.
Article
Cell Biology
Serena Dato, Francesco De Rango, Paolina Crocco, Stefano Pallotti, Michael E. Belloy, Yann Le Guen, Michael D. Greicius, Giuseppe Passarino, Giuseppina Rose, Valerio Napolioni
Summary: Advanced age is the biggest risk factor for late-onset Alzheimer's disease (LOAD), and it shares genetic signatures with longevity. The study found evidence that pathways leading to longevity also contribute to LOAD, and identified interacting genes that are associated with survival to old age. The findings suggest that interactions of risk factors may drive different trajectories of cognitive aging.
Article
Mathematical & Computational Biology
Alena Orlenko, Jason H. Moore
Summary: The study compared different methods for feature importance estimation in real and simulated datasets with non-additive interactions. The results showed that the permutation feature importance metric provides more precise feature importance rank estimation in the presence of non-additive interactions, particularly in simulated datasets.
Article
Genetics & Heredity
Yang Da, Zuoxiang Liang, Dzianis Prakapenka
Summary: The rapid growth in genomic selection data presents unprecedented opportunities to discover and utilize complex genetic effects for improving phenotypes, but there is a lack of methodology. This study developed multifactorial methods to investigate the contributions of global low-order and local high-order epistasis effects to phenotypic variance and the accuracy of genomic prediction of quantitative traits. These methods provide a capability to evaluate the contributions of complex genetic effects to phenotypic variance and prediction accuracy and discover and utilize complex genetic effects for improving quantitative trait phenotypes.
FRONTIERS IN GENETICS
(2022)
Review
Computer Science, Interdisciplinary Applications
R. Manavalan, S. Priya
Summary: Genome-wide association studies (GWAS) help in understanding genetic variations and environmental factors in human diseases, with cancer epistasis being a significant research area. Computational methods to infer genetic interactions and the evaluation of these methods are crucial for cancer research and diagnosis.
MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING
(2021)
Article
Multidisciplinary Sciences
Brooke Sheppard, Nadav Rappoport, Po-Ru Loh, Stephan J. Sanders, Noah Zaitlen, Andy Dahl
Summary: The study introduces a model for structured polygenic epistasis called Coordinated Epistasis (CE) and proves that several recent theories of genetic architecture fall under CE. By proposing the Even-Odd (EO) test and calibrating it in various realistic biological models, evidence of CE is found in 18 out of 26 traits in the UK Biobank. The study concludes that CE is a genetic architecture dimension capturing structured, systemic forms of epistasis in complex human traits.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Public, Environmental & Occupational Health
Shiqi Lin, Xingjian Gao, Frauke Degenhardt, Yu Qian, Tianzi Liu, Xavier Farre Ramon, Syed Sibte Hadi, Manuel Romero-Gomez, Javier Fernandez, Agustin Albillos, Maria Buti Ferret, Luis Bujanda, Antonio Julia, Rafael de Cid, Rosanna Asselta, Andre Franke, Fan Liu
Summary: This study conducted a genome-wide epistasis study of COVID-19 severity and identified three significant interactions between different genes. The most significant interaction was found between rs9792388 upstream of PDGFRL and rs3025892 downstream of SNAP25, indicating a possible molecular mechanism by which SARS-CoV-2 affects the nervous system.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Demetrius DiMucci, Mark Kon, Daniel Segre
Summary: Machine learning is used to interpret biological complexity by training algorithms, and BowSaw algorithm helps identify variable combinations used for classification.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Clinical Neurology
Shuqiong Zheng, Jia Guo, Qianqian Xin, Hanga Galfalvy, Youran Ye, Na Yan, Rongrong Qian, J. John Mann, Enze Li, Xiang Xue, Honglei Yin
Summary: This study investigated the association of EPHX2 and P2X2 polymorphisms and mRNA expression with depression and suicidal behavior, as well as the mediating role of cognition in these associations. The results showed that cognitive function played a significant mediator role in the genetic effect on depression. The rs202059124 C allele was associated with increased depression risk, and P2X2 mRNA expression was related to depression. Furthermore, a haploblock (rs9331942 and rs2279590) was associated with suicide attempts. These findings suggest that EPHX2 and P2X2 genes are implicated in depression and suicidal behavior.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Article
Neurosciences
Kye Won Park, Ho-Sung Ryu, Eunsoon Shin, Yoongi Park, Sang Ryong Jeon, Seong Yoon Kim, Jae Seung Kim, Seong-Beom Koh, Sun Ju Chung
Summary: This study conducted an ethnicity-specific and sex-specific GWAS on PD in the Korean population and identified several SNPs associated with PD, including SNCA, PARK16, and LRRK2 loci. The sex-specific analysis revealed a strong association between SNCA and PARK16 loci and PD in females, while no significant SNP was found in males.
NPJ PARKINSONS DISEASE
(2023)
Article
Multidisciplinary Sciences
Chia-Ling Kuo, Olga A. Vsevolozhskaya, Dmitri V. Zaykin
Article
Cell Biology
Jeffrey S. Wieskopf, Jayanti Mathur, Walrati Limapichat, Michael R. Post, Mona Al-Qazzaz, Robert E. Sorge, Loren J. Martin, Dmitri V. Zaykin, Shad B. Smith, Kelen Freitas, Jean-Sebastien Austin, Feng Dai, Jie Zhang, Jaclyn Marcovitz, Alexander H. Tuttle, Peter M. Slepian, Sarah Clarke, Ryan M. Drenan, Jeff Janes, Shakir Al Sharari, Samantha K. Segall, Eske K. Aasvang, Weike Lai, Reinhard Bittner, Christopher I. Richards, Gary D. Slade, Henrik Kehlet, John Walker, Uwe Maskos, Jean-Pierre Changeux, Marshall Devor, William Maixner, Luda Diatchenko, Inna Belfer, Dennis A. Dougherty, Andrew I. Su, Sarah C. R. Lummis, M. Imad Damaj, Henry A. Lester, Ardem Patapoutian, Jeffrey S. Mogil
SCIENCE TRANSLATIONAL MEDICINE
(2015)
Editorial Material
Oncology
C. R. Weinberg, D. Zaykin
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2015)
Article
Oncology
Min Shi, Katie M. O'Brien, Dale P. Sandler, Jack A. Taylor, Dmitri V. Zaykin, Clarice R. Weinberg
BREAST CANCER RESEARCH AND TREATMENT
(2017)
Article
Biochemistry & Molecular Biology
Katie M. O'Brien, Min Shi, Dale P. Sandler, Jack A. Taylor, Dmitri V. Zaykin, Jean Keller, Alison S. Wise, Clarice R. Weinberg
EUROPEAN JOURNAL OF HUMAN GENETICS
(2016)
Article
Genetics & Heredity
Olga A. Vsevolozhskaya, Dmitri V. Zaykin, David A. Barondess, Xiaoren Tong, Sneha Jadhav, Qing Lu
GENETIC EPIDEMIOLOGY
(2016)
Article
Neurosciences
Jing Dong, Annah Wyss, Jingyun Yang, T. Ryan Price, Aude Nicolas, Michael Nalls, Greg Tranah, Nora Franceschini, Zongli Xu, Claudia Schulte, Alvaro Alonso, Steven R. Cummings, Myriam Fornage, Dmitri Zaykin, Leping Li, Xuemei Huang, Stephen Kritchevsky, Yongmei Liu, Thomas Gasser, Robert S. Wilson, Philip L. De Jager, Andrew B. Singleton, Jayant M. Pinto, Tamara Harris, Thomas H. Mosley, David A. Bennett, Stephanie London, Lei Yu, Honglei Chen
MOLECULAR NEUROBIOLOGY
(2017)
Article
Genetics & Heredity
Olga A. Vsevolozhskaya, Chia-Ling Kuo, Gabriel Ruiz, Luda Diatchenko, Dmitri V. Zaykin
GENETIC EPIDEMIOLOGY
(2017)
Article
Medicine, Research & Experimental
Loren J. Martin, Shad B. Smith, Arkady Khoutorsky, Claire A. Magnussen, Alexander Samoshkin, Robert E. Sorge, Chulmin Cho, Noosha Yosefpour, Sivaani Sivaselvachandran, Sarasa Tohyama, Tiffany Cole, Thang M. Khuong, Ellen Mir, Dustin G. Gibson, Jeffrey S. Wieskopf, Susana G. Sotocinal, Jean Sebastien Austin, Carolina B. Meloto, Joseph H. Gitt, Christos Gkogkas, Nahum Sonenberg, Joel D. Greenspan, Roger B. Fillingim, Richard Ohrbach, Gary D. Slade, Charles Knott, Ronald Dubner, Andrea G. Nackley, Alfredo Ribeiro-da-Silva, G. Gregory Neely, William Maixner, Dmitri V. Zaykin, Jeffrey S. Mogil, Luda Diatchenko
JOURNAL OF CLINICAL INVESTIGATION
(2017)
Article
Psychiatry
Olga Vsevolozhskaya, Gabriel Ruiz, Dmitri Zaykin
TRANSLATIONAL PSYCHIATRY
(2017)
Article
Biochemistry & Molecular Biology
Katerina Zorina-Lichtenwalter, Ryan N. Lichtenwalter, Dima V. Zaykin, Marc Parisien, Simon Gravel, Andrey Bortsov, Luda Diatchenko
HUMAN MOLECULAR GENETICS
(2019)
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Anesthesiology
Shad B. Smith, Marc Parisien, Eric Bair, Inna Belfer, Anne-Julie Chabot-Dore, Pavel Gris, Samar Khoury, Shannon Tansley, Yelizaveta Torosyan, Dmitri Zaykin, Olaf Bernhardt, Priscila de Oliveira Serrano, Richard Gracely, Deepti Jain, Marjo-Riitta Jaervelin, Linda Kaste, Kathleen Kerr, Thomas Kocher, Raija Lahdesmaki, Nadia Laniado, Cathy Laurie, Cecelia Laurie, Minna Mannikko, Carolina Meloto, Andrea Nackley, Sarah Nelson, Paula Pesonen, Margarete Ribeiro-Dasilva, Celia Rizzatti-Barbosa, Anne Sanders, Christian Schwahn, Kirsi Sipila, Tamar Sofer, Alexander Teumer, Jeffrey Mogil, Roger Fillingim, Joel Greenspan, Richard Ohrbach, Gary Slade, William Maixner, Luda Diatchenko
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Anesthesiology
Rodrigo Benavides, Olga Vsevolozhskaya, Stefano Cattaneo, Dmitri Zaykin, Ashley Brenton, Marc Parisien, Vivek Verma, Samar Khoury, Ian Gilron, Luda Diatchenko
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Genetics & Heredity
Olga A. Vsevolozhskaya, Fengjiao Hu, Dmitri Zaykin
FRONTIERS IN GENETICS
(2019)
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Genetics & Heredity
Olga A. Vsevolozhskaya, Dmitri V. Zaykin
GENETIC EPIDEMIOLOGY
(2020)