Article
Genetics & Heredity
Seyed Mehdi Esmaeili-Fard, Mohsen Gholizadeh, Seyed Hasan Hafezian, Rostam Abdollahi-Arpanahi
Summary: In this study, alternative genome-wide association study (GWAS) approaches were used on the genome of Baluchi sheep to identify genes affecting pregnancy outcomes and lamb growth. The results revealed that calcium ion transport during pregnancy and feeding lambs by milk after parturition have the greatest impact on weight gain.
FRONTIERS IN GENETICS
(2021)
Article
Microbiology
Hongjiao Liu, Wodan Ling, Xing Hua, Jee-Young Moon, Jessica S. S. Williams-Nguyen, Xiang Zhan, Anna M. M. Plantinga, Ni Zhao, Angela Zhang, Rob Knight, Qibin Qi, Robert D. D. Burk, Robert C. C. Kaplan, Michael C. C. Wu
Summary: This study proposes a novel approach called the covariate-adjusted KRV framework to map genetic variants associated with microbiome beta-diversity. The framework evaluates the association between genetics and microbes by comparing similarity in genetic profiles to similarity in microbiome profiles across individuals. The study identifies an immunity-related gene IL23R and three other novel genes involved in immune functions or autoimmune disorders. Simulation studies show that the covariate-adjusted KRV has a greater power than other microbiome GWAS methods.
Article
Biotechnology & Applied Microbiology
Jia Wang, Yueling Fan, Lin Mao, Cunmin Qu, Kun Lu, Jiana Li, Liezhao Liu
Summary: Through genome-wide association studies (GWAS) and transcriptome analysis, we explored the genetic basis of silique length (SL) in rapeseed, identifying candidate genes related to starch and sucrose metabolism, plant hormone signal transmission, and phenylpropanoid biosynthesis. Photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play important roles in the development of rapeseed siliques.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Review
Biochemical Research Methods
Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernandez
Summary: Pathway enrichment analysis is widely used for interpreting biomedical data, but its results are influenced by various factors. Benchmark studies have evaluated these factors and identified key influences on the analysis results.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Yang Xi, Qifan Wu, Yutian Zeng, Jingjing Qi, Junpeng Li, Hua He, Hengyong Xu, Jiwei Hu, Xiping Yan, Lili Bai, Chunchun Han, Shenqiang Hu, Jiwen Wang, Hehe Liu, Liang Li
Summary: This study performed a genome wide association study to identify the genetic basis of growth rate in ducks. They found 41 significant SNPs related to growth rate, with ASAP1 and LYN genes being important candidate genes. The study also showed that growth rate can be used as a reliable predictor of adult weight.
Review
Biochemistry & Molecular Biology
Micah Silberstein, Nicholas Nesbit, Jacquelyn Cai, Phil H. Lee
Summary: Pathway analysis, also known as gene-set enrichment analysis, integrates biological knowledge into statistical analysis of high-throughput genetics data. It has led to discoveries of genes and biological mechanisms underlying common and complex disorders. Challenges include utilizing multiple layers of high-throughput genomics data and improving existing pathway analysis methods.
JOURNAL OF GENETICS AND GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Anna Kisielnicka, Marta Sobalska-Kwapis, Dorota Purzycka-Bohdan, Boguslaw Nedoszytko, Monika Zablotna, Michal Seweryn, Dominik Strapagiel, Roman J. Nowicki, Adam Reich, Dominik Samotij, Justyna Szczech, Dorota Krasowska, Joanna Bartosinska, Joanna Narbutt, Aleksandra Lesiak, Paulina Barasinska, Agnieszka Owczarczyk-Saczonek, Joanna Czerwinska, Jacek C. Szepietowski, Aleksandra Batycka-Baran, Rafal Czajkowski, Magdalena Gorecka-Sokolowska, Lidia Rudnicka, Joanna Czuwara, Aneta Szczerkowska-Dobosz
Summary: This study used a Genome-Wide Association Study (GWAS) to compare the genetic background related to obesity among psoriatic patients and healthy controls. The results identified several genetic signals associated with BMI in psoriatic patients and provided insights into the understanding of the pathogenesis of obesity among this group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Chenyu Zhao, Xiaocan Jia, Yuping Wang, Zixiao Luo, Jingwen Fan, Xuezhong Shi, Yongli Yang
Summary: This study used SPU testing technique to identify shared genetic susceptibility for seven autoimmune diseases and discovered pleiotropic genes and shared pathways, which may aid in the development of common treatment approaches.
Article
Biotechnology & Applied Microbiology
Yixin Zhang, James B. Meigs, Ching-Ti Liu, Josee Dupuis, Chloe Sarnowski
Summary: Considering family history may enhance the accuracy and power of CC-GWAS in detecting disease-associated genetic variants. The methods incorporating family history showed higher power than CC-GWAS, especially in older age groups. These methods detected known genetic variants and increased their significance in real data applications, demonstrating the importance of including family history in genetic association studies.
Article
Plant Sciences
Idan Sabag, Gota Morota, Zvi Peleg
Summary: Our study investigated a sesame panel with wide phenotypic variation, identifying genetic signals associated with flowering date and yield traits, highlighting the importance of flowering date in productivity. Our results provide insights into the genetic architecture of sesame traits under Mediterranean climate conditions and may inform future breeding programs in the region.
Article
Biotechnology & Applied Microbiology
Hehe Liu, Jianmei Wang, Jian Hu, Lei Wang, Zhanbao Guo, Wenlei Fan, Yaxi Xu, Dapeng Liu, Yunsheng Zhang, Ming Xie, Jing Tang, Wei Huang, Qi Zhang, Zhengkui Zhou, Shuisheng Hou
Summary: The study found that age and sunlight can induce melanin deposition in bird beak skin, which is determined by genetic factors. Two major loci affecting melanin deposition were identified, and potential causative genes were discovered. Additionally, the study highlighted the importance of the melanin metabolism pathway in skin pigmentation.
Article
Biochemical Research Methods
Xueyuan Cao, Stan Pounds
Summary: GSDA is a powerful method for evaluating the association of gene sets with variables, capable of identifying complex non-monotonic gene-set associations that may be missed by other methods.
BMC BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Venkata Rami Reddy Yannam, Marlon Caicedo, Rosa Ana Malvar, Bernardo Ordas
Summary: The study used GWAS and genome-wide association analysis to elucidate the genetic characteristics of senescence and its impact on agronomic traits. Core senescence genes could serve as crucial candidates for future gene editing and breeding purposes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Urology & Nephrology
Stella Koutros, Lambertus A. Kiemeney, Parichoy Pal Choudhury, Roger L. Milne, Evangelina Lopez de Maturana, Yuanqing Ye, Vijai Joseph, Oscar Florez-Vargas, Lars Dyrskjot, Jonine Figueroa, Diptavo Dutta, Graham G. Giles, Michelle A. T. Hildebrandt, Kenneth Offit, Manolis Kogevinas, Elisabete Weiderpass, Marjorie L. McCullough, Neal D. Freedman, Demetrius Albanes, Charles Kooperberg, Victoria K. Cortessis, Margaret R. Karagas, Alison Johnson, Molly R. Schwenn, Dalsu Baris, Helena Furberg, Dean F. Bajorin, Olivier Cussenot, Geraldine Cancel-Tassin, Simone Benhamou, Peter Kraft, Stefano Porru, Angela Carta, Timothy Bishop, Melissa C. Southey, Giuseppe Matullo, Tony Fletcher, Rajiv Kumar, Jack A. Taylor, Philippe Lamy, Frederik Prip, Mark Kalisz, Stephanie J. Weinstein, Jan G. Hengstler, Silvia Selinski, Mark Harland, Mark Teo, Anne E. Kiltie, Adonina Tardon, Consol Serra, Alfredo Carrato, Reina Garcia-Closas, Josep Lloreta, Alan Schned, Petra Lenz, Elio Riboli, Paul Brennan, Anne Tjonneland, Thomas Otto, Daniel Ovsiannikov, Frank Volkert, Sita H. Vermeulen, K. K. Aben, Tessel E. Galesloot, Constance Turman, Immaculata De Vivo, Edward Giovannucci, David J. Hunter, Chancellor Hohensee, Rebecca Hunt, Alpa V. Patel, Wen-Yi Huang, Gudmar Thorleifsson, Manuela Gago-Dominguez, Pilar Amiano, Klaus Golka, Mariana C. Stern, Wusheng Yan, Jia Liu, Shengchao Alfred, Shilpa Katta, Amy Hutchinson, Belynda Hicks, William A. Wheeler, Mark P. Purdue, Katherine A. McGlynn, Cari M. Kitahara, Christopher A. Haiman, Mark H. Greene, Thorunn Rafnar, Nilanjan Chatterjee, Stephen J. Chanock, Xifeng Wu, Francisco X. Real, Debra T. Silverman, Montserrat Garcia-Closas, Kari Stefansson, Ludmila Prokunina-Olsson, Nuria Malats, Nathaniel Rothman
Summary: A meta-analysis of 32 studies identified novel genetic variants associated with bladder cancer risk and constructed a polygenic risk score (PRS) to stratify lifetime risk. These findings provide insights into the biological underpinnings of bladder cancer and have the potential to inform future preventive strategies.
Article
Plant Sciences
Chuanji Zhao, Meili Xie, Longbing Liang, Li Yang, Hongshi Han, Xinrong Qin, Jixian Zhao, Yan Hou, Wendong Dai, Caifu Du, Yang Xiang, Shengyi Liu, Xianqun Huang
Summary: In this study, the genetic basis of seed oil content (SOC) in rapeseed was investigated using a natural population and recombinant inbred lines (RILs). A high-density linkage map was constructed and a major QTL for SOC was identified. RNA-seq analysis revealed the metabolic pathways and candidate genes that are associated with SOC.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Neurosciences
Yiwen Zhu, Min-Jung Wang, Katherine M. Crawford, Juan Carlos Ramirez-Tapia, Alexandre A. Lussier, Kathryn A. Davis, Christiaan de Leeuw, Anne E. Takesian, Takao K. Hensch, Jordan W. Smoller, Erin C. Dunn
Summary: The study found that genes regulating sensitive periods are associated with increased depression risk, with a gene set opening sensitive periods particularly linked to vulnerability. There was also a statistical interaction identified between caregiver abuse during ages 1-5 and genetic risk for depression. These findings highlight the importance of gene-by-development interplay in understanding the complexity of depression etiology.
NEUROPSYCHOPHARMACOLOGY
(2022)
Article
Genetics & Heredity
Duncan S. Palmer, Daniel P. Howrigan, Sinead B. Chapman, Rolf Adolfsson, Nick Bass, Douglas Blackwood, Marco P. M. Boks, Chia-Yen Chen, Claire Churchhouse, Aiden P. Corvin, Nicholas Craddock, David Curtis, Arianna Di Florio, Faith Dickerson, Nelson B. Freimer, Fernando S. Goes, Xiaoming Jia, Ian Jones, Lisa Jones, Lina Jonsson, Rene S. Kahn, Mikael Landen, Adam E. Locke, Andrew M. McIntosh, Andrew McQuillin, Derek W. Morris, Michael C. O'Donovan, Roel A. Ophoff, Michael J. Owen, Nancy L. Pedersen, Danielle Posthuma, Andreas Reif, Neil Risch, Catherine Schaefer, Laura Scott, Tarjinder Singh, Jordan W. Smoller, Matthew Solomonson, David St Clair, Eli A. Stahl, Annabel Vreeker, James T. R. Walters, Weiqing Wang, Nicholas A. Watts, Robert Yolken, Peter P. Zandi, Benjamin M. Neale
Summary: Exome sequencing analysis of individuals with bipolar disorder reveals enrichment of ultra-rare protein-truncating variants in constrained genes. AKAP11 is identified as a risk gene for both bipolar disorder and schizophrenia. This study highlights the importance of rare coding variation in the development of bipolar disorder.
Article
Neurosciences
Yongbin Wei, Siemon C. de Lange, Jeanne E. Savage, Elleke Tissink, Ting Qi, Jonathan Repple, Marius Gruber, Tilo Kircher, Udo Dannlowski, Danielle Posthuma, Martijn P. van den Heuvel
Summary: This study examines the impact of genetic susceptibility to schizophrenia and bipolar disorder on brain connectivity. The findings suggest that the genetic liability of SCZ and BD is associated with normative variations in brain circuitry.
BIOLOGICAL PSYCHIATRY
(2023)
Article
Clinical Neurology
Nike Zoe Welander, Gull Rukh, Mathias Rask-Andersen, Aster V. E. Harder, Arn M. J. M. van den Maagdenberg, Helgi Birgir Schioth, Jessica Mwinyi
Summary: This study found no evidence of a shared genetic basis or of a causal association between migraine and either IBD or celiac disease. However, there were indications of causal associations between celiac disease and migraine subtypes. Further research is needed to investigate these associations.
Review
Neurosciences
Matthieu C. de Hemptinne, Danielle Posthuma
Summary: Genome-wide association studies have provided valuable insights into brain and behavioral traits, but they also raise ethical concerns regarding privacy and misuse. Better regulation and guidelines are needed to ensure responsible use of genetic data, and researchers should be cautious about the potential negative impacts of their findings.
NATURE NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Douglas P. Wightman, Jeanne E. Savage, Christiaan A. de Leeuw, Iris E. Jansen, Danielle Posthuma
Summary: Proxy phenotypes based on parental diagnosis status have been used to identify common variants associated with Alzheimer's disease, but rare variants have not been investigated. In this study, a proxy phenotype for Alzheimer's disease/dementia was generated for a large population cohort and rare variant aggregation analyses successfully identified genes associated with the proxy phenotype. Three of these genes were replicated in an independent cohort and have been previously linked to clinically diagnosed Alzheimer's disease. This study demonstrates the utility of proxy phenotypes in identifying genes associated with Alzheimer's disease through rare variant aggregation.
SCIENTIFIC REPORTS
(2023)
Editorial Material
Multidisciplinary Sciences
Emil Uffelmann, Danielle Posthuma, Wouter J. Peyrot
SCIENTIFIC REPORTS
(2023)
Article
Psychiatry
Pritesh Jain, Tyne Miller-Fleming, Apostolia R. Topaloudi, Dongmei K. Yu, Petros Drineas, Marianthi Georgitsi, Zhiyu Yang, Renata Rizzo, Kirsten R. Mueller-Vahl, Zeynep A. Tumer, Nanette Mol Debes, Andreas S. Hartmann, Christel E. Depienne, Yulia S. Worbe, Pablo Mir, Danielle C. Cath, Dorret Boomsma, Veit Roessner, Tomasz Wolanczyk, Piotr Janik, Natalia Szejko, Cezary Zekanowski, Csaba Barta, Zsofia Nemoda, Zsanett Tarnok, Joseph D. Buxbaum, Dorothy Grice, Jeffrey Glennon, Hreinn Stefansson, Bastian Hengerer, Noa Benaroya-Milshtein, Francesco Cardona, Tammy Hedderly, Isobel Heyman, Chaim Huyser, Astrid Morer, Norbert Mueller, Alexander Munchau, Kerstin J. Plessen, Cesare Porcelli, Susanne Walitza, Anette Schrag, Davide Martino, Andrea Dietrich, Carol A. Mathews, Jeremiah M. Scharf, Pieter J. Hoekstra, Lea K. Davis, Peristera Paschou
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Neurosciences
Elleke Tissink, Josefin Werme, Siemon C. de Lange, Jeanne E. Savage, Yongbin Wei, Christiaan A. de Leeuw, Mats Nagel, Danielle Posthuma, Martijn P. van den Heuvel
Summary: This study explores the genetic component of structural and functional connections within resting-state networks (RSNs) and their potential impact on brain disorders. It identifies genes involved in axon guidance and synaptic functioning in the visual network, and reveals the genetic overlap between RSN-FC alterations and brain disorders.
Article
Biochemistry & Molecular Biology
Daniel S. Malawsky, Eva van Walree, Benjamin M. Jacobs, Teng Hiang Heng, Qin Qin Huang, Ataf H. Sabir, Saadia Rahman, Saghira Malik Sharif, Ahsan Khan, Masa Umicevic Mirkov, Hiroyuki Kuwahara, Xin Gao, Fowzan S. Alkuraya, Danielle Posthuma, William G. Newman, Christopher J. Griffiths, Rohini Mathur, David A. van Heel, Sarah Finer, Jared O'Connell, Hilary C. Martin
Summary: This study investigated the association between autozygosity and common diseases, and discovered an effective method to reduce confounding. The results suggest that autozygosity has significant impact on common diseases, especially for type 2 diabetes among British Pakistanis.
Article
Geriatrics & Gerontology
Douglas P. Wightman, Jeanne E. Savage, Elleke Tissink, Cato Romero, Iris E. Jansen, Danielle Posthuma
Summary: Neurodegenerative diseases are a group of disorders characterized by neuronal cell death, causing various physical and mental problems. This study identified genetic overlap between three or more neurodegenerative disorders, including shared genetic loci, important genes, and tissues. These findings are important for understanding and treating neurodegenerative diseases.
NEUROBIOLOGY OF AGING
(2023)
Article
Neurosciences
Vera Fominykh, Alexey A. Shadrin, Piotr P. Jaholkowski, Shahram Bahrami, Lavinia Athanasiu, Douglas P. Wightman, Emil Uffelmann, Danielle Posthuma, Geir Selbaek, Anders M. Dale, Srdjan Djurovic, Oleksandr Frei, Ole A. Andreassen
Summary: This study found shared genetic loci between Alzheimer's disease (AD) and Multiple Sclerosis (MS), indicating the commonalities and associations between these diseases in terms of genetic susceptibility. These shared loci are involved in inflammation and neurodegeneration, suggesting potential shared pathological mechanisms.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Clinical Neurology
Lei S. Zhao, Wenhui Zhao, Jin Cao, Yiheng Tu
Summary: This study used genetic data and Mendelian randomization (MR) to reveal the causal relationship between migraine and microstructural white matter (WM). Specifically, the study found that the mode of anisotropy (MO) of the left inferior fronto-occipital fasciculus and the orientation dispersion index (OD) of the right posterior thalamic radiation exerted significant causal effects on migraine. Migraine also had a significant causal effect on the OD of the left superior cerebellar peduncle.
JOURNAL OF HEADACHE AND PAIN
(2023)
