Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Behavioral Sciences
Konstantinos Voskarides, Nefeli Giannopoulou, Rasha Eid, Konstantinos Parperis, Andreas Chatzittofis
Summary: Several studies have confirmed the association between autoimmune diseases and psychiatric disorders, with genetic evidence supporting this link. This study aimed to investigate the genetic linkage between genetic variants predisposing to autoimmune diseases and psychiatric disorders by constructing common haplotypes. The results showed multiple chromosomal regions containing genetic variants associated with both diseases, and specific genetic haplotypes were identified. Notably, six autoimmune diseases shared a common haplotype with psychiatric diseases at the HLA locus 6p21-22.
BRAIN AND BEHAVIOR
(2023)
Article
Clinical Neurology
Gie Ken-Dror, Ioana Cotlarciuc, Ida Martinelli, Elvira Grandone, Sini Hiltunen, Erik Lindgren, Maurizio Margaglione, Veronique Le Cam Duchez, Aude Bagan Triquenot, Marialuisa Zedde, Michelangelo Mancuso, Ynte M. Ruigrok, Thomas Marjot, Brad Worrall, Jennifer J. Majersik, Tiina M. Metso, Jukka Putaala, Elena Haapaniemi, Susanna M. Zuurbier, Matthijs C. Brouwer, Serena M. Passamonti, Maria Abbattista, Paolo Bucciarelli, Braxton D. Mitchell, Steven J. Kittner, Robin Lemmens, Christina Jern, Emanuela Pappalardo, Paolo Costa, Marina Colombi, Diana Aguiar de Sousa, Sofia Rodrigues, Patricia Canhao, Aleksander Tkach, Rosa Santacroce, Giovanni Favuzzi, Antonio Arauz, Donatella Colaizzo, Kostas Spengos, Amanda Hodge, Reina Ditta, Alessandro Pezzini, Stephanie Debette, Jonathan M. Coutinho, Vincent Thijs, Katarina Jood, Guillaume Pare, Turgut Tatlisumak, Jose M. Ferro, Pankaj Sharma
Summary: A genome-wide association study identified new genetic variants influencing susceptibility to CVT, with the discovery validated in an independent European cohort. These findings provide important new insights into the pathophysiology of CVT.
ANNALS OF NEUROLOGY
(2021)
Article
Genetics & Heredity
Michal Marczyk, Agnieszka Macioszek, Joanna Tobiasz, Joanna Polanska, Joanna Zyla
Summary: The study evaluated the impact of different integration methods and linkage disequilibrium correction on multiple GSA algorithms, with CERNO and MAGENTA combined with Stouffer method showing the most efficiency. LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. The best performance was observed when using Fisher or Stouffer integration with LD correction.
FRONTIERS IN GENETICS
(2021)
Article
Clinical Neurology
Alexander M. Kulminski, Ian Philipp, Yury Loika, Liang He, Irina Culminskaya
Summary: The protective role of the apolipoprotein E (APOE) epsilon 2 allele in Alzheimer's disease (AD) may be influenced by different immunomodulation functions of TOMM40 and APOE variants in a sex-specific manner, defining a more homogeneous AD-protective epsilon 2/epsilon 3-bearing profile in men.
ALZHEIMERS & DEMENTIA
(2021)
Article
Plant Sciences
Qiuping Tan, Sen Li, Yuzheng Zhang, Min Chen, Binbin Wen, Shan Jiang, Xiude Chen, Xiling Fu, Dongmei Li, Hongyu Wu, Yong Wang, Wei Xiao, Ling Li
Summary: This study presents de novo genome assemblies for five Prunus species and identifies associations between key agricultural traits and specific genetic loci, such as the OVATE transcription factor, NAC transcription factor, and microRNA172d. The findings suggest the importance of parallel evolution in the diversification of commercially important domesticated species. These genomic resources will aid in functional genomics, evolutionary research, and agronomic improvement. Structural variant-based GWASs can be used across various plant species, animals, and humans for precise identification of candidate genes and genetic architecture components.
HORTICULTURE RESEARCH
(2021)
Article
Biology
Francesc Coll, Theodore Gouliouris, Sebastian Bruchmann, Jody Phelan, Kathy E. Raven, Taane G. Clark, Julian Parkhill, Sharon J. Peacock
Summary: PowerBacGWAS is a computational pipeline that performs power calculations for bacterial genome-wide association studies using existing genomic data. This tool implements two alternative approaches for power calculations and can determine sample sizes required to detect causal variants of different minor allele frequencies, effect sizes, and phenotype heritability. It can also be applied to other bacterial populations to determine statistically significant associations or detectable associations with a given sample size.
COMMUNICATIONS BIOLOGY
(2022)
Review
Genetics & Heredity
William R. Reay, Murray J. Cairns
Summary: Genome-wide association studies have provided important biological insights into complex diseases, offering opportunities for drug repurposing. Leveraging common variant genetics through approaches such as single-loci mapping to drug targets, transcriptome-wide association studies, gene-set association, causal inference by Mendelian randomization, and polygenic scoring, researchers aim to identify new treatment options more efficiently.
NATURE REVIEWS GENETICS
(2021)
Article
Nutrition & Dietetics
Jiawen Xu, Shuai Li, Yi Zeng, Haibo Si, Yuangang Wu, Shaoyun Zhang, Bin Shen
Summary: Osteoporosis (OP) is the most common bone disease. This study explored the relationship between OP and dietary habits using a large-scale genome-wide association study (GWAS). The analysis identified seven candidate dietary habits that showed genetic associations with OP, and found a causal relationship between OP and certain dietary habits such as butter consumption, decaffeinated coffee consumption, overall processed meat intake, monthly alcohol consumption, and daily servings of raw vegetables.
Article
Plant Sciences
Behailu Mulugeta, Kassahun Tesfaye, Rodomiro Ortiz, Eva Johansson, Teklehaimanot Hailesilassie, Cecilia Hammenhag, Faris Hailu, Mulatu Geleta
Summary: The growing global demand for wheat for food is rising due to population growth and climate change. A genome-wide association study (GWAS) using 10,045 SNP markers was conducted to identify genomic regions associated with grain yield and related traits in Ethiopian durum wheat. The study revealed high heritability estimates and identified novel marker-trait associations (MTAs) that could potentially improve durum wheat production globally. The research also highlighted the importance of the Ethiopian durum wheat gene pool in this improvement.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Friedrich Teuscher
Summary: This study improves parts of the theory underlying the use of contingency tables by introducing the linkage disequilibrium parameter as a measure of two-way interactions applied to three-way tables. It also presents a simple formula to quantify Simpson's paradox. Additionally, the study addresses the determination of fixed cells in a contingency table and the limitations of methods simulating contingency tables with given pairwise associations.
Article
Genetics & Heredity
Robin J. Hofmeister, Diogo M. Ribeiro, Simone Rubinacci, Olivier Delaneau
Summary: SHAPEIT5, a new phasing method, accurately processes large sequencing datasets and improves imputation accuracy by generating reference panels of haplotypes. The method was applied to UK Biobank data, which resulted in the identification of 549 genes with compound heterozygous loss-of-function events. The use of UK Biobank as a reference panel, coupled with SHAPEIT5 phasing, further enhances genotype imputation accuracy.
Article
Plant Sciences
Versha Rohilla, Rajesh Kumar Yadav, Atman Poonia, Ravika Sheoran, Gita Kumari, P. S. Shanmugavadivel, Aditya Pratap
Summary: This study evaluates the genetic diversity among mung bean genotypes and identifies genomic regions associated with yield attributing traits and yellow mosaic disease resistance through association mapping. Population genetic structure analysis, genetic diversity analysis, and estimation of average linkage disequilibrium indicate significant genetic variation and markers associated with yield-related traits and disease resistance. The findings provide valuable information for mung bean improvement and breeding programs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Prooksa Ananchuensook, Sirinporn Suksawatamnauy, Panarat Thaimai, Supachaya Sriphoosanaphan, Kessarin Thanapirom, Chinachote Teerapakpinyo, Yong Pooworawan, Piyawat Komolmit
Summary: The study identified the association between VDR gene polymorphisms and inactive carrier (IC) and chronic hepatitis (CH) in patients with chronic Hepatitis B virus infection. CdX-2 G/A genotypes were independently associated with IC status in Thai patients with chronic HBV infection.
Article
Clinical Neurology
Vincent Damotte, Antoine Lizee, Matthew Tremblay, Alisha Agrawal, Pouya Khankhanian, Adam Santaniello, Refujia Gomez, Robin Lincoln, Wendy Tang, Tiffany Chen, Nelson Lee, Pablo Villoslada, Jill A. Hollenbach, Carolyn D. Bevan, Jennifer Graves, Riley Bove, Douglas S. Goodin, Ari J. Green, Sergio E. Baranzini, Bruce A. C. Cree, Roland G. Henry, Stephen L. Hauser, Jeffrey M. Gelfand, Pierre-Antoine Gourraud
MULTIPLE SCLEROSIS JOURNAL
(2019)
Article
Clinical Neurology
Vincent Damotte, Antoine Lizee, Matthew Tremblay, Alisha Agrawal, Pouya Khankhanian, Adam Santaniello, Refujia Gomez, Robin Lincoln, Wendy Tang, Tiffany Chen, Nelson Lee, Pablo Villoslada, Jill A. Hollenbach, Carolyn D. Bevan, Jennifer Graves, Riley Bove, Douglas S. Goodin, Ari J. Green, Sergio E. Baranzini, Bruce A. C. Cree, Roland G. Henry, Stephen L. Hauser, Jeffrey M. Gelfand, Pierre-Antoine Gourraud
MULTIPLE SCLEROSIS JOURNAL
(2019)
Article
Biochemical Research Methods
Estelle Geffard, Sophie Limou, Alexandre Walencik, Michelle Daya, Harold Watson, Dara Torgerson, Kathleen C. Barnes, Anne Cesbron Gautier, Pierre-Antoine Gourraud, Nicolas Vince
Article
Allergy
Nicolas Vince, Sophie Limou, Michelle Daya, Wataru Morii, Nicholas Rafaels, Estelle Geffard, Venceslas Douillard, Alexandre Walencik, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E. Ortega, James G. Wilson, Leslie A. Lange, Harold Watson, Dan L. Nicolae, Deborah A. Meyers, Nadia N. Hansel, Jean G. Ford, Mezbah U. Faruque, Eugene R. Bleecker, Monica Campbell, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Margaret A. Taub, Carole Ober, Emiko Noguchi, Kathleen C. Barnes, Dara Torgerson, Pierre-Antoine Gourraud
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2020)
Article
Multidisciplinary Sciences
Guillaume Guimbretiere, Simon Nusinovici, Antoine Monnot, Jonathan Sobocinski, Thomas Senage, Pascal Delsart, Pierre-Antoine Gourraud, Blandine Maurel
SCIENTIFIC REPORTS
(2020)
Article
Immunology
Emmanuel Montassier, Gabriel A. Al-Ghalith, Camille Mathe, Quentin Le Bastard, Venceslas Douillard, Abel Garnier, Remi Guimon, Bastien Raimondeau, Yann Touchefeu, Emilie Duchalais, Nicolas Vince, Sophie Limou, Pierre-Antoine Gourraud, David A. Laplaud, Arnaud B. Nicot, Jean-Paul Soulillou, Laureline Berthelot
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Clinical Neurology
Alireza Akhbardeh, Jennifer K. Arjona, Kristen M. Krysko, Bardia Nourbakhsh, Pierre Antoine Gourraud, Jennifer S. Graves
ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY
(2020)
Article
Cell Biology
Paloma Gomez-Fernandez, Aitzkoa Lopez de Lapuente Portilla, Ianire Astobiza, Jorge Mena, Andoni Urtasun, Vivian Altmann, Fuencisla Matesanz, David Otaegui, Elena Urcelay, Alfredo Antiguedad, Sunny Malhotra, Xavier Montalban, Tamara Castillo-Trivino, Laura Espino-Paisan, Orhan Aktas, Mathias Buttmann, Andrew Chan, Bertrand Fontaine, Pierre-Antoine Gourraud, Michael Hecker, Sabine Hoffjan, Christian Kubisch, Tania Kuempfel, Felix Luessi, Uwe K. Zettl, Frauke Zipp, Iraide Alloza, Manuel Comabella, Christina M. Lill, Koen Vandenbroeck
Article
Gastroenterology & Hepatology
C. Le Berre, A. Bourreille, M. Flamant, G. Bouguen, L. Siproudhis, M. Dewitte, N. Dib, E. Cesbron-Metivier, T. Goronflot, M. Hanf, P. -A. Gourraud, E. Kerdreux, A. Poinas, C. Trang-Poisson
BMC GASTROENTEROLOGY
(2020)
Article
Gastroenterology & Hepatology
Catherine Le Berre, Mathurin Flamant, Guillaume Bouguen, Laurent Siproudhis, Marie Dewitte, Nina Dib, Elodie Cesbron-Metivier, Thomas Goronflot, Matthieu Hanf, Pierre-Antoine Gourraud, Elise Kerdreux, Alexandra Poinas, Arnaud Bourreille, Caroline Trang-Poisson
JOURNAL OF CROHNS & COLITIS
(2020)
Article
Genetics & Heredity
Nicolas Vince, Venceslas Douillard, Estelle Geffard, Diogo Meyer, Erick C. Castelli, Steven J. Mack, Sophie Limou, Pierre-Antoine Gourraud
GENETIC EPIDEMIOLOGY
(2020)
Article
Clinical Neurology
Olivia Rousseau, Matilde Karakachoff, Alban Gaignard, Lise Bellanger, Philippe Bijlenga, Pacome Constant Dit Beaufils, Vincent L'Allinec, Olivier Levrier, Pierre Aguettaz, Jean-Philippe Desilles, Caterina Michelozzi, Gaultier Marnat, Anne-Clemence Vion, Gervaise Loirand, Hubert Desal, Richard Redon, Pierre-Antoine Gourraud, Romain Bourcier
Summary: Through analyzing a large amount of patient data, it was found that the location of intracranial aneurysms is the most significant factor associated with the risk of rupture, while size and treatment intake are less relevant. The use of machine-learning methods can help predict rupture risks more accurately.
JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY
(2021)
Article
Genetics & Heredity
D. S. Goodin, P. Khankhanian, P. A. Gourraud, N. Vince
Summary: The study found that different combinations of risk haplotypes result in MS risk closer to an additive model, indicating that the individual combination of risk haplotypes is crucial for the development of MS, and this interaction plays a key role in determining whether MS develops or not.
BMC MEDICAL GENOMICS
(2021)
Article
Clinical Neurology
Stanislas Demuth, Joris Mueller, Veronique Quenardelle, Valerie Lauer, Roxana Gheoca, Malwina Trzeciak, Irene Pierre-Paul, Jerome De Seze, Pierre-Antoine Gourraud, Valerie Wolff
Summary: Strokecopilot is a literature-based clinical decision support system developed to assist neurologists in managing the acute phase of AIS. By providing information and outcomes of reference populations that match patient characteristics, the system helps neurologists make evidence-based medical reasoning to determine the indications of intravenous thrombolysis and endovascular treatments.
JOURNAL OF NEUROLOGY
(2023)
Article
Cell Biology
Venceslas Douillard, Nayane dos Santos Brito Silva, Sonia Bourguiba-Hachemi, Michel S. Naslavsky, Marilia O. Scliar, Yeda A. O. Duarte, Mayana Zatz, Maria Rita Passos-Bueno, Sophie Limou, Pierre-Antoine Gourraud, Elise Launay, Erick C. Castelli, Nicolas Vince
Summary: Human genomics has advanced rapidly, driving genome-wide association studies (GWASs). However, SNP-based GWASs are limited in capturing the polymorphism of HLA genes. This study evaluated the accuracy of using the 1000 Genomes data as a reference panel to impute HLA genotypes in admixed individuals and highlighted the importance of using genetically specific models for imputation.
