Article
Genetics & Heredity
Erika D'haenens, Sarah Vergult, Bjorn Menten, Annelies Dheedene, R. Frank Kooy, Bert Callewaert
Summary: Dystroglycanopathies are a group of congenital muscular dystrophies that show a wide range of phenotypes. They are not only clinically heterogeneous but also genetically heterogeneous. This study identifies a novel mutation in the B3GALNT2 gene associated with CMDs. Through a study on uniparental disomy, a unique case is discovered. Additionally, an overview of previously reported cases is provided, expanding the phenotypic spectrum.
Article
Biotechnology & Applied Microbiology
Mo Li, Yi Hu, Baihui Zhao, Luan Chen, Hailiang Huang, Cong Huai, Xiaoqing Zhang, Jinghong Zhang, Wei Zhou, Lu Shen, Qi Zhen, Bao Li, Wenjun Wang, Lin He, Shengying Qin
Summary: A two-stage study identified genetic markers associated with TB susceptibility in 616 TB patients and 709 healthy controls. The study confirmed 6 nominally significant SNPs and a HLA-II allele as predisposing factors for TB. The research provides insight into the genetic variants linked to TB susceptibility and sheds light on tuberculosis pathogenesis.
Article
Biology
Korin Sahinyan, Darren M. Blackburn, Marie-Michelle Simon, Felicia Lazure, Tony Kwan, Guillaume Bourque, Vahab D. Soleimani, Y. M. Dennis Lo
Summary: Myofibers are versatile components of skeletal muscle, undergoing key chromatin alterations under various biological and disease conditions. Single-cell sequencing techniques offer a window into the epigenome of myonuclei, while single myofiber ATAC-Seq allows for in-depth analysis of chromatin accessibility and comparative studies between physiological and disease states. These methods reveal significant differences in chromatin regulation in muscle fibers, with implications for developmental processes and muscle-wasting diseases.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Genetics & Heredity
Chujie Chen, Bo Zhu, Xiangwei Tang, Bin Chen, Mei Liu, Ning Gao, Sheng Li, Jingjing Gu
Summary: By analyzing the patterns of genome-wide ROH, we found that both ancient and recent inbreeding events had varying degrees of impact on different horse breeds. However, recent inbreeding events were rare, especially among indigenous horse breeds. Therefore, the ROH-based genomic inbreeding coefficient can help monitor the level of inbreeding. Through our study on the Thoroughbred population, we identified 24 ROH islands containing 72 candidate genes associated with artificial selection traits. Our findings provide insight into horse breed characteristics and future breeding strategies.
Review
Biochemistry & Molecular Biology
Natsuko Aida, Akiko Saito, Toshifumi Azuma
Summary: The development of next-generation sequencing (NGS) has greatly improved the speed and capacity of genetic analysis, expanding its applications to include genome, epigenome, metagenome, and transcriptome analyses. Bone tissue, as a crucial unit supporting the body, is susceptible to genetic diseases. The relationship between age-related bone fragility and genetic factors has recently gained attention.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Obstetrics & Gynecology
M. D. Kilby
Summary: This paper reviews the role of NGS in investigating fetal malformations, emphasizing the importance of prospective case selection and informative pre-test counseling, as well as the crucial role of regulated laboratory sequencing and bioinformatic pathways in clinical practice.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Nicola Zilio, Helle D. Ulrich
Summary: Mapping the genome-wide distribution of single-strand breaks is crucial for understanding damage signaling and DNA repair. This article reviews classical and newly developed high-resolution methods for mapping single-strand breaks, highlighting the valuable insights they provide into the impact of this type of damage on the genome.
Article
Biochemical Research Methods
Muhammad Tahir, Muhammad Sardaraz, Zahid Mehmood, Muhammad Saud Khan
Summary: This paper proposed an efficient error estimation computational model ESREEM to assess error rates in NGS data. The model is based on a probabilistic error model integrated with Hidden Markov Model, and experimental results show that it efficiently estimates errors compared to state-of-the-art algorithms.
CURRENT BIOINFORMATICS
(2021)
Review
Genetics & Heredity
Alexandra Emms, James Castleman, Stephanie Allen, Denise Williams, Esther Kinning, Mark Kilby
Summary: Congenital malformations diagnosed by ultrasound screening have an underlying genetic cause in many cases. Next generation sequencing as a secondary prenatal genetic test offers additional diagnostic yield for congenital abnormalities potentially associated with genetic causes, especially in cases involving cardiac and neurological anomalies, large nuchal translucency, and non-immune fetal hydrops. The use of exome sequencing has shown significant incremental yield in single-system anomalies, making it a valuable tool for routine clinical care in fetuses with congenital abnormalities.
Article
Oncology
Yu Zhang, Takahiko Nishiyama, Eric N. Olson, Rhonda Bassel-Duby
Summary: Muscular dystrophies are a group of neuromuscular disorders with genetic causes that lead to muscle loss and degeneration. The CRISPR/Cas system offers a new path for treatment, potentially correcting genetic mutations permanently and benefiting skeletal muscle due to its post-mitotic and multinucleated features. However, challenges remain for translating CRISPR/Cas genome editing into a viable therapy for muscular dystrophies.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Genetics & Heredity
Jifeng Zhu, Junying Zhang, Meiyan Jiang, Weirong Wang, Jianxia Jiang, Yanli Li, Liyong Yang, Xirong Zhou
Summary: Rapeseed is an important oil crop with a huge genome. Next generation sequencing technology was used to develop SSR markers in rapeseed, which were validated and tested for polymorphism, demonstrating their usefulness in genetic studies of rapeseed.
Article
Microbiology
Madjid Morsli, Christine Zandotti, Aurelie Morand, Philippe Colson, Michel Drancourt
Summary: In this case report, metagenomic next-generation sequencing successfully identified Echovirus 12 as an etiological agent of acute meningitis in pediatric population, highlighting the potential of this method in improving the accuracy of viral diagnosis.
Article
Clinical Neurology
Yu-lian Fang, Na Li, Xiu-fang Zhi, Jie Zheng, Yang Liu, Lin-jie Pu, Chun-yu Gu, Jian-bo Shu, Chun-quan Cai
Summary: This study identified mutations in adjacent genes of the SMN1 gene and other genes that may be associated with the onset of SMA through analysis of SMA family samples, including novel mutations not previously reported.
NEUROLOGICAL SCIENCES
(2021)
Article
Cell Biology
Hedwig S. Kruitwagen, Loes A. Oosterhoff, Monique E. van Wolferen, Chen Chen, Sathidpak Nantasanti Assawarachan, Kerstin Schneeberger, Anne Kummeling, Giora van Straten, Ies C. Akkerdaas, Christel R. Vinke, Frank G. van Steenbeek, Leonie W. L. van Bruggen, Jeannette Wolfswinkel, Guy C. M. Grinwis, Sabine A. Fuchs, Helmuth Gehart, Niels Geijsen, Robert G. Vries, Hans Clevers, Jan Rothuizen, Baukje A. Schotanus, Louis C. Penning, Bart Spee
Article
Chemistry, Multidisciplinary
Shicheng Ye, Jochem W. B. Boeter, Marko Mihajlovic, Frank G. van Steenbeek, Monique E. van Wolferen, Loes A. Oosterhoff, Ary Marsee, Massimiliano Caiazzo, Luc J. W. van der Laan, Louis C. Penning, Tina Vermonden, Bart Spee, Kerstin Schneeberger
ADVANCED FUNCTIONAL MATERIALS
(2020)
Article
Pharmacology & Pharmacy
Marjan A. E. van Hagen, Louska Schipper, Marjolein A. M. Oosterveer-van der Doelen, Manon Vos-Loohuis, Ronette Gehring, Peter A. Leegwater
JOURNAL OF VETERINARY PHARMACOLOGY AND THERAPEUTICS
(2020)
Article
Genetics & Heredity
Jasmin Nessler, Petra Hug, Paul J. J. Mandigers, Peter A. J. Leegwater, Vidhya Jagannathan, Anibh M. Das, Marco Rosati, Kaspar Matiasek, Adrian C. Sewell, Marion Kornberg, Marina Hoffmann, Petra Wolf, Andrea Fischer, Andrea Tipold, Tosso Leeb
Article
Genetics & Heredity
Anna Letko, Katie M. Minor, Steven G. Friedenberg, G. Diane Shelton, Jill Pesayco Salvador, Paul J. J. Mandigers, Peter A. J. Leegwater, Paige A. Winkler, Simon M. Petersen-Jones, Bryden J. Stanley, Kari J. Ekenstedt, Gary S. Johnson, Liz Hansen, Vidhya Jagannathan, James R. Mickelson, Cord Drogemueller
Article
Genetics & Heredity
P. J. J. Mandigers, F. G. Van Steenbeek, W. Bergmann, M. Vos-Loohuis, P. A. Leegwater
Summary: A juvenile form of paroxysmal dyskinesia was identified in the Markiesje dog breed, with a frameshift mutation in the SOD1 gene being the underlying cause. The mutation showed full penetrance in affected dogs but was not found in other analyzed dogs of the breed. This genetic defect leads to a distinct juvenile neurologic disease, different from the related diseases seen in humans and other dog breeds.
Article
Multidisciplinary Sciences
Francesca Genova, Simona Nonnis, Elisa Maffioli, Gabriella Tedeschi, Maria Giuseppina Strillacci, Michela Carisetti, Giuseppe Sironi, Francesca Anna Cupaioli, Noemi Di Nanni, Alessandra Mezzelani, Ettore Mosca, Christopher R. Helps, Peter A. J. Leegwater, Laetitia Dorso, Maria Longeri, Reuben M. Buckley, Danielle Aberdein, Paulo C. Alves, Asa Ohlsson Andersson, Gregory S. Barsh, Rebecca R. Bellone, Tomas F. Bergstrom, Adam R. Boyko, Jeffrey A. Brockman, Margret L. Casal, Marta G. Castelhano, Ottmar Distl, Nicholas H. Dodman, N. Matthew Ellinwood, Jonathan E. Fogle, Oliver P. Forman, Dorian J. Garrick, Edward Ginns, Bianca Haase, Jens Haggstrom, Robert J. Harvey, Daisuke Hasegawa, Isabel Hernandez, Marjo K. Hytonen, Maria Kaukonen, Christopher B. Kaelin, Tomoki Kosho, Emilie Leclerc, Teri L. Lear, Tosso Leeb, Ronald H. L. Li, Hannes Lohi, Mark A. Magnuson, Richard Malik, Shrinivasrao P. Mane, John S. Munday, William J. Murphy, Niels C. Pedersen, Simon M. Peterson-Jones, Max F. Rothschild, Clare Rusbridge, Beth Shapiro, Joshua A. Stern, William F. Swanson, Karen A. Terio, Rory J. Todhunter, Wesley C. Warren, Elizabeth A. Wilcox, Julia H. Wildschutte, Yoshihiko Yu, Leslie A. Lyons
Summary: The study utilized multi-omics analyses to explore unknown pathogenetic processes in Abyssinian cats with amyloidosis, revealing genomic variants, protein expression differences, and differential miRNA expression. The familial amyloid renal form is not a simple monogenic trait and amyloid deposition is triggered by a mix of proteins coded by wild-type genes. This form of amyloidosis in Abyssinian cats can be biochemically classified as AA amyloidosis.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
J. Pei, M. Schuldt, E. Nagyova, Z. Gu, S. el Bouhaddani, L. Yiangou, M. Jansen, J. J. A. Calis, L. M. Dorsch, C. Snijders Blok, N. A. M. van den Dungen, N. Lansu, B. J. Boukens, I. R. Efimov, M. Michels, M. C. Verhaar, R. de Weger, A. Vink, F. G. van Steenbeek, A. F. Baas, R. P. Davis, H. W. Uh, D. W. D. Kuster, C. Cheng, M. Mokry, J. van der Velden, F. W. Asselbergs, M. Harakalova
Summary: Through integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks driving pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.
CLINICAL EPIGENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Christopher A. Jenkins, Ellen C. Schofield, Cathryn S. Mellersh, Luisa De Risio, Sally L. Ricketts
Summary: Genotype imputation using a reference panel combining high-density array data with publicly available whole genome sequence consortium variant data is shown to be an effective and accurate method to increase the density of lower-density array datasets in dogs. The study demonstrates high accuracy in imputation, utilizing reference panels consisting of breed-specific array data and multi-breed variant data. The findings provide evidence and support for the efficacy of this approach in canine genetics.
Review
Agriculture, Dairy & Animal Science
Karen R. Gaar-Humphreys, Talitha C. F. Spanjersberg, Giorgia Santarelli, Guy C. M. Grinwis, Viktor Szatmari, Bernard A. J. Roelen, Aryan Vink, J. Peter van Tintelen, Folkert W. Asselbergs, Hille Fieten, Magdalena Harakalova, Frank G. van Steenbeek
Summary: Heart disease is a major cause of death in both humans and dogs, with genetic cardiomyopathies like dilated cardiomyopathy (DCM) accounting for a portion of these cases. DCM in both species is characterized by ventricular enlargement and dysfunction, leading to heart failure and arrhythmias. Despite similarities in disease progression and subtypes, the genetic background of DCM has been more extensively studied in humans than in dogs. Different dog breeds have been found to develop distinct DCM phenotypes, providing a unique opportunity for modeling. Understanding DCM in dogs can improve breeding selection and overall care for both human and canine DCM patients. This review examines the feasibility of using dogs as a naturally occurring bidirectional disease model for DCM and discusses the potential use of engineered stem cells for disease modeling and treatment.
Article
Biochemistry & Molecular Biology
Manon C. Bouwmeester, Yu Tao, Susana Proenca, Frank G. van Steenbeek, Roos-Anne Samsom, Sandra M. Nijmeijer, Theo Sinnige, Luc J. W. van der Laan, Juliette Legler, Kerstin Schneeberger, Nynke I. Kramer, Bart Spee
Summary: In vitro toxicity testing using hepatocyte-like intrahepatic cholangiocyte organoids (HL-ICOs) allows for the evaluation of drug metabolism gene expression and activity, providing insights into the extent of drug-induced hepatotoxicity.
Article
Veterinary Sciences
Karin Sanders, Hans S. Kooistra, Marieke van den Heuvel, Michal Mokry, Guy C. M. Grinwis, Noortje A. M. van den Dungen, Frank G. van Steenbeek, Sara Galac
Summary: Cushing's syndrome (CS) is more common in dogs and is caused by cortisol-secreting adrenocortical tumours (csACTs) in a significant percentage of cases. By performing RNA sequencing on csACTs and normal adrenal cortices (NACs) of dogs, differentially expressed genes were identified that can improve prognosis and serve as treatment targets. Cytochrome P450 26B1 (CYP26B1) was found to be significantly associated with survival in both canine and human csACTs. Further research could explore the potential use of CYP26B1 inhibitors for inhibiting csACT growth in dogs and humans.
VETERINARY AND COMPARATIVE ONCOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Maud A. J. de Kinderen, Johann Soelkner, Gabor Meszaros, Setegn W. Alemu, Wondmeneh Esatu, John W. M. Bastiaansen, Hans Komen, Tadelle Dessie
Summary: Ethiopia, a developing nation, could benefit greatly from improving smallholder poultry farming. G*E analyses were conducted to determine the best chicken strain for different Ethiopian environments in terms of predicted body weight (BW). The study found significant G*E effects, with the Sasso strain performing best in terms of predicted BW.
Article
Biology
Xiaoyan Wu, Elise R. den Boer, Manon Vos-Loohuis, Frank G. van Steenbeek, Glen R. Monroe, Isaac J. Nijman, Peter. A. J. Leegwater, Hille Fieten