Article
Biotechnology & Applied Microbiology
Shinji Sasaki, Youko Miki, Takayuki Ibi, Hiroyuki Wakaguri, Yuichi Yoshida, Yoshikazu Sugimoto, Yutaka Suzuki
Summary: A study identified a CNV associated with calf mortality, affecting susceptibility to infectious diseases. CNVR_221 homozygotes had lower complement activity and higher risk allele frequency in dead calves with infectious diseases.
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Biology
Milovan Suvakov, Arijit Panda, Colin Diesh, Ian Holmes, Alexej Abyzov
Summary: CNVpytor is an extension of CNVnator that improves performance and functionality, allowing for filtering, annotation, and merging of CNV calls across multiple samples. Its modular architecture enables use in shared and cloud environments, and data can be exported to JBrowse for visualization and analysis.
Article
Multidisciplinary Sciences
Mitchell R. Vollger, Xavi Guitart, Philip C. Dishuck, Ludovica Mercuri, William T. Harvey, Ariel Gershman, Mark Diekhans, Arvis Sulovari, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, David Porubsky, Ruiyang Li, Sergey Nurk, Sergey Koren, Karen H. Miga, Adam M. Phillippy, Winston Timp, Mario Ventura, Evan E. Eichler
Summary: This study presents a comprehensive view of human segmental duplication (SD) organization using a complete human genome dataset. SDs are an important component of the genome, accounting for one-third of the total sequence, and they exhibit evolutionary differences and structural diversity between humans and other primates.
Review
Genetics & Heredity
Edward J. Hollox, Luciana W. Zuccherato, Serena Tucci
Summary: Structural variation (SV) refers to large differences in genomic structure between two genomes, including both copy number variations and variations that do not change copy number, such as inversions. Recent advances in reference genomes and sequencing technologies have renewed interest in SV research, highlighting its role in human evolution. Studies have shown the impact of SV on changes in human brain, population-specific responses to the environment, and contributions from archaic hominin admixture to present-day human SV.
TRENDS IN GENETICS
(2022)
Article
Biochemical Research Methods
Junping Li, Lin Gao, Yusen Ye
Summary: The researchers developed a control-free method called HiSV for identifying large-scale structural variations from Hi-C samples. HiSV achieved superior accuracy and sensitivity through evaluations on simulated data sets and cancer cell lines, and effectively captured complex SVs. HiSV can also supplement the results of WGS methods.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Ziyu Tao, Shixiang Wang, Chenxu Wu, Tao Wu, Xiangyu Zhao, Wei Ning, Guangshuai Wang, Jinyu Wang, Jing Chen, Kaixuan Diao, Fuxiang Chen, Xue-Song Liu
Summary: This study developed a mechanism-agnostic method to categorize CNAs based on various fragment properties and revealed novel patterns of CNA. The activities of some CNA signatures consistently predicted cancer patients' prognosis. This study provides important insights into the role of CNA in cancer and its potential implications for cancer prognosis, evolution, and etiology.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Cell Biology
Wesley M. Marin, Danillo G. Augusto, Kristen J. Wade, Jill A. Hollenbach
Summary: The C4 gene loci encode for complement component 4 (C4) proteins and play a crucial role in the complement system. The C4A and C4B genes exhibit copy number variation and size variation, and are associated with autoimmune and pathogenic diseases.
Article
Genetics & Heredity
Foad J. Rouhani, Xueqing Zou, Petr Danecek, Tauanne Dias Amarante, Gene Koh, Qianxin Wu, Yasin Memari, Richard Durbin, Inigo Martincorena, Andrew R. Bassett, Daniel Gaffney, Serena Nik-Zainal
Summary: The study explores human induced pluripotent stem cells derived from different tissues, finding UV-related damage and mutations in skin fibroblast-derived cells, while blood-derived cells show a high prevalence of acquired mutations.
Article
Biochemistry & Molecular Biology
Agnieszka Piotrowska-Nowak, Krzysztof Safranow, Jakub G. Adamczyk, Ireneusz Soltyszewski, Pawel Cieszczyk, Katarzyna Tonska, Cezary Zekanowski, Beata Borzemska
Summary: Energy efficiency is crucial for athletic performance. This study investigated the relationship between mitochondrial DNA (mtDNA) variants and athletic performance among Polish male athletes. The analysis revealed no correlation between mtDNA variants and athletic performance, but showed a lower mtDNA copy number in both power and endurance athletes compared to controls.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Manuela Moraru, Adriana Perez-Portilla, Karima Al-Akioui Sanz, Alfonso Blazquez-Moreno, Antonio Arnaiz-Villena, Hugh T. Reyburn, Carlos Vilches
Summary: Fc gamma receptors (FcγR) are cell-surface glycoproteins that play a role in immune responses. The CNR5 deletion on the FCGR locus can lead to loss and recombination of FCGR genes, potentially affecting immune function. The distribution of FCGR polymorphism shows significant variation in the highlands of Ecuador, with CNR5 deletion being relatively common.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Aditi Hazra, Andrea O'Hara, Kornelia Polyak, Faina Nakhlis, Beth T. Harrison, Antonio Giordano, Beth Overmoyer, Filipa Lynce
Summary: The goal of this study was to identify biomarkers associated with de novo inflammatory breast cancer (IBC). Through examination of breast biopsies, significant copy number variations (CNVs) on chromosome 7p11.2 and 21 were identified. These findings provide insights into the biology of IBC and may lead to the optimization of treatment strategies.
Article
Genetics & Heredity
Martin Kerick, Marialbert Acosta-Herrera, Carmen Pilar Simeon-Aznar, Jose Luis Callejas, Shervin Assassi, Susanna M. Proudman, Mandana Nikpour, Nicolas Hunzelmann, Gianluca Moroncini, Jeska K. de Vries-Bouwstra, Gisela Orozco, Anne Barton, Ariane L. Herrick, Chikashi Terao, Yannick Allanore, Carmen Fonseca, Marta Eugenia Alarcon-Riquelme, Timothy R. D. J. Radstake, Lorenzo Beretta, Christopher P. Denton, Maureen D. Mayes, Javier Martin
Summary: This study investigated the association of C4 CN with systemic sclerosis risk, finding that higher C4 CN provides protection to SSc, while deviations from CN parity of C4A and C4B increase risk. Gender differences were observed in the protection conferred by C4A and C4B.
NPJ GENOMIC MEDICINE
(2022)
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Oscar L. Rodriguez, Yana Safonova, Catherine A. Silver, Kaitlyn Shields, William S. Gibson, Justin T. Kos, David Tieri, Hanzhong Ke, Katherine J. L. Jackson, Scott D. Boyd, Melissa L. Smith, Wayne A. Marasco, Corey T. Watson
Summary: Variation in the antibody response is linked to disease outcomes, vaccine and therapeutic responsiveness. Polymorphisms within the immunoglobulin heavy chain locus have an impact on the antibody repertoire, indicating genetic predisposition. Understanding IGH genetics can help comprehend the regulation, function, and dynamics of the antibody response.
NATURE COMMUNICATIONS
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Inga Voges, Amke Caliebe, Sophia Hinz, Simona Boroni Grazioli, Daniel Dominik Gabbert, Philip Wegner, Anselm Sebastian Uebing, Piers E. F. Daubeney, Dudley J. Pennell, Sylvia Krupickova
Summary: This study aimed to establish reference values for atrial volumes in pediatric patients using MRI. The study analyzed data from 155 healthy children and found that body surface area and sex were significantly associated with atrial volumes. The study provides average values for atrial volumes and establishes percentile charts.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Gastroenterology & Hepatology
Stephan Buch, Hamish Innes, Philipp Ludwig Lutz, Hans Dieter Nischalke, Jens U. Marquardt, Janett Fischer, Karl Heinz Weiss, Jonas Rosendahl, Astrid Marot, Marcin Krawczyk, Markus Casper, Frank Lammert, Florian Eyer, Arndt Vogel, Silke Marhenke, Johann von Felden, Rohini Sharma, Stephen Rahul Atkinson, Andrew McQuillin, Jacob Nattermann, Clemens Schafmayer, Andre Franke, Christian Strassburg, Marcella Rietschel, Heidi Altmann, Stefan Sulk, Veera Raghavan Thangapandi, Mario Brosch, Carolin Lackner, Rudolf E. Stauber, Ali Canbay, Alexander Link, Thomas Reiberger, Mattias Mandorfer, Georg Semmler, Bernhard Scheiner, Christian Datz, Stefano Romeo, Stefano Ginanni Corradini, William Lucien Irving, Joanne R. Morling, Indra Neil Guha, Eleanor Barnes, M. Azim Ansari, Jocelyn Quistrebert, Luca Valenti, Sacha A. Mueller, Marsha Yvonne Morgan, Jean-Francois Dufour, Jonel Trebicka, Thomas Berg, Pierre Deltenre, Sebastian Mueller, Jochen Hampe, Felix Stickel
Summary: This study identifies rs2242652 in TERT as a novel protective factor for HCC in patients with alcohol-related cirrhosis.
Article
Radiology, Nuclear Medicine & Medical Imaging
Inga Voges, Amke Caliebe, Sophia Hinz, Simona Boroni Grazioli, Dominik D. Gabbert, Piers E. F. Daubeney, Anselm S. Uebing, Dudley J. Pennell, Sylvia Krupickova
Summary: This study aims to provide reference values for MRI measurement of ventricular volumes in children and compares two different post-processing techniques. The results show significant correlations between ventricular volumes and factors such as height, body surface area, and weight. These reference values are important for the diagnosis, follow-up, and research of heart disease.
JOURNAL OF MAGNETIC RESONANCE IMAGING
(2023)
Article
Genetics & Heredity
Alina Senst, Amke Caliebe, Matthias Drum, Christian Cossu, Martin Zieger, Eva Scheurer, Iris Schulz
Summary: This study aimed to provide evidence-based recommendations for the successful identification of altered human remains by investigating commonly used tissues from altered bodies. The study found differences between tissue types and DNA extraction methods, with blood samples outperforming others. Additionally, Next Generation Sequencing provided higher profile completeness compared to standard genotyping methods.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Gastroenterology & Hepatology
Juliane Glaubitz, Anika Wilden, Fabian Frost, Sabine Ameling, Georg Homuth, Hala Mazloum, Malte Christoph Ruehlemann, Corinna Bang, Ali A. Aghdassi, Christoph Budde, Tilmann Pickartz, Andre Franke, Barbara M. Broeker, Uwe Voelker, Julia Mayerle, Markus M. Lerch, Frank-Ulrich Weiss, Matthias Sendler
Summary: Understanding the role of T-reg/Th17 balance in maintaining intestinal barrier function is important for reducing the risk of severe disease and late death in acute pancreatitis (AP). Depletion of T-reg cells enhances the proinflammatory response and reduces bacterial translocation to the pancreas in a mouse model of AP. Targeting T-regs may help improve the course of the disease.
Article
Gastroenterology & Hepatology
Philipp Rausch, Sarah Ellul, Anthea Pisani, Corinna Bang, Trevor Tabone, Claire Marantidis Cordina, Graziella Zahra, Andre Franke, Pierre Ellul
Summary: Background: Microbial communities are believed to influence inflammatory processes in patients with inflammatory bowel disease (IBD), but these effects are often influenced by treatments and rarely studied in treatment-naive patients. Methods: Untreated IBD onset patients and healthy controls were recruited from Malta. Stool samples were collected and analyzed via sequencing to assess microbial communities. Results: Differences in community composition, variability, and diversity were observed between healthy and diseased individuals, but minimal differences were found between newly diagnosed UC and CD cohorts. Network analyses revealed changes in bacterial interactions, suggesting disease-specific alterations in community dynamics. Additionally, microbial community characteristics were identified as predictors for future treatments. Conclusion: Treatment-naive IBD onset patients from Malta show differences in microbial communities compared to healthy individuals, and future treatment options can be predicted based on microbial community characteristics.
INFLAMMATORY BOWEL DISEASES
(2023)
Article
Oncology
Stefanie V. V. Junk, Elke Schaeffeler, Martin Zimmermann, Anja Moericke, Rita Beier, Peter Schuette, Birthe Fedders, Julia Alten, Laura Hinze, Norman Klein, Andreas Kulozik, Martina U. U. Muckenthaler, Rolf Koehler, Arndt Borkhardt, Jayaram Vijayakrishnan, David Ellinghaus, Michael Forster, Andre Franke, Astrid Wintering, Christian P. P. Kratz, Martin Schrappe, Matthias Schwab, Richard S. S. Houlston, Gunnar Cario, Martin Stanulla
Summary: This study analyzed the impact of therapy-related hyperbilirubinemia on the treatment outcome of pediatric patients with acute lymphoblastic leukemia (ALL) and identified the contributing genetic risk factors. The study found that high hyperbilirubinemia had a negative impact on treatment outcome, and the rs6744284 variant in the UGT1A gene cluster was strongly associated with the risk of hyperbilirubinemia.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Article
Clinical Neurology
Nils G. Margraf, Justina Dargvainiene, Emily Theel, Frank Leypoldt, Wolfgang Lieb, Andre Franke, Klaus Berger, Jens Kuhle, Gregor Kuhlenbaeumer
Summary: This study investigates the potential of neurofilament light chain (NfL) in serum and cerebrospinal fluid as a biomarker for neurodestruction in status epilepticus. The results suggest that the concentration of NfL is mainly determined by the duration of status epilepticus, rather than the type of status or treatment refractoriness.
JOURNAL OF NEUROLOGY
(2023)
Article
Cell Biology
Daniel Kolbe, Nicolas A. da Silva, Janina Dose, Guillermo G. Torres, Amke Caliebe, Ben Krause-Kyora, Almut Nebel
Summary: By analyzing ancient samples up to 12,000 years old, this study revealed the evolutionary history of the three major APOE alleles in Europe. Significant allele frequency shifts were detected between populations and over time. The differences in allele distributions between early European populations (i.e., hunter-gatherers vs. first farmers) were likely influenced by changes in diet/lifestyle, while admixture played an important role in shaping current APOE variation from around 4000 BCE onwards.
Article
Multidisciplinary Sciences
Christine Eimer, Knut G. Rump, Gunnar Elke, Tobias H. Becher, Norbert Weiler, Amke Caliebe, Dirk Schaedler
Summary: The purpose of this study was to assess the effect of different levels of positive end-expiratory pressure (PEEP) on the distance from the subclavian vein (SCV) to the parietal pleura (DVP) and on the cross-sectional area (CSA) of the SCV. The results showed that an increase in PEEP did not have clinically relevant effects on DVP and CSA. Therefore, PEEP optimization is not indicated for subclavian vein cannulation.
Article
Multidisciplinary Sciences
Younghun Y. Han, Jinyoung J. Byun, Catherine Zhu, Ryan R. Sun, Julia Y. Roh, Heather Cordell, Hyun-Sung A. Lee, Vikram R. Shaw, Sung Wook Kang, Javad Razjouyan, Matthew A. Cooley, Manal M. Hassan, Katherine A. Siminovitch, Trine Folseraas, David Ellinghaus, Annika Bergquist, Simon M. Rushbrook, Andre Franke, Tom H. Karlsen, Konstantinos N. Lazaridis, Katherine A. McGlynn, Lewis R. Roberts, Christopher Amos, Christoph Schramm, David Shapiro, Elizabeth Goode
Summary: This study used multitrait joint analyses to explore the genetic contribution and correlations between various clinical and epidemiological traits associated with PSC. Several new risk loci and potential susceptibility genes such as MANBA and IRF5 were identified, and in silico drug screening provided candidate agents for further investigation of pharmacological effects in PSC.
NATURE COMMUNICATIONS
(2023)
Article
Clinical Neurology
Yasmine Sommerer, Valerija Dobricic, Marcel Schilling, Olena Ohlei, Sanaz Sedghpour Sabet, Tanja Wesse, Janina Fuss, Soeren Franzenburg, Andre Franke, Laura Parkkinen, Christina M. Lill, Lars Bertram
Summary: This study conducted an epigenome-wide association study (EWAS) using DNAm profiles in entorhinal cortex (EC) from AD patients and control brains, and found several genomic loci associated with disease onset and progression. By integrating DNAm levels with mRNA expression data, significant correlations were observed for 6 of the significant CpGs. Additionally, accelerated epigenetic aging was found in the brains of AD patients compared to controls.
ALZHEIMERS RESEARCH & THERAPY
(2023)
Article
Immunology
Hesham ElAbd, Petra Bacher, Andreas Tholey, Tobias L. Lenz, Andre Franke
Summary: The HLA proteins play a crucial role in adaptive immunity by presenting self and foreign peptides to T cells. Genetic variation in the HLA region is associated with many complex diseases, highlighting the importance of specific HLA-presented peptides in disease etiology. Identifying the immunopeptidome, the set of peptides presented by an individual's HLA proteins in vivo, has garnered increasing attention for various reasons, such as cancer immunotherapy, vaccine development, and understanding autoimmunity. Despite significant progress, there are still unanswered questions and challenges in peptide presentation analysis and T cell immunogenicity. Addressing these challenges would enhance our understanding of disease etiology and lead to advancements in vaccine engineering and immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2023)
Correction
Cardiac & Cardiovascular Systems
Verena Limperger, Gili Kenet, Bettina Kiesau, Max Koether, Malin Schmeiser, Florian Langer, David Juhl, Maria Shneyder, Andre Franke, Ulrich C. Klostermeier, Rolf Mesters, Frank Ruehle, Monika Stoll, Dagmar Steppat, Dorothee Kowalski, Angela Rocke, Piotr Kuta, Tido Bajorat, Antje Torge, Bruno Neuner, Ralf Junker, Ulrike Nowak-Goettl
JOURNAL OF THROMBOSIS AND THROMBOLYSIS
(2023)
Article
Medicine, Research & Experimental
Hajrullah Ahmeti, Amke Caliebe, Christoph Rocken, Olav Jansen, Maximilian H. Mehdorn, Michael Synowitz
Summary: This study systematically examined 696 patients with primary intracranial meningiomas to assess the effect of preoperative peritumoral brain edema (PTBE) on preoperative symptoms, neurological deficits, postoperative complications, and long-term outcomes. Results showed that PTBE significantly increased the incidences of specific preoperative symptoms, neurological deficits, and postoperative complications. Patients with preoperative PTBE required more medical support after surgery, but all patients had favorable outcomes.
EUROPEAN JOURNAL OF MEDICAL RESEARCH
(2023)