Article
Multidisciplinary Sciences
Peng Ni, Fan Nie, Zeyu Zhong, Jinrui Xu, Neng Huang, Jun Zhang, Haochen Zhao, You Zou, Yuanfeng Huang, Jinchen Li, Chuan-Le Xiao, Feng Luo, Jianxin Wang
Summary: The authors develop a deep learning tool ccsmeth and a Nextflow pipeline ccsmethphase for accurate detection and phasing of DNA 5mCpG using CCS reads in human. Existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. By training ccsmeth with PacBio CCS reads, the authors achieve high accuracy in 5mCpG detection at single-molecule resolution and strong correlations with bisulfite sequencing and nanopore sequencing at the genome-wide level.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Teresa De Jesus Martinez, Elliot A. Hershberg, Emma Guo, Garrett J. Stevens, Colin Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M. Buels, Lincoln D. Stein, Ian H. Holmes
Summary: JBrowse Jupyter is a package that aims to bridge the gap between Python programming and genomic visualization. It provides a Python interface to quickly set up, launch and customize JBrowse views in Jupyter notebooks. Users can also share their data through Google's Colab notebooks, ensuring reproducible interactive views.
Article
Biochemistry & Molecular Biology
Baekgyu Choi, Chang Kyung Kang, Seongwan Park, Dohoon Lee, Andrew J. Lee, Yuji Ko, Suk-Jo Kang, Kyuho Kang, Sun Kim, Youngil Koh, Inkyung Jung
Summary: A blood condition called CHIP, which is related to aging, can increase the susceptibility to severe COVID-19. Patients with CHIP showed a strong proinflammatory response in certain white blood cells, exacerbating systemic inflammation. Targeting these responses with anti-inflammatory therapies may offer potential treatments.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Article
Multidisciplinary Sciences
Daria Kostiniuk, Hely Tamminen, Pashupati P. Mishra, Saara Marttila, Emma Raitoharju
Summary: The nc886 locus is not polymorphically imprinted in non-human primates and guinea pigs, unlike in humans, suggesting that animal models are not applicable for nc886 research. The data obtained suggests that the nc886 region may be classically imprinted in great apes and potentially also in Old World monkeys.
Article
Oncology
Roberta Giordo, Rida Gulsha, Sarah Kalla, George A. Calin, Leonard Lipovich
Summary: The genome-wide association study identified six genetic variants significantly associated with both type 2 diabetes and cancer in non-coding regions, including lncRNA genes. These variants provide evidence of a shared genetic architecture between the two diseases and may serve as potential drug targets.
Article
Multidisciplinary Sciences
Samuel Mathieu, Mewen Briend, Erik Abner, Christian Couture, Zhonglin Li, Yohan Bosse, Sebastien Theriault, Tonu Esko, Benoit J. Arsenault, Patrick Mathieu
Summary: A genome-wide association analysis was conducted on a large sample size to identify genetic risk loci associated with hypothyroidism. The study found multiple risk loci involved in lymphocyte function. Candidate genes associated with hypothyroidism were identified using molecular quantitative trait loci, co-localization, and enhancer-promoter chromatin looping. Mendelian randomization analysis identified blood expressed genes and circulating proteins as potential causal molecules for hypothyroidism. Drug-gene interaction analysis revealed that certain cancer therapy drugs increase the risk of hypothyroidism. This study provides important genetic evidence for drug-induced hypothyroidism and identifies potential drug targets.
Article
Multidisciplinary Sciences
Zhikun Wu, Zehang Jiang, Tong Li, Chuanbo Xie, Liansheng Zhao, Jiaqi Yang, Shuai Ouyang, Yizhi Liu, Tao Li, Zhi Xie
Summary: This study conducted long-read sequencing-based structural variant analysis on 405 unrelated Chinese individuals, identifying 132,312 nonredundant structural variants, of which 45.2% are novel. The study also discovered rare deletions associated with anemia and structural variants related to immunity that differentiate the northern and southern Chinese populations.
NATURE COMMUNICATIONS
(2021)
Article
Orthopedics
Scott Kulm, Austin C. Kaidi, David Kolin, Mark T. Langhans, Mathias P. Bostrom, Olivier Elemento, Tony S. Shen
Summary: A genome-wide association study was conducted to characterize the genetic risk factors associated with end-stage hip osteoarthritis in patients undergoing total hip arthroplasty. Multiple genetic variants, including 5 novel loci, were found to be associated with the disease, but the effect of genetics was lower compared to age and body mass index.
JOURNAL OF ARTHROPLASTY
(2023)
Article
Biochemistry & Molecular Biology
Veronique Geoffroy, Jean-Baptiste Lamouche, Thomas Guignard, Samuel Nicaise, Arnaud Kress, Sophie Scheidecker, Antony Le Bechec, Jean Muller
Summary: Much of the human genetics variant repertoire is composed of single nucleotide variants (SNV) and small insertion/deletions (indel) but structural variants (SV) remain a major part of our modified DNA. SV detection has often been a complex question to answer either because of the necessity to use different technologies (array CGH, SNP array, Karyotype, Optical Genome Mapping horizontal ellipsis ) to detect each category of SV or to get an appropriate resolution (Whole Genome Sequencing). The AnnotSV webserver aims at being an efficient tool to annotate and interpret SV potential pathogenicity in the context of human diseases, recognize potential false positive variants from all the SV identified, and visualize the patient variants repertoire. The most recent developments in the AnnotSV webserver include updated annotations sources and ranking, three novel output formats for diverse utilization, and two novel user interfaces including an interactive circos view.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Brian T. Lee, Galt P. Barber, Anna Benet-Pages, Jonathan Casper, Hiram Clawson, Mark Diekhans, Clay Fischer, Jairo Navarro Gonzalez, Angie S. Hinrichs, Christopher M. Lee, Pranav Muthuraman, Luis R. Nassar, Beagan Nguy, Tiana Pereira, Gerardo Perez, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent
Summary: The UCSC Genome Browser is a graphical viewer for exploring genome annotations, providing integrated tools for visualizing, comparing, analyzing, and sharing genomic datasets. Updates this year include new public hub assemblies for new organisms, updated clinical tracks, a new Track Sets feature, enhanced variant displays, and a tool for placing new SARS-CoV-2 genomes in a global phylogenetic tree. Other improvements focus on usability features such as informative mouseover displays and new fonts.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Andrew J. Harris, Nicole M. Foley, Tiffani L. Williams, William J. Murphy
Summary: Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. Users can visualize genome-wide variation in evolutionary histories and genetic divergence, and compare it with gene annotations and other customizable features.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Gastroenterology & Hepatology
Connor A. Emdin, Mary Haas, Veeral Ajmera, Tracey G. Simon, Julian Homburger, Cynthia Neben, Lan Jiang, Wei-Qi Wei, Qiping Feng, Alicia Zhou, Joshua Denny, Kathleen Corey, Rohit Loomba, Sekar Kathiresan, Amit Khera
Summary: This study identified 12 independent genetic variants, including 7 newly identified ones, that confer risk for cirrhosis. A polygenic score based on these variants can identify a subset of the population at substantially increased risk, particularly those susceptible to the hepatotoxic effects of excess alcohol consumption or obesity.
Article
Biochemical Research Methods
Elliot A. Hershberg, Garrett Stevens, Colin Diesh, Peter Xie, Teresa De Jesus Martinez, Robert Buels, Lincoln Stein, Ian Holmes
Summary: This study developed an R package that provides an interface to the JBrowse 2 genome browser, allowing configuration and customization entirely with R code. The browser can be deployed from the R console and embedded in Shiny applications or R Markdown documents.
Article
Psychiatry
Hill F. Ip, Camiel M. van der Laan, Eva M. L. Krapohl, Isabell Brikell, Cristina Sanchez-Mora, Ilja M. Nolte, Beate St Pourcain, Koen Bolhuis, Teemu Palviainen, Hadi Zafarmand, Lucia Colodro-Conde, Scott Gordon, Tetyana Zayats, Fazil Aliev, Chang Jiang, Carol A. Wang, Gretchen Saunders, Ville Karhunen, Anke R. Hammerschlag, Daniel E. Adkins, Richard Border, Roseann E. Peterson, Joseph A. Prinz, Elisabeth Thiering, Ilkka Seppala, Natalia Vilor-Tejedor, Tarunveer S. Ahluwalia, Felix R. Day, Jouke-Jan Hottenga, Andrea G. Allegrini, Kaili Rimfeld, Qi Chen, Yi Lu, Joanna Martin, Maria Soler Artigas, Paula Rovira, Rosa Bosch, Gemma Espanol, Josep Antoni Ramos Quiroga, Alexander Neumann, Judith Ensink, Katrina Grasby, Jose J. Morosoli, Xiaoran Tong, Shelby Marrington, Christel Middeldorp, James G. Scott, Anna Vinkhuyzen, Andrey A. Shabalin, Robin Corley, Luke M. Evans, Karen Sugden, Silvia Alemany, Laerke Sass, Rebecca Vinding, Kate Ruth, Jess Tyrrell, Gareth E. Davies, Erik A. Ehli, Fiona A. Hagenbeek, Eveline De Zeeuw, Toos C. E. M. Van Beijsterveldt, Henrik Larsson, Harold Snieder, Frank C. Verhulst, Najaf Amin, Alyce M. Whipp, Tellervo Korhonen, Eero Vuoksimaa, Richard J. Rose, Andre G. Uitterlinden, Andrew C. Heath, Pamela Madden, Jan Haavik, Jennifer R. Harris, Oyvind Helgeland, Stefan Johansson, Gun Peggy S. Knudsen, Pal Rasmus Njolstad, Qing Lu, Alina Rodriguez, Anjali K. Henders, Abdullah Mamun, Jackob M. Najman, Sandy Brown, Christian Hopfer, Kenneth Krauter, Chandra Reynolds, Andrew Smolen, Michael Stallings, Sally Wadsworth, Tamara L. Wall, Judy L. Silberg, Allison Miller, Liisa Keltikangas-Jarvinen, Christian Hakulinen, Laura Pulkki-Raback, Alexandra Havdahl, Per Magnus, Olli T. Raitakari, John R. B. Perry, Sabrina Llop, Maria-Jose Lopez-Espinosa, Klaus Bonnelykke, Hans Bisgaard, Jordi Sunyer, Terho Lehtimaki, Louise Arseneault, Marie Standl, Joachim Heinrich, Joseph Boden, John Pearson, L. John Horwood, Martin Kennedy, Richie Poulton, Lindon J. Eaves, Hermine H. Maes, John Hewitt, William E. Copeland, Elizabeth J. Costello, Gail M. Williams, Naomi Wray, Marjo-Riitta Jarvelin, Matt McGue, William Iacono, Avshalom Caspi, Terrie E. Moffitt, Andrew Whitehouse, Craig E. Pennell, Kelly L. Klump, S. Alexandra Burt, Danielle M. Dick, Ted Reichborn-Kjennerud, Nicholas G. Martin, Sarah E. Medland, Tanja Vrijkotte, Jaakko Kaprio, Henning Tiemeier, George Davey Smith, Catharina A. Hartman, Albertine J. Oldehinkel, Miquel Casas, Marta Ribases, Paul Lichtenstein, Sebastian Lundstrom, Robert Plomin, Meike Bartels, Michel G. Nivard, Dorret I. Boomsma
Summary: Childhood aggressive behavior has a high heritability of around 50% and a genome-wide association metaanalysis was conducted in this study. Three significant genes associated with educational traits were identified and polygenic scores based on the analysis could predict aggression significantly. Aggression showed genetic correlations with various psychiatric and psychological traits, while having a negative correlation with cognitive traits and age at first birth. Genetic correlations were stronger for aggression with smoking phenotypes, while weaker for teacher-reported aggression compared to mother- and self-reported aggression.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Genetics & Heredity
Genevieve H. L. Roberts, Raghavendran Partha, Brooke Rhead, Spencer C. Knight, Danny S. Park, Marie Coignet, Miao Zhang, Nathan Berkowitz, David A. Turrisini, Michael Gaddis, Shannon R. McCurdy, Milos Pavlovic, Luong Ruiz, Chodon Sass, Asher K. Haug Baltzell, Harendra Guturu, Ahna R. Girshick, Catherine A. Ball, Eurie L. Hong, Kristin A. Rand
Summary: GWAS based on self-reported phenotypes reveal distinct associations between risk loci and COVID-19 outcomes, suggesting genetic differences in susceptibility and severity. Collecting deep COVID-19 phenotype data can aid in identifying therapeutic targets.
Article
Medicine, General & Internal
Silvia Di Maio, Claudia Lamina, Stefan Coassin, Lukas Forer, Reinhard Wuerzner, Sebastian Schoenherr, Florian Kronenberg
Summary: The study found that SARS-CoV-2 infections enforce the association between high Lp(a) and IHD, but the risk for thromboembolic events is not influenced by Lp(a.
JOURNAL OF INTERNAL MEDICINE
(2022)
Article
Emergency Medicine
Nikolas Beck, Miriam Michel, Elisabeth Binder, Klaus Kapelari, Michael Maurer, Claudia Lamina, Thomas Mueller, Daniela Karall, Sabine Scholl-Buergi
Summary: This retrospective study analyzes the urgency of patient visits at the emergency department of the Clinic for Pediatrics at the Medical University of Innsbruck. The majority of visits were classified as nonurgent, with more visits recorded during regular office hours and on weekends. Likelihoods of inpatient admission and hospital stay lengths increased with urgency levels.
PEDIATRIC EMERGENCY CARE
(2022)
Article
Medicine, General & Internal
Lukas Lunger, Andreas Melmer, Wolfgang Sturm, Claudia Lamina, Alexander Tschoner, Julia Engl, Armin Honlinger, Clemens Engler, Peter Willeit, Stefan Kiechl, Johann Willeit, Dietmar Ofner, Heinz Wykypiel, Markus Laimer, Herbert Tilg, Christoph Ebenbichler
Summary: The study demonstrates that weight loss induced by bariatric surgery can halt the natural progression of carotid intima media thickness (C-IMT) over a 10-year observation period, compared to a population-based control cohort.
WIENER KLINISCHE WOCHENSCHRIFT
(2023)
Article
Cardiac & Cardiovascular Systems
Johanna F. Schachtl-Riess, Sebastian Schoenherr, Claudia Lamina, Lukas Forer, Stefan Coassin, Gertraud Streiter, Azin Kheirkhah, Yong Li, Heike Meiselbach, Silvia Di Maio, Kai-Uwe Eckardt, Anna Koettgen, Florian Kronenberg
Summary: This study aimed to identify the genetic and non-genetic determinants of HDL-mediated cholesterol efflux capacity (CEC). CEC was measured using serum samples from participants in the German Chronic Kidney Disease (GCKD) study. The results showed that HDL-cholesterol and triglycerides were the main determinants of CEC, and the KLKB1 and CLSTN2 loci were significantly associated with CEC.
Article
Medical Laboratory Technology
Ioannis Dikaios, Harald Althaus, Eduardo Angles-Cano, Uta Ceglarek, Stefan Coassin, Christa M. Cobbaert, Vincent Delatour, Benjamin Dieplinger, Matthias Grimmler, Andrew N. Hoofnagle, Gerhard M. Kostner, Florian Kronenberg, Zsusanna Kuklenyik, Alicia N. Lyle, Urban Prinzing, L. Renee Ruhaak, Hubert Scharnagl, Hubert W. Vesper, Liesbet Deprez
Summary: Elevated concentrations of Lp(a) are directly related to increased risk of cardiovascular diseases, but the lack of global standardization of current measurement procedures hinders consistent patient care. This study aims to develop a next-generation SI-traceable reference measurement system for Lp(a) using peptide-calibrated measurement procedures and serum-based reference materials. The results show that unspiked human serum pools are the preferred secondary reference materials for the future SI-traceable Lp(a) measurement system.
CLINICAL CHEMISTRY
(2023)
Article
Medical Laboratory Technology
L. Renee Ruhaak, Fred P. H. T. M. Romijn, Ilijana Begcevic Brkovic, Zsusanna Kuklenyik, Julia Dittrich, Uta Ceglarek, Andrew N. Hoofnagle, Harald Althaus, Eduardo Angles-Cano, Stefan Coassin, Vincent Delatour, Liesbet Deprez, Ioannis Dikaios, Gerhard M. Kostner, Florian Kronenberg, Alicia Lyle, Urban Prinzing, Hubert W. Vesper, Christa M. Cobbaert, Int Federation Clinical Chem Lab Med Working Grp Apolipoproteins Mass Spect
Summary: In order to ensure the accuracy and reliability of medical results from in vitro diagnostic and in-house tests, a higher order reference measurement system traceable to endorsed reference measurement procedures and reference materials is needed. A candidate reference measurement procedure for serum apolipoprotein(a) [apo(a)] based on mass spectrometry was developed and provisionally validated. The method demonstrated accurate quantitation of serum apo(a) and fulfilled predefined analytical performance specifications.
CLINICAL CHEMISTRY
(2023)
Article
Cardiac & Cardiovascular Systems
Patrick B. Mark, Juan J. Carrero, Kunihiro Matsushita, Yingying Sang, Shoshana H. Ballew, Morgan E. Grams, Josef Coresh, Aditya Surapaneni, Nigel J. Brunskill, John Chalmers, Lili Chan, Alex R. Chang, Rajkumar Chinnadurai, Gabriel Chodick, Massimo Cirillo, Dick de Zeeuw, Marie Evans, Amit X. Garg, Orlando M. Gutierrez, Hiddo J. L. Heerspink, Gunnar H. Heine, William G. Herrington, Junichi Ishigami, Florian Kronenberg, Jun Young Lee, Adeera Levin, Rupert W. Major, Angharad Marks, Girish N. Nadkarni, David M. J. Naimark, Christoph Nowak, Mahboob Rahman, Charumathi Sabanayagam, Mark Sarnak, Simon Sawhney, Markus P. Schneider, Varda Shalev, Jung-Im Shin, Moneeza K. Siddiqui, Nikita Stempniewicz, Keiichi Sumida, Jose M. Valdivielso, Jan van den Brand, Angela Yee-Moon Wang, David C. Wheeler, Lihua Zhang, Frank L. J. Visseren, Benedicte Stengel
Summary: This study investigated the association between cardiovascular disease (CVD) and future risk of kidney failure with replacement therapy (KFRT). It found that both prevalent and incident CVD were strongly associated with KFRT risk, with incident HF showing the strongest association.
EUROPEAN HEART JOURNAL
(2023)
Article
Cardiac & Cardiovascular Systems
Florian Kronenberg, Samia Mora, Erik S. G. Stroes, Brian A. Ference, Benoit J. Arsenault, Lars Berglund, Marc R. Dweck, Marlys L. Koschinsky, Gilles Lambert, Francois Mach, Catherine J. McNeal, Patrick M. Moriarty, Pradeep Natarajan, Borge G. Nordestgaard, Klaus G. Parhofer, Salim S. Virani, Arnold von Eckardstein, Gerald F. Watts, Jane K. Stock, Kausik K. Ray, Lale S. Tokgozoglu, Alberico L. Catapano
Summary: In 2022, the European Atherosclerosis Society (EAS) released a new consensus statement on the relationship between lipoprotein(a) [Lp(a)] and atherosclerotic cardiovascular disease (ASCVD) and aortic stenosis. This statement highlights the importance of understanding Lp(a) concentration and its impact on lifetime risk for ASCVD. It also provides practical advice on using Lp(a) concentration to manage risk factors, despite the lack of currently available targeted therapies to lower Lp(a).
Article
Cardiac & Cardiovascular Systems
Can Gollmann-Tepekoeylue, Michael Graber, Jakob Hirsch, Sophia Mair, Andreas Naschberger, Leo Poelzl, Felix Naegele, Elke Kirchmair, Gerald Degenhart, Egon Demetz, Richard Hilbe, Hao-Yu Chen, James C. Engert, Anna Boehm, Nadja Franz, Daniela Lobenwein, Daniela Lener, Christiane Fuchs, Anna Weihs, Sonja Toechterle, Georg F. Vogel, Victor Schweiger, Jonas Eder, Peter Pietschmann, Markus Seifert, Florian Kronenberg, Stefan Coassin, Michael Blumer, Hubert Hackl, Dirk Meyer, Gudrun Feuchtner, Rudolf Kirchmair, Jakob Troppmair, Markus Krane, Guenther Weiss, Sotirios Tsimikas, George Thanassoulis, Michael Grimm, Bernhard Rupp, Lukas A. Huber, Shen-Ying Zhang, Jean-Laurent Casanova, Ivan Tancevski, Johannes Holfeld
Summary: TLR3 is identified as a central molecular regulator of calcification in valvular interstitial cells, and BGN is revealed as a new endogenous agonist of TLR3. BGN activates TLR3 through XYLT1-dependent posttranslational modification and induces the transdifferentiation of valvular interstitial cells into bone-forming osteoblasts through TLR3-dependent induction of type I interferons.
Article
Biochemistry & Molecular Biology
Sebastian Schoenherr, Hansi Weissensteiner, Florian Kronenberg, Lukas Forer
Summary: This paper presents a major upgrade to the Haplogrep software, including added features such as haplogroup summary statistics and variant annotations from various genome databases, improved algorithms for large-scale data, and a new web framework. These improvements allow researchers to classify and investigate thousands of samples more conveniently.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, General & Internal
Ferdinand J. Donhauser, Martina E. Zimmermann, Anna B. Steinkirchner, Simon Wiegrebe, Alexander Dietl, Caroline Brandl, Ralph Burkhardt, Andre Gessner, Frank Schweda, Tobias Bergler, Elke Schaeffner, Carsten A. Boeger, Florian Kronenberg, Andreas Luchner, Klaus J. Stark, Iris M. Heid
Summary: Cardiovascular risk factors are common in old-aged individuals, but there is limited population-based data on their control in this population. The AugUR cohort study analyzed the cardiovascular risk factor control in the 70+-year-old population of/near Regensburg. The study found that a significant proportion of participants had high LDL-cholesterol, HbA1c, or blood pressure levels beyond recommended levels, and these factors were associated with impaired kidney function.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Pharmacology & Pharmacy
Marlys L. Koschinsky, Erik S. G. Stroes, Florian Kronenberg
Summary: This review focuses on the causal association between Lipoprotein(a) (Lp(a)) and cardiovascular outcomes, the mechanisms by which elevated Lp(a) contributes to cardiovascular diseases, the metabolic insights on the production and clearance of Lp(a), and the current and future therapeutic approaches to lower Lp(a) concentrations.
PHARMACOLOGICAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Adriana Koller, Claudia Lamina, Caroline Brandl, Martina E. Zimmermann, Klaus J. Stark, Hansi Weissensteiner, Reinhard Wuerzner, Iris M. Heid, Florian Kronenberg, Jay Stewart
Summary: This study suggests that mtDNA copy number in blood may serve as a more accessible biomarker for age-related macular degeneration (AMD) than mtDNA copy number in the retina, providing new insights into the relationship between mtDNA-CN and AMD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
