Article
Agriculture, Dairy & Animal Science
Jun Teng, Changheng Zhao, Dan Wang, Zhi Chen, Hui Tang, Jianbin Li, Cheng Mei, Zhangping Yang, Chao Ning, Qin Zhang
Summary: This study evaluated the performance of several imputation methods in Holstein cattle using LCS data and found that GLIMPSE, QUILT, and STITCH performed better than other methods, with an imputation accuracy over 0.9.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King, Charles Cox
Summary: The study found that low-pass sequencing to a depth above 0.4x coverage achieves higher power for association studies in pharmacogenetics compared to genotyping arrays.
Article
Multidisciplinary Sciences
Rui Marcalo, Sonya Neto, Miguel Pinheiro, Ana J. Rodrigues, Nuno Sousa, Manuel A. S. Santos, Paula Simao, Carla Valente, Lilia Andrade, Alda Marques, Gabriela R. Moura
Summary: This study reveals a high genetic heterogeneity for COVID-19 susceptibility and severity across global populations, and it suggests that the prognosis of patients with COPD is not related to genetic risk.
Article
Public, Environmental & Occupational Health
Kylie Getz, Rebecca A. Hubbard, Kristin A. Linn
Summary: This study compares multiple imputation methods using plasmode simulations based on a nationwide EHR-derived de-identified database. The results show that under missingness completely at random, chained equations and random forest methods have low bias and similar standard errors. However, denoising autoencoders have higher bias under missingness at random. In the case of missingness not at random, all methods exhibit substantial bias.
Article
Biochemical Research Methods
Kristiina Ausmees, Carl Nettelblad
Summary: The study investigates the benefits of an imputation method based on haplotype frequencies in ancient DNA analysis, showing improved accuracy and ability to capture rare variation at lower coverages. The software prophaser is optimized for parallel processing on GPUs, offering reasonable runtimes in experiments.
Article
Fisheries
Baltasar F. Garcia, Grazyella M. Yoshida, Roberto Carvalheiro, Jose M. Yanez
Summary: This study evaluated the feasibility of genotype imputation from medium density to sequence level in Nile tilapia and investigated the impacts of size and origin of reference population in the accuracy of imputation. The results showed that using more animals from the same population as reference improved the accuracy of imputation, while using information from other populations had minor effect on imputation accuracy.
Article
Biochemistry & Molecular Biology
Zhichao Li, Xiaosen Jiang, Mingyan Fang, Yong Bai, Siyang Liu, Shujia Huang, Xin Jin
Summary: The Chinese Millionome Database (CMDB) is a database that contains low-coverage whole-genome sequencing (WGS) data from 141,431 unrelated healthy Chinese individuals, covering 9.04 million single nucleotide variants (SNV) with allele frequency information. The CMDB is the most representative and comprehensive Chinese population genome database to date, housing data from a multi-ethnic Chinese population with wide geographical distribution.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Psychiatry
Bettina Konte, James T. R. Walters, Dan Rujescu, Sophie E. Legge, Antonio F. Pardinas, Dan Cohen, Munir Pirmohamed, Jari Tiihonen, Annette M. Hartmann, Jan P. Bogers, Jan van der Weide, Karen van der Weide, Anu Putkonen, Eila Repo-Tiihonen, Tero Hallikainen, Ed Silva, Oddur Ingimarsson, Engilbert Sigurdsson, James L. Kennedy, Patrick F. Sullivan, Marcella Rietschel, Gerome Breen, Hreinn Stefansson, Kari Stefansson, David A. Collier, Michael C. O'Donovan, Ina Giegling
Summary: The study suggests that the HLA-DQB1 gene plays a significant role in clozapine-induced agranulocytosis and neutropenia, indicating the involvement of immune system factors. Using local ancestry estimates can help identify risk variants and improve the prediction of hematological adverse effects.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Chemistry, Multidisciplinary
Jose Vidal-Paz, Benigno Antonio Rodriguez-Gomez, Jose A. Orosa
Summary: A GIS-based application is being developed to develop models involving environmental variables in the Galicia region of Spain. The study evaluated four imputation methods to estimate missing rainfall data, and found that the missForest method provided the best results.
APPLIED SCIENCES-BASEL
(2023)
Article
Biology
Rongrong Ding, Rodrigo Savegnago, Jinding Liu, Nanye Long, Cheng Tan, Gengyuan Cai, Zhanwei Zhuang, Jie Wu, Ming Yang, Yibin Qiu, Donglin Ruan, Jianping Quan, Enqin Zheng, Huaqiang Yang, Zicong Li, Suxu Tan, Mohammed Bedhane, Robert Schnabel, Juan Steibel, Cedric Gondro, Jie Yang, Wen Huang, Zhenfang Wu
Summary: The SWine IMputation (SWIM) haplotype reference panel and web server provide a valuable resource for improving imputation and genetic discoveries in pigs. By developing a reference haplotype panel based on 2259 whole genome-sequenced animals representing 44 pig breeds, this study overcomes the limitation of low density genotyped variant sites, resulting in improved genetic mapping resolution. The use of this resource for genotype imputation demonstrates significant improvements in genetic mapping resolution.
COMMUNICATIONS BIOLOGY
(2023)
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
Multidisciplinary Sciences
Sho Hosoya, Sota Yoshikawa, Mana Sato, Kiyoshi Kikuchi
Summary: The study found that the prediction accuracy of genomic selection for standard length, body weight, and testes weight in tiger pufferfish was within an acceptable range when using 4000 or 1200 SNPs. However, predictive abilities decreased with less than 1200 SNPs due to reduced accuracy in estimating genetic relationships among individuals.
SCIENTIFIC REPORTS
(2021)
Article
Computer Science, Information Systems
Preeti Saini, Bharti Nagpal
Summary: The study focuses on imputing missing data in the Wheat crop yield Dataset to improve crop estimation or production forecasting. Different imputation techniques are explored and evaluated for their performance. The results show that the Arithmetic Average Replacement method performs well among the statistical methods, while Miss Forest and MICE methods perform well among the Machine Learning based methods.
MULTIMEDIA TOOLS AND APPLICATIONS
(2023)
Article
Agriculture, Multidisciplinary
Zhang Kai-li, Peng Xia, Zhang Sai-xian, Zhan Hui-wen, Lu Jia-hui, Xie Sheng-song, Zhao Shu-hong, Li Xin-yun, Ma Yun-long
Summary: Genotype imputation has become an essential part of genomic data analysis. This study investigates the impact of various influencing factors on imputation accuracy using the Illumina PorcineSNP50 Bead Chip and compares the performance of four commonly used imputation software programs. The results show that imputation accuracy is influenced by validation population marker density, reference population sample size, and minor allele frequency (MAF).
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Biology
Francisco M. Ortuno, Carlos Loucera, Carlos S. Casimiro-Soriguer, Jose A. Lepe, Pedro Camacho Martinez, Laura Merino Diaz, Adolfo de Salazar, Natalia Chueca, Federico Garcia, Javier Perez-Florido, Joaquin Dopazo
Summary: The ongoing global initiative for SARS-CoV-2 whole-genome sequencing has led to many incomplete or low-quality sequences due to the urgency of sequencing in emergency situations. The developed impuSARS application can impute missing data from the available massive viral genome sequences, improving the pace of sequencing production.
Article
Emergency Medicine
Guido Heyne, Sebastian Ewens, Holger Kirsten, Johannes Karl Maria Fakler, Orkun Ozkurtul, Gunther Hempel, Sebastian Kramer, Manuel Florian Struck
Summary: Short body height and high body mass index are associated with endobronchial intubation. The possibility of unrecognized endobronchial intubation should be considered in intubated major trauma patients suspected of pneumothorax before tube thoracostomy.
EMERGENCY MEDICINE JOURNAL
(2022)
Article
Pediatrics
Felix Blume, Holger Kirsten, Peter Ahnert, Trinad Chakraborty, Arnd Gross, Katrin Horn, Mohammad Reza Toliat, Peter Nurnberg, Eva-Maria Westenfelder, Wolfgang Goepel, Markus Scholz
Summary: The study verified the association of immunology-related genes with bronchopulmonary dysplasia (BPD), identifying 5 candidate SNPs associated with BPD phenotypes, with 4 genes involved in cell adhesion. The strongest association was found between rs45538638 of the ABCA3 gene and CPAP.
PEDIATRIC RESEARCH
(2022)
Article
Genetics & Heredity
Andreas Kuehnapfel, Katrin Horn, Ulrike Klotz, Michael Kiehntopf, Maciej Rosolowski, Markus Loeffler, Peter Ahnert, Norbert Suttorp, Martin Witzenrath, Markus Scholz
Summary: This study is the first context-specific genetic association study of blood cytokine concentrations in CAP patients, revealing numerous biologically plausible candidate genes.
Article
Multidisciplinary Sciences
Michael Thelwell, Alice Bullas, Andreas Kuehnapfel, John Hart, Peter Ahnert, Jon Wheat, Markus Loeffler, Markus Scholz, Simon Choppin
Summary: Traditional body measurement techniques may not fully capture the complexity of human body shape, while 3D imaging systems provide a more comprehensive representation. Geometric morphometrics offer an improved method of analyzing variation in human body shape by quantifying biological shape after accounting for non-shape variation.
Article
Multidisciplinary Sciences
Sibylle Schirm, Arash Haghikia, Markus Brack, Peter Ahnert, Geraldine Nouailles, Norbert Suttorp, Markus Loeffler, Martin Witzenrath, Markus Scholz
Summary: Atherosclerosis is a leading cause of death worldwide, and biomathematical modeling can help develop and improve prevention and treatment approaches. This study presents a biomathematical model of murine atherosclerosis, which can predict the disease progression and treatment outcomes under different diet and treatment conditions. By translating known biological mechanisms into mathematical equations and fitting model parameters using experimental data, the model accurately simulates the dynamics of atherosclerotic lesions.
Article
Virology
Yuri Kheifetz, Holger Kirsten, Markus Scholz
Summary: This study proposes a method based on a nonlinear dynamical system to predict the development of the pandemic, addressing the issues of parameter estimation bias caused by incomplete data and delayed reporting. The method can estimate and compare the effectiveness of non-pharmaceutical interventions and provide scenarios for the future course of the epidemic.
Article
Medicine, General & Internal
Manuel Florian Struck, Christian Kleber, Sebastian Ewens, Sebastian Ebel, Holger Kirsten, Sebastian Kraemer, Stefan Schob, Georg Osterhoff, Felix Girrbach, Peter Hilbert-Carius, Benjamin Ondruschka, Gunther Hempel
Summary: This study aims to investigate the rate of occult pneumothorax in trauma patients before initial computed tomography (CT) and analyze the role of chest CT in assessing thoracic pathology and injury severity. The results show that clinical decisions for chest tube placement (CTP) before CT are associated with significant false-negative and false-positive cases, indicating that a combination of clinical assessment and CT imaging is important for CTP decisions.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Respiratory System
Peter Pennitz, Holger Kirsten, Vincent D. Friedrich, Emanuel Wyler, Cengiz Goekeri, Benedikt Obermayer, Gitta A. Heinz, Mir-Farzin Mashreghi, Maren Buettner, Jakob Trimpert, Markus Landthaler, Norbert Suttorp, Andreas C. Hocke, Stefan Hippenstiel, Mario Toennies, Markus Scholz, Wolfgang M. Kuebler, Martin Witzenrath, Katja Hoenzke, Geraldine Nouailles
Summary: Single-cell RNA sequencing is important for studying biological processes, especially in lung research. We compared single-cell transcriptomes from six different species' lungs and identified marker genes using integrative approaches. This method helps identify transcriptomic signatures in different species' lung tissue and select appropriate models for future respiratory research.
EUROPEAN RESPIRATORY REVIEW
(2022)
Article
Multidisciplinary Sciences
Matthias Wuttke, Eva Koenig, Maria-Alexandra Katsara, Holger Kirsten, Saeed Khomeijani Farahani, Alexander Teumer, Yong Li, Martin Lang, Burulca Goecmen, Cristian Pattaro, Dorothee Guenzel, Anna Koettgen, Christian Fuchsberger
Summary: A genotype imputation approach was applied to whole exome sequencing data from the UK Biobank, resulting in the discovery of 158 rare variants and 105 genes significantly associated with kidney function traits. This approach boosts statistical power and provides a comprehensive resource for directing experimental and clinical studies of kidney disease.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Cengiz Goekeri, Peter Pennitz, Wibke Groenewald, Ulrike Behrendt, Holger M. Kirsten, Christian Zobel, Sarah A. Berger, Gitta Heinz, Mir-Farzin Mashreghi, Sandra-Maria Wienhold, Kristina Dietert, Anca D. Dorhoi, Achim Gruber, Markus Scholz, Gernot Rohde, Norbert Suttorp, Geraldine CAPNETZ Study Grp, Martin Witzenrath, Geraldine Nouailles
Summary: This study aimed to investigate the role of microRNA-223 in orchestrating pulmonary inflammation during pneumococcal pneumonia. It was found that low levels of serum microRNA-223 correlated with increased disease severity in patients. In murine experiments, the absence of microRNA-223 led to increased neutrophilic influx into the lungs, resulting in aggravated histopathology and acute lung injury.
Article
Immunology
Elisa Regenhardt, Holger Kirsten, Melanie Weiss, Christoph Luebbert, Sebastian N. Stehr, Yvonne Remane, Corinna Pietsch, Mario Hoenemann, Amrei von Braun
Summary: Understanding breakthrough infections of SARS-CoV-2 in vaccinated healthcare workers is crucial in controlling the impact of the COVID-19 pandemic in healthcare facilities. A cohort study was conducted to investigate acute SARS-CoV-2 infections in vaccinated employees. The majority of breakthrough infections were symptomatic, with high viral loads and prolonged shedding. Neutralizing antibody titers were highest for the wildtype, intermediate for Delta, and lowest for Omicron variants. Lower levels of anti-RBD-IgG were associated with higher viral loads for both variants. Overall, the clinical course of infection was mild to moderate, but immune response waned over time.
Article
Pediatrics
Manuel Florian Struck, Franziska Rost, Thomas Schwarz, Peter Zimmermann, Manuela Siekmeyer, Daniel Graefe, Sebastian Ebel, Holger Kirsten, Christian Kleber, Martin Lacher, Bernd Donaubauer
Summary: This study analyzed the performance of different vascular access procedures in severely injured pediatric trauma patients from the scene to admission. The results showed that successful IV or IO access was achieved by emergency medical service physicians at the scene, but there were some issues upon ED admission. Mechanical complications were also observed in the OR and ICU. Therefore, special preparedness is necessary in prehospital, ED, ICU, and OR environments.
Article
Oncology
Manuel Florian Struck, Robert Werdehausen, Holger Kirsten, Holger Goessmann, Rhea Veelken, Florian van Boemmel, Sebastian Stehr, Timm Denecke, Sebastian Ebel
Summary: This retrospective analysis found that high perioperative infusion volumes and the omission of heparin reversal with protamine were associated with postoperative bleeding complications. High infusion volumes also contributed to a length of stay in the intensive care unit of more than one day. Our findings suggest a restrictive perioperative infusion regime and support the use of postoperative protamine for heparin reversal in chemosaturation procedures.
Article
Biochemistry & Molecular Biology
Andreas Kuehnapfel, Peter Ahnert, Katrin Horn, Holger Kirsten, Markus Loeffler, Markus Scholz
Summary: Body height, body mass index, hip and waist circumference are important risk factors or outcome variables in clinical and epidemiological research. However, there is limited research on other traits with potentially higher functional specificity. This study used a three-dimensional body scanner to assess participants and identified genetic loci associated with various anthropometric traits. The findings suggest that 3D laser-based anthropometry is promising for discovering new loci and improving the understanding of established ones.
Meeting Abstract
Respiratory System
P. Pennitz, H. Kirsten, E. Wyler, C. Goekeri, B. Obermayer, A. G. Heinz, F. M. Mashreghi, J. Trimpert, M. Landthaler, N. Suttorp, C. A. Hocke, S. Hippenstiel, M. Toennies, M. Scholz, M. W. Kuebler, M. Witzenrath, K. Hoenzke, G. Nouailles
