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
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.
Review
Biochemistry & Molecular Biology
Imane Lalami, Carole Abo, Bruno Borghese, Charles Chapron, Daniel Vaiman
Summary: This review discusses the genetics of endometriosis, a common feminine disease with a genetic heritability estimated at around 50%. Large GWAS studies have identified some genes and loci associated with the disease, but a significant portion of the heritability remains unexplained. Additional efforts such as exome sequencing may be needed to fully elucidate the genetic factors of endometriosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Allergy
Antonino Romano, Abderrahim Oussalah, Celine Chery, Rosa-Maria Gueant-Rodriguez, Francesco Gaeta, Jose-Antonio Cornejo-Garcia, Pierre Rouyer, Thomas Josse, Cristobalina Mayorga, Maria-Jose Torres, Jean-Louis Gueant
Summary: The study revealed a strong association between the HLA-DRB3 gene locus and an increased risk of delayed penicillin hypersensitivity, with specific alleles increasing the risk of delayed reactions. The potential value of the HLA-DRB3*02:02 allele in the risk management of delayed hypersensitivity to penicillins was suggested for further evaluation in larger population samples of diverse origins.
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)
Review
Microbiology
Navisha Dookie, Azraa Khan, Nesri Padayatchi, Kogieleum Naidoo
Summary: This review discusses the potential of next generation whole genome sequencing (WGS) in accelerating individualized care for tuberculosis (TB), as well as the challenges and mechanisms of drug resistance and its implications on diagnosis and treatment.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Oncology
Richard J. Marrero, Jatinder K. Lamba
Summary: Acute myeloid leukemia (AML) is a rare blood cancer that develops from malignant myeloid precursor cells in the bone marrow. There is a lack of genome-wide association studies specifically focused on AML, despite the increasing number of studies in other types of cancer. This review summarizes recent genome-wide studies in AML and highlights the challenges and limitations in researching this rare and heterogeneous disease.
Article
Biotechnology & Applied Microbiology
Jie Gao, Xin Hu, Chunyan Gao, Guang Chen, Hui Feng, Zhen Jia, Peimin Zhao, Haiyang Yu, Huaiwen Li, Zedong Geng, Jingbo Fu, Jun Zhang, Yikeng Cheng, Bo Yang, Zhanghan Pang, Daoquan Xiang, Jizeng Jia, Handong Su, Hailiang Mao, Caixia Lan, Wei Chen, Wenhao Yan, Lifeng Gao, Wanneng Yang, Qiang Li
Summary: This study used a non-invasive and high-throughput phenotyping platform to monitor a diverse wheat panel and investigate the genetic controls of growth and yield-related traits. By conducting whole genome re-sequencing and a genome-wide association analysis, the study identified numerous marker-trait associations and quantitative trait loci (QTLs) that contribute to wheat growth and yield production. The temporal dynamics of these QTLs were also revealed. This research provides insights into optimizing wheat growth and yield, and offers the potential for high-throughput early selection to accelerate breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Vylyny Chat, Robert Ferguson, Leah Morales, Tomas Kirchhoff
Summary: Ultra low-coverage whole-genome sequencing (ulcWGS) has shown comparable or superior performance to traditional genotyping arrays in genotype accuracy, with lower cost. It is considered an attractive alternative in next-generation GWAS design.
FRONTIERS IN GENETICS
(2022)
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)
Review
Biotechnology & Applied Microbiology
Chao Ye, Xinyu Wei, Tianqiong Shi, Xiaoman Sun, Nan Xu, Cong Gao, Wei Zou
Summary: This article reviews the development of genome-scale metabolic network models and discusses their importance in industrial biotechnology and human health applications. The challenges and future trends of GSMMs are also addressed.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
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
Genetics & Heredity
Guangyuan Zhou, Tianfei Liu, Yan Wang, Hao Qu, Dingming Shu, Xinzheng Jia, Chenglong Luo
Summary: This study identifies a genomic location on chromosome 1 that is significantly associated with hyperpigmentation of the visceral peritoneum in yellow-feathered chickens. Multiple SNP markers related to functional genes were found in this region. Additionally, a melanoma-associated gene, CYP2D6, was also found to be possibly involved in the development of HVP.
FRONTIERS IN GENETICS
(2022)
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)
Article
Pharmacology & Pharmacy
Bayew Tsega Abebe, Michael Weiss, Christiane Modess, Tobias Tadken, Danilo Wegner, Marleen J. Meyer, Ulrich Schwantes, Claudia Neumeister, Eberhard Scheuch, Hans-Ulrich Schulz, Mladen Tzvetkov, Werner Siegmund
JOURNAL OF CLINICAL PHARMACOLOGY
(2020)
Article
Pharmacology & Pharmacy
Ole Jensen, Johannes Matthaei, Felix Blome, Matthias Schwab, Mladen V. Tzvetkov, Juergen Brockmoeller
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2020)
Article
Pharmacology & Pharmacy
Sarah Romer, Marleen J. Meyer, Kathrin Klein, Lennart V. Schneider, Johannes Matthaei, Ana Tzvetkova, Joanna Lapczuk-Romanska, Jochen Gaedcke, Marek Drozdzik, Jurgen Brockmoeller, Anne T. Nies, Mladen V. Tzvetkov
Summary: rs35854239 variant partially affects OCT1 splicing, leading to moderate changes in OCT1 expression in the human liver. The alternative spliced OCT1 transcript is not correctly localized in the plasma membrane and unable to transport substrates. However, this variant does not significantly impact the pharmacokinetics of drugs like sumatriptan and fenoterol.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Ole Jensen, Johannes Matthaei, Henry G. Klemp, Marleen J. Meyer, Jurgen Brockmoller, Mladen V. Tzvetkov
Summary: This study confirmed IBC as an endogenous biomarker of OCT1 activity in humans, with OCT1 potentially regulating cellular concentrations of specific regulators or co-substrates in lipid and energy metabolism. Unlike in mice, OCT1 in humans may not directly mediate the efflux of IBC, suggesting a different mechanism for the association between blood concentrations of carnitine derivatives and OCT1 genotype in humans.
FRONTIERS IN PHARMACOLOGY
(2021)
Editorial Material
Pharmacology & Pharmacy
Marleen J. Meyer, Mladen V. Tzvetkov
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Johannes Matthaei, Juergen Brockmoeller, Werner Steimer, Konstanze Pischa, Stefan Leucht, Maria Kullmann, Ole Jensen, Typhaine Ouethy, Mladen Vassilev Tzvetkov, Muhammad Rafehi
Summary: The pharmacokinetics of the tricyclic antidepressant amitriptyline is primarily influenced by the genotypes of CYP2D6 and CYP2C19, with OCT1 genetic variation playing a minor role. Inhibition of OCT1 by amitriptyline and nortriptyline in vitro was observed, but significant effects of OCT1 genetic polymorphism on drug pharmacokinetics were not found in clinical studies with healthy volunteers and depressive disorder patients.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemical Research Methods
Saskia Floerl, Annett Kuehne, Joachim Geyer, Juergen Brockmoeller, Mladen V. Tzvetkov, Yohannes Hagos
Summary: The study revealed a strong correlation in transport kinetics and inhibition pattern between human NTCP and mouse Ntcp, but specific compounds like benzbromarone showed significant species differences. Such differences need to be taken into consideration when transferring pharmacokinetic data from rodents to humans.
Article
Immunology
Eileen Moritz, Gabriele Jedlitschky, Josefine Negnal, Mladen Tzvetkov, Guenter Daum, Marcus Doerr, Stephan B. Felix, Henry Voelzke, Matthias Nauck, Edzard Schwedhelm, Peter Meisel, Thomas Kocher, Bernhard H. Rauch, Birte Holtfreter
Summary: The study found that S1P serum concentrations were significantly increased in patients with periodontitis and were correlated with high-sensitivity C-reactive protein levels. There was no significant association with caries variables, but the expression of the S1P-generating enzyme was elevated in inflamed gingival tissue compared to normal tissue.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Carolin Seifert, Ellen Balz, Susann Herzog, Anna Korolev, Sebastian Gassmann, Heiko Paland, Matthias A. Fink, Markus Grube, Sascha Marx, Gabriele Jedlitschky, Mladen Tzvetkov, Bernhard H. Rauch, Henry W. S. Schroeder, Sandra Bien-Moeller
Summary: Research has shown that PIM1 kinase plays a significant role in the behavior of glioblastoma stem cells, and its inhibition can lead to the death of these stem-like cells, suggesting a potential approach for glioblastoma therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, General & Internal
Caspar Mewes, Tessa Alexander, Benedikt Buttner, Jose Hinz, Ayelet Alpert, Aron-F Popov, Tim Beissbarth, Mladen Tzvetkov, Marian Grade, Michael Quintel, Ingo Bergmann, Ashham Mansur
Summary: The study investigated the impact of the rs951818 SNP of the LAG-3 gene on sepsis mortality and disease severity. AA-homozygote patients had lower 28-day mortality and more often required invasive mechanical ventilation compared to C-allele carriers. The findings suggest genetic profiling of LAG-3 variants could be a promising approach for risk stratification in sepsis patients and personalized therapeutic targeting of immune checkpoints may be a future component of sepsis therapy.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Pharmacology & Pharmacy
Adrian Rump, Franziska N. Weiss, Louisa Schulz, Marie-Luise Kromrey, Eberhard Scheuch, Mladen V. Tzvetkov, Tyler White, Shane Durkee, Kevin W. Judge, Vincent Jannin, Aouatef Bellamine, Werner Weitschies, Michael Grimm
Summary: Controlling the timing and location of release of active ingredients in the gastrointestinal tract after oral administration remains a challenge. This study used MRI and salivary tracing techniques to investigate the impact of different combinations of capsule sizes and materials on the disintegration site and time. Results suggested that variability in the gastrointestinal localization of disintegration was lowest for the DUOCAP(R) capsule-in-capsule configuration using DRcaps(R) designed release capsules, enabling targeted delivery to the distal small intestine.
Article
Biochemistry & Molecular Biology
Marleen Julia Meyer, Simon Falk, Sarah Roemer, Clarissa Prinzinger, Sabine Tacke, Joachim Geyer, Stefan Simm, Mladen Vassilev Tzvetkov
Summary: In this study, the cloned dog OCT1 and OCT2 were compared to their human and mouse orthologs, revealing significant differences in transport kinetics. The functional characterization of dog OCT1 and OCT2 provides valuable insights for the use of dogs as pre-clinical models and for drug therapy in dogs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Marleen J. Meyer, Pascale C. F. Schreier, Mert Basaran, Stefaniia Vlasova, Tina Seitz, Juergen Brockmoeller, Barbara Zdrazil, Mladen V. Tzvetkov
Summary: This study analyzed the differences between human and mouse OCT1 orthologs and identified nonconserved amino acids Cys36 and Phe32 as determinants of OCT1 polyspecificity. It also found that the second phenol ring in Cys36 is essential for the affinity of fenoterol. This is the first study to report single amino acids as determinants of OCT1 polyspecificity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Eik Schaefer, Christian Scheer, Karen Salje, Anja Fritz, Thomas Kohlmann, Nils-Olaf Huebner, Matthias Napp, Lizon Fiedler-Lacombe, Dana Stahl, Bernhard Rauch, Matthias Nauck, Uwe Voelker, Stephan Felix, Guglielmo Lucchese, Agnes Floeel, Stefan Engeli, Wolfgang Hoffmann, Klaus Hahnenkamp, Mladen Tzvetkov
Summary: In this study, we analyzed the symptoms and comorbidities of COVID-19 patients in North-East Germany and found that ageusia without anosmia was associated with the highest risk of hospitalization. Other symptoms such as dyspnea, vomiting, and fever were also significantly associated with increased hospitalization risk. Age > 60 years and comorbidities such as COPD, prior stroke, diabetes, kidney, and cardiac diseases were further identified as risk factors for hospitalization. These findings highlight the importance of considering both symptoms and comorbidities in identifying patients at high risk of hospitalization.
SCIENTIFIC REPORTS
(2022)
Article
Endocrinology & Metabolism
Angelique Kragl, Anke Hannemann, Matthias Nauck, Uwe Voelker, Heide Siggelkow, Alexander Teumer, Mladen V. Tzvetkov
Summary: Osteporosis is a chronic disease characterized by reduced bone mineral density and increased fracture risk. This study found significant associations between certain genetic variants and bone properties, supporting the role of genetic disposition in osteoporosis development. The study also identified a novel causal role of SCD expression in adipose tissue on bone integrity.
CALCIFIED TISSUE INTERNATIONAL
(2023)