Article
Immunology
Ferhat Guzel, Micol Romano, Erdi Keles, David Piskin, Seza Ozen, Hakan Poyrazoglu, Ozgur Kasapcopur, Erkan Demirkaya
Summary: This study describes the development and validation of an NGS-based multiplex array for targeted sequencing of nine genes associated with common AIDs, offering a cost-effective, comprehensive, and informative screening tool compared to other methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Review
Biotechnology & Applied Microbiology
Chu Cheng, Zhongjie Fei, Pengfeng Xiao
Summary: Next-generation sequencing (NGS) is widely used in life science research and clinical diagnosis. However, its high error rate poses challenges for detecting SNPs and low-abundance mutations, limiting its clinical applications. Sanger sequencing is still considered the gold standard and is used to verify the results of NGS in practice. Improvements have been made in template preparation, sequencing strategy, and data processing to ensure high-quality NGS data. Challenges and future development of NGS in clinical application are also discussed.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Cell Biology
Tamer Butto, Kanak Mungikar, Peter Baumann, Jennifer Winter, Beat Lutz, Susanne Gerber
Summary: In the last decade, there has been a significant increase in nuclei-based studies, especially in combination with next-generation sequencing. These studies aim to understand the molecular states in heterogeneous cell populations using more affordable sequencing approaches and optimized nuclei isolation methods. While these powerful new methods offer unprecedented insights, it is important to consider the associated challenges critically. This article provides a comprehensive overview of the rise of nuclei-based studies and discusses their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improving experimental designs and using various strategies appropriately will lead to biologically accurate and meaningful information.
Article
Chemistry, Analytical
Eleen Y. Shum, Janice H. Lai, Sixing Li, Haeun G. Lee, Jesse Soliman, Vedant K. Raol, Cavina K. Lee, Stephen P. A. Fodor, H. Christina Fan
Summary: UltraPCR is a next-generation dPCR system that enables single-molecule DNA counting with a swift and parallelized workflow. Each reaction is divided into over 30 million partitions, allowing for single-template occupancy, and the use of unique emulsion chemistry and three-dimensional imaging technique for rapid detection. This system has the potential for high precision, accuracy, and reproducibility, making it suitable for noninvasive prenatal screening.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Isolde van Riemsdijk, Jan W. Arntzen, Wieslaw Babik, Serge Bogaerts, Michael Franzen, Konstantinos Kalaentzis, Spartak N. Litvinchuk, Kurtulus Olgun, Jan Willem P. M. Wijnands, Ben Wielstra
Summary: This study utilizes parallel tagged amplicon sequencing to obtain nuclear DNA markers for banded newts and investigates population structure, interspecific gene flow, and phylogenetic relationships. The results confirm the genetic distinctiveness of the three proposed species and suggest a sister relationship between O. nesterovi and O. ophryticus. Limited introgression between the two species is found. Intraspecific structuring is extensive, with the recognized subspecies O. vittatus cilicensis representing the most distinct lineage. Mitochondrial DNA shows some discrepancies with nuclear DNA patterns among the banded newt species.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Cell Biology
Yuechun Yu, Ke Wang, Aamir Fahira, Qiangzhen Yang, Renliang Sun, Zhiqiang Li, Zhuo Wang, Yongyong Shi
Summary: The HLA system plays a crucial role in transplantation and immunotherapy, but HLA typing remains challenging. New algorithms and software tools have been developed, yet there is a lack of systematic comparative studies. Research compared eight HLA typing software tools across different scenarios, assisting researchers in selecting the most appropriate tool for specific datasets.
Article
Immunology
William F. Wright, Patricia J. Simner, Karen C. Carroll, Paul G. Auwaerter
Summary: Despite the continued prevalence of infectious diseases as the main cause of fever of unknown origin, advancements in molecular technologies offer hope in transforming the investigation of this condition by potentially replacing traditional microbial identification methods.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Genetics & Heredity
So Young Kang, Deok Geun Kim, Hyunjin Kim, Yoon Ah Cho, Sang Yun Ha, Ghee Young Kwon, Kee-Taek Jang, Kyoung-Mee Kim
Summary: This study validates the sensitivity of PCR for detecting TERT promoter mutations by comparing the results of PCR kit and NGS. The presence of TERT mutations was successfully verified in all 103 cases using PCR. The average read depth of the TERT promoter region was lower compared to other genes, with significantly higher depth at C250 compared to C228.
BMC MEDICAL GENOMICS
(2022)
Review
Plant Sciences
Philomena Chu, Sarah Zanon Agapito-Tenfen
Summary: Classical genetic engineering and new genome editing techniques, especially CRISPR/Cas technology, have increased the possibilities for modifying genetic material in organisms, potentially offering novel agricultural traits. However, concerns arise from unintended genetic modifications reported as side-effects. This systematic review of scientific literature on unintended genomic alterations in plants modified through various techniques reveals a wide range of effects, from small nucleotide polymorphisms to large structural variations, with a potential underestimation due to limited use of comprehensive sequencing methods. Future research should focus on more thorough examination of analytical methods to provide regulators with valuable information for detection and identification of genomic interventions.
Review
Infectious Diseases
Koay Chun Giok, Rohit Kunnath Menon
Summary: It is beneficial to use mechanical debridement augmented with antibiotics for the treatment of peri-implantitis. The microbial profile plays a key role in selecting the appropriate antibiotics. Further studies with standardization and universal clinical parameters are needed for a better understanding of peri-implantitis.
Review
Oncology
Anisha Luthra, Brooke Mastrogiacomo, Shaleigh A. Smith, Debyani Chakravarty, Nikolaus Schultz, Francisco Sanchez-Vega
Summary: NGS technologies have been widely adopted in cancer research and clinical care in the past decade, enabling patient stratification, biomarker identification, heritable cancer risk assessment, and treatment monitoring. The development of novel algorithms, computational pipelines, and structured knowledge bases has been crucial for downstream data processing and interpretation. Collaborations across institutions have led to the creation of large pooled datasets that offer valuable insights into the genomics of rare cancers.
GENES CHROMOSOMES & CANCER
(2022)
Article
Food Science & Technology
Rosalia Rodriguez-Riveiro, Amaya Velasco, Carmen G. Sotelo
Summary: This study compares five DNA extraction methods based on quantity, quality, and simplicity to determine the most suitable method for species identification. Significant differences were found among the methods in terms of yield, efficiency, and purity, but not in terms of the species employed. The Wizard kit showed the highest yield, while other methods stood out for affordability (Chelex) and automation (Mpure).
Review
Biology
Haeun Lee, Jun Won Min, Seyoung Mun, Kyudong Han
Summary: This review discusses the recently studied and utilized NGS technologies and effective computational approaches for discovering retrotransposons. NGS has provided new perspectives for detecting retrotransposon-mediated SVs and various computational methods have been developed for accurately detecting insertions and deletions in the human genome.
Review
Cardiac & Cardiovascular Systems
Liam W. McQueen, Shameem S. Ladak, Riccardo Abbasciano, Sarah J. George, M-Saadeh Suleiman, Gianni D. Angelini, Gavin J. Murphy, Mustafa Zakkar
Summary: This review assesses the use of single-cell and next-generation sequencing techniques in studying atherosclerosis and vascular inflammation. The results show that these methods provide high-resolution analysis of the disease and have potential for application in other vascular diseases. However, there is significant heterogeneity in the results of single-cell sequencing.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Letter
Clinical Neurology
Felix Kleefeld, Anja von Renesse, Carsten Dittmayer, Lutz Harms, Josefine Radke, Helena Radbruch, Hans-Hilmar Goebel, Florence Pache, Udo Schneider, Markus Schuelke, Akinori Uruha, Werner Stenzel
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2022)
Article
Genetics & Heredity
Guido Vogt, Sarah Verheyen, Sarina Schwartzmann, Nadja Ehmke, Cornelia Potratz, Anette Schwerin-Nagel, Barbara Plecko, Manuel Holtgrewe, Dominik Seelow, Jasmin Blatterer, Michael R. Speicher, Uwe Kornak, Denise Horn, Stefan Mundlos, Bjorn Fischer-Zirnsak, Felix Boschann
Summary: Pathogenic variants in the ATP9A gene cause a novel autosomal recessive neurodevelopmental disorder characterized by postnatal microcephaly. ATP9A plays a crucial role in endosomal transport, with variants leading to a reduction in mRNA expression and altered gene expression of components related to endosomes.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Clinical Neurology
Annegret Quade, Kevin Rostasy, Ronny Wickstrom, Omer Faruk Aydin, Stefano Sartori, Margherita Nosadini, Ellen Knierim, Gerhard Kluger, Rudolf Korinthenberg, Burkhard Stueve, Stephan Waltz, Steffen Leiz, Martin Haeusler
Summary: This study reports 15 patients with autoimmune encephalitis associated with NMDAR1 autoantibodies, who presented with movement abnormalities or neuropsychiatric symptoms as major complaints following herpes encephalitis. Early diagnosis and treatment of autoimmune encephalitis may be associated with a better outcome.
Article
Neurosciences
Ellen Knierim, Johannes Vogt, Michael Kintscher, Alexey Ponomarenko, Jan Baumgart, Prateep Beed, Tatiana Korotkova, Thorsten Trimbuch, Axel Panzer, Ortrud K. Steinlein, Ulrich Stephani, Andrew Escayg, Mahmoud Koko, Yuanyuan Liu, Holger Lerche, Dietmar Schmitz, Robert Nitsch, Markus Schuelke
Summary: The PLPPR4 gene encodes the PRG-1 protein, which modulates cortical excitatory transmission. Variants in the PLPPR4 gene are associated with BFNS/BFIS. The study found that partial loss-of-function of the Plppr4 gene has an impact on the development of BFNS/BFIS.
Article
Biochemistry & Molecular Biology
Henrike L. Sczakiel, Max Zhao, Brigitte Wollert-Wulf, Magdalena Danyel, Nadja Ehmke, Corinna Stoltenburg, Nadirah Damseh, Motee Al-Ashhab, Tugce B. Balci, Matthew Osmond, Andrea Andrade, Jens Schallner, Joseph Porrmann, Kimberly McDonald, Mingjuan Liao, Henry Oppermann, Konrad Platzer, Nadine Dierksen, Majid Mojarrad, Atieh Eslahi, Behnaz Bakaeean, Daniel G. Calame, James R. Lupski, Zahra Firoozfar, Seyed Mohammad Seyedhassani, Seyed Ahmad Mohammadi, Najwa Anwaar, Fatima Rahman, Dominik Seelow, Martin Janz, Denise Horn, Reza Maroofian, Felix Boschann
Summary: FINCA syndrome is an autosomal recessive multisystem disorder characterized by fibrosis, neurodegeneration, and cerebral angiomatosis. This study presents 15 individuals from 12 families with an overlapping phenotype associated with nine novel NHLRC2 variants. The study also proposes a potential genotype-phenotype correlation, with a greater reduction in protein expression being associated with a more severe phenotype.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Clinical Neurology
Felix Kleefeld, Andreas Hentschel, Arpad von Moers, Katrin Hahn, Rita Horvath, Hans-Hilmar Goebel, Corinna Preusse, Jens Schallner, Markus Schuelke, Andreas Roos, Werner Stenzel
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2023)
Editorial Material
Biochemistry & Molecular Biology
Dominik Seelow
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell & Tissue Engineering
Marie-Therese Henke, Annika Zink, Sebastian Diecke, Alessandro Prigione, Markus Schuelke
Summary: We generated two pairs of mother-child iPSCs lines carrying the m.8993 T > G and m.9176 T > G mutations in the MT-ATP6 gene for Maternally Inherited Leigh Syndrome (MILS) using Sendai virus-mediated delivery of reprogramming factors OCT4, SOX2, KLF4, and c-MYC. All iPSCs lines exhibited a normal karyotype, expressed pluripotency markers, and differentiated into the three germ layers. The patient-iPSCs retained the same levels of heteroplasmy as the source fibroblasts (>97.0%), with the heteroplasmy remaining at 0.0% for the m.8993 T > G mutation and decreasing from 55.0% to 1.0% for the m.9176 T > G mutation in maternal iPSCs.
STEM CELL RESEARCH
(2023)
Article
Cell Biology
Sofia Schnell, Ellen Knierim, Petra Bittigau, Jakob Kreye, Kathrin Hauptmann, Patrick Hundsdoerfer, Susanne Morales-Gonzalez, Markus Schuelke, Marc Nikolaus
Summary: Ophelia syndrome is characterized by the coincidence of severe neuropsychiatric symptoms, classical Hodgkin lymphoma, and the presence of antibodies to the metabotropic glutamate 5 receptor (mGluR5). The expression of mGluR5 differs among classical Hodgkin lymphoma cell lines and is associated with upregulation of signaling pathways involved in lymphoma progression. Increased expression of mGluR5 is observed in the lymphoma tissue of Ophelia syndrome patients, suggesting a potential role in the development of autoimmune encephalitis. Further studies are needed to investigate the exact mechanisms underlying the pathogenesis of Ophelia syndrome.
Review
Clinical Neurology
Nina-Maria Wilpert, Ana Luisa de Almeida Marcelino, Ellen Knierim, Pasquale Incoronato, Elisa Sanchez-Sendin, Olga Staudacher, Anne Drenckhahn, Petra Bittigau, Jakob Kreye, Harald Pruess, Markus Schuelke, Andrea A. Kuehn, Angela M. Kaindl, Marc Nikolaus
Summary: In the fourth year of the COVID-19 pandemic, mortality rates decreased while the risk of neuropsychiatric disorders remained the same in pediatric cases, with a prevalence of 3.8%. A case study revealed a 10-year-old girl developing hemichorea after SARS-CoV-2 infection, and immunostaining of murine brain also showed the presence of unknown antigens in the patient's CSF. A scoping review identified 32 additional children with movement disorders or ataxia after COVID-19, and the etiology was suspected to be autoimmune in most cases.
JOURNAL OF NEUROLOGY
(2023)
Article
Clinical Neurology
Felix Kleefeld, Andreas Hentschel, Arpad von Moers, Katrin Hahn, Rita Horvath, Hans-Hilmar Goebel, Corinna Preusse, Jens Schallner, Markus Schuelke, Andreas Roos, Werner Stenzel
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2023)
Review
Clinical Neurology
Nina -Maria Wilpert, Davide Tonduti, Ylenia Vaia, Heiko Krude, Catherine Sarret, Markus Schuelke
Summary: This study involved patient families in defining patient-relevant outcomes for MCT8 deficiency. The most important therapeutic goals identified by the parents were improvement in development, particularly in gross motor skills. Other goals included head control, sitting ability, weight gain, improvement in expressive language skills, and reduction of dystonia/spasticity, dysphagia, and reflux. The importance of patient-centered clinical endpoints in treatment trials was emphasized.
NEUROPSYCHIATRIC DISEASE AND TREATMENT
(2023)
Article
Mathematical & Computational Biology
Samuele Garda, Freyda Lenihan-Geels, Sebastian Proft, Stefanie Hochmuth, Markus Schuelke, Dominik Seelow, Ulf Leser
Summary: Researchers have created RegEl, a freely available corpus annotated with regulatory DNA elements, to aid in the development of information extraction algorithms. Their entity detection models performed well and extracted large collections of genes or diseases associated with regulatory elements.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Gastroenterology & Hepatology
Marlene Panzer, Andre Viveiros, Benedikt Schaefer, Nadja Baumgartner, Klaus Seppi, Atbin Djamshidian, Theodor Todorov, William J. H. Griffiths, Eckart Schott, Markus Schuelke, Dennis Eurich, Albert Friedrich Stattermayer, Adrian Bomford, Pierre Foskett, Julia Vodopiutz, Rudolf Stauber, Elke Pertler, Bernhard Morell, Herbert Tilg, Thomas Mueller, Stefan Kiechl, Raul Jimenez-Heredia, Karl Heinz Weiss, Si Houn Hahn, Andreas Janecke, Peter Ferenci, Heinz Zoller
Summary: This study evaluated the prevalence and disease mechanism of the synonymous variant c.2292C>T (p.Phe764=) in Wilson disease. It was found that this variant has a higher allele frequency in Wilson disease patients and causes abnormal mRNA processing of ATP7B transcripts.
HEPATOLOGY COMMUNICATIONS
(2022)