Review
Biology
Adrian Munoz-Barrera, Luis A. Rubio-Rodriguez, Ana Diaz-de Usera, David Jaspez, Jose M. Lorenzo-Salazar, Rafaela Gonzalez-Montelongo, Victor Garcia-Olivares, Carlos Flores
Summary: This article provides a technical review of next-generation sequencing (NGS) applications in cancer research, particularly melanoma. It covers various methodological approaches, including library preparation, sequence variation assessment, and bioinformatics processing. The article also highlights key applications and compares the pros and cons of different sequencing platforms.
Article
Oncology
Margherita Rimini, Eleonora Loi, Carles Fabregat-Franco, Valentina Burgio, Sara Lonardi, Monica Niger, Mario Scartozzi, Ilario G. Raposelli, Giuseppe Aprile, Francesca Ratti, Federica Pedica, Helena Verdaguer, Mario Rizzato, Federico Nichetti, Eleonora Lai, Alessandro Cappetta, Teresa Macarulla, Matteo Fassan, Filippo De Braud, Andrea Pretta, Francesca Simionato, Francesco De Cobelli, Luca Aldrighetti, Lorenzo Fornaro, Stefano Cascinu, Zavattari Patrizia, Andrea Casadei-Gardini
Summary: This study identified three mutation-based clusters in IDH1-mutated intrahepatic cholangiocarcinomas (IDH1m iCCAs) and demonstrated their prognostic significance.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Health Care Sciences & Services
Antonio Juan Ribelles, Pablo Gargallo, Pablo Berlanga, Vanessa Segura, Yania Yanez, Barbara Juan, Marta Salom, Margarita Llavador, Jaime Font de Mora, Victoria Castel, Adela Canete
Summary: The study analyzed 70 pediatric sarcoma patients and detected 30 pathogenic mutations in 18 different genes through histopathological analysis and NGS testing. Targeted treatment was implemented in 6 patients, leading to a disease control rate of 78%, demonstrating feasibility of personalized therapy for pediatric sarcomas.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
Article
Genetics & Heredity
Manal Alaamery, Jahad Alghamdi, Salam Massadeh, Mona Alsawaji, Nora Aljawini, Nour Albesher, Bader Alghamdi, Mansour Almutairi, Fayez Hejaili, Majid Alfadhel, Batoul Baz, Bader Almuzzaini, Adel F. Almutairi, Mubarak Abdullah, Francisco J. Quintana, Abdullah Sayyari
Summary: This study aimed to investigate the genetic causes of end-stage renal disease (ESRD) in Saudi kidney disease patients, using a targeted next-generation sequencing gene panel. The results identified several genetic variants associated with ESRD and CKD in this population, including novel variants not previously reported in other populations. Further studies are needed to validate these findings in larger sample sizes and different ethnic groups.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Sara-Sophie Poethe, Julia Holtel, Jan-Philip Biermann, Trine Riemer, Melanie Grabmueller, Burkhard Madea, Ralf Thiele, Richard Jaeger
Summary: Forensic DNA profiles are typically established using multiplex PCR amplification and capillary electrophoresis (CE) analysis, but high-throughput next generation sequencing (NGS) techniques have recently been used as an alternative. In this study, an alternative NGS assay called maSTR assay was developed that is cost-effective and performs well in samples with low DNA content, mixed DNA, or PCR inhibitors. The maSTR assay, in conjunction with the SNiPSTR bioinformatics pipeline, is a simple and robust NGS-based STR typing method for human identification in forensic and biomedical contexts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Shuji Murakami, Tomoyuki Yokose, Daiji Nemoto, Masaki Suzuki, Ryou Usui, Yoshiro Nakahara, Tetsuro Kondo, Terufumi Kato, Haruhiro Saito
Summary: For patients with advanced non-small-cell lung cancer, having a tissue surface area of >= 1 mm^2 is sufficient for successful testing with NGS, regardless of the device used. The success rate of DNA and RNA sequencing was high overall, with large EBUS-GS demonstrating the highest success rates.
Article
Cell Biology
Jiang Xiulin, Chunyan Wang, Jishu Guo, Chenyang Wang, Chenglong Pan, Zhi Nie
Summary: The study found that 11 HOXAs were consistently up-regulated in both LGG and GBM tissues. Higher expression of HOXAs was significantly associated with advanced tumor stage, IDH mutation status, 1p/19q co-deletion, histological type, and primary therapy outcome. Survival analyses showed that elevated expression of various HOXAs correlated with shorter overall survival, disease-specific survival, and progression-free survival in LGG patients. Furthermore, the study revealed HOXAs' involvement in inflammatory response and immune regulation signaling pathways, as well as their correlation with immune cell infiltration, immune modulator, and drug sensitivity.
Article
Virology
Manasi Majumdar, Cristina Celma, Elaine Pegg, Krunal Polra, Jake Dunning, Javier Martin
Summary: The study focused on a detection method for enteroviruses using NGS analysis of clinical samples, showing high concordance with conventional Sanger sequencing and good sensitivity and specificity for different EV types. The NGS method identified previously untyped EVs and potential co-infections, demonstrating its potential for comprehensive EV detection and genetic analysis.
Article
Pathology
Junyan Tao, Dantong Sun, Hai Zhou, Jingjuan Zhu, Xiaochun Zhang, Helei Hou
Summary: The study showed that 39.7% of HGSOC patients harbored at least one actionable genetic alteration, with 25.0% of patients having mutations beyond BRCA1 that may require off-label therapy or participation in clinical trials. NGS assays are necessary to screen actionable genetic alterations in HGSOC patients for personalized and precise treatment.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Medical Laboratory Technology
Xiaohua Fang, Chaofeng Zhu, Xiaofan Zhu, Yin Feng, Zhihui Jiao, Huikun Duan, Xiangdong Kong, Ning Liu
Summary: This study evaluated gene variations in Chinese MPS patients using targeted NGS technology and identified 11 novel variants associated with disease. MPS II was found to be the most common type in China. The study expands the variation spectrum of MPS, which is important for disease management and genetic counseling.
CLINICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Pierre-Julien Viailly, Vincent Sater, Mathieu Viennot, Elodie Bohers, Nicolas Vergne, Caroline Berard, Helene Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie-Delphine Lanic, Sydney Dubois, Dominique Penther, Herve Tilly, Sylvain Mareschal, Fabrice Jardin
Summary: This study introduces a new method called molecular Copy Number Alteration (mCNA) for detecting copy number changes using unique molecular identifiers (UMI). The algorithm consists of four main steps: constructing UMI count matrices, using control samples to construct a pseudo-reference, computing log-ratios, segmenting, and statistically inferring abnormal segmented breaks. The success of mCNA was demonstrated on a dataset of patients with Diffuse Large B-cell Lymphoma, showing strong correlation with comparative genomic hybridization results.
BMC BIOINFORMATICS
(2021)
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.
Article
Virology
Sten Calvelage, Niina Tammiranta, Tiina Nokireki, Tuija Gadd, Elisa Eggerbauer, Luca M. Zaeck, Madlin Potratz, Claudia Wylezich, Dirk Hoeper, Thomas Mueller, Stefan Finke, Conrad M. Freuling
Summary: A new bat lyssavirus, Kotalahti bat lyssavirus (KBLV), was identified with high genetic similarity to EBLV-2, KHUV, and BBLV. It is classified as phylogroup I lyssavirus and likely associated with Brandt's bat, fulfilling criteria for species demarcation. Cross-neutralization studies suggest that conventional rabies vaccines may provide protection against KBLV.
Article
Infectious Diseases
Pauline Dianne Santos, Friederike Michel, Claudia Wylezich, Dirk Hoper, Markus Keller, Cora M. Holicki, Claudia A. Szentiks, Martin Eiden, Aemero Muluneh, Antonie Neubauer-Juric, Sabine Thalheim, Anja Globig, Martin Beer, Martin H. Groschup, Ute Ziegler
Summary: The emergence of WNV and USUV in Europe caused significant outbreaks leading to avifauna mortality and human infections. In Germany, a bird surveillance network was established to monitor these zoonotic arthropod-borne viruses. Co-infections of WNV and USUV were detected in dead birds, with WNV strains classified as lineage 2 and USUV strains as lineages Africa 2, Africa 3, and Europe 2. Further reports of co-infections in animals and humans are expected in the future.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Infectious Diseases
Mahmoud M. Naguib, Dirk Hoeper, Magdy F. Elkady, Manal A. Afifi, Ahmed Erfan, Hassanein H. Abozeid, Wafaa M. Hasan, Abdel-Satar Arafa, Momtaz Shahein, Martin Beer, Timm C. Harder, Christian Grund
Summary: The study investigated the differences between genotype VII and genotype XXI of NDV in Egyptian poultry, focusing on antigenic sites in the HN protein. It found limited variations in antigen sites but more mutations in other protein domains among these two genotypes.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Sten Calvelage, Conrad M. Freuling, Anthony R. Fooks, Dirk Hoeper, Denise A. Marston, Lorraine McElhinney, Thomas Bruun Rasmussen, Stefan Finke, Martin Beer, Thomas Mueller
Summary: European bat lyssavirus type 1 (EBLV-1) is the main causative agent of rabies in European bats. A study utilizing high-throughput sequencing on archived Danish EBLV-1 samples revealed they belong to the EBLV-1a subtype, and indicated a close phylogenetic relationship with Dutch and German isolates in the region. This study emphasized the importance of full-genome phylogenetic analyses for understanding genetic geography of lyssaviruses.
Article
Microbiology
Jacob Schoen, Angele Breithaupt, Dirk Hoeper, Jacqueline King, Anne Pohlmann, Rokshana Parvin, Klaus-Peter Behr, Bernd-Andreas Schwarz, Martin Beer, Juergen Stech, Timm Harder, Christian Grund
Summary: The H3N1 low pathogenicity avian influenza virus caused repeated outbreaks in Belgium in 2019, resulting in high chicken mortality and unusual systemic replication capability. Unlike traditional LPAIVs, the H3N1 virus undergoes HA cleavage without intracellular proteases, and its replication is inhibited by a plasmin inhibitor. Plasminogen recruitment by the viral neuraminidase leads to systemic replication and high pathogenicity phenotype in natural chicken strains.
Article
Biotechnology & Applied Microbiology
Fabian Billenkamp, Karina Schnabel, Liane Huether, Jana Frahm, Dirk von Soosten, Ulrich Meyer, Dirk Hoeper, Martin Beer, Christian Seyboldt, Heinrich Neubauer, Sven Daenicke
Summary: Glyphosate-based herbicides are widely used non-selective herbicides that inhibit synthesis of aromatic amino acids in various organisms. Controversies have arisen regarding potential health effects, especially on gut microbiomes. However, a study analyzing glyphosate effects on the rumen microbiome did not observe any adverse effects on composition, diversity, or microbial metabolites, despite using feedstuffs with differing dietary fiber and energy content.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Article
Virology
Julia E. Holper, Finn Grey, John Kenneth Baillie, Tim Regan, Nicholas J. Parkinson, Dirk Hoper, Thiprampai Thamamongood, Martin Schwemmle, Katrin Pannhorst, Lisa Wendt, Thomas C. Mettenleiter, Barbara G. Klupp
Summary: A genome-wide CRISPR/Cas9 forward screen identified sphingomyelin synthase 1 (SMS1) as a key factor in the replication of pseudorabies virus (PrV), highlighting its importance in PrV infection when the gD-mediated entry pathway is blocked.
Article
Infectious Diseases
Claudia Wylezich, Tina Schaller, Rainer Claus, Klaus Hirschbuehl, Bruno Markl, Elisabeth Kling, Oliver Spring, Dirk Hoeper, Jurgen Schlegel, Martin Beer, Sebastian Dintner
Summary: This study retrospectively conducted whole-genome sequencing on samples from SARS-CoV-2 cases, revealing identical sequences in some individuals between upper and lower respiratory tract samples, while others showed low-level intra-host genomic evolution and unique nucleotide deletions.
DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE
(2021)
Article
Infectious Diseases
Herbert Weissenboeck, Arnt Ebinger, Anna Maria Gager, Denise Thaller, Dirk Hoeper, Katharina Lichtmannsperger, Christiane Weissenbacher-Lang, Julia Matt, Martin Beer
Summary: An Austrian organic dairy sheep farm experienced cases of recumbency and sudden deaths in 3- to 4-week-old lambs. Pathological analysis identified a new enterovirus causing severe myelitis in affected motoneurons of the spinal cord, indicating a causative role of the novel virus. The reverse-transcription quantitative PCR assay for the recently discovered ovine picornavirus showed negative results, leading to the detection of the new enterovirus through next-generation sequencing-based metagenomics.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Virology
Sabine Nitschel, Luca M. Zaeck, Madlin Potratz, Tobias Nolden, Verena te Kamp, Kati Franzke, Dirk Hoeper, Florian Pfaff, Stefan Finke
Summary: The study investigated the adaptation of field rabies virus to cell culture replication, revealing that adaptive mutations could be acquired through passages to overcome replication bottlenecks in cell culture. The limited release of infectious virus at the plasma membrane was identified as a defined characteristic of highly virulent field rabies viruses.
Article
Microbiology
Florian Pfaff, Angele Breithaupt, Dennis Rubbenstroth, Sina Nippert, Christina Baumbach, Sascha Gerst, Christoph Langner, Claudia Wylezich, Arnt Ebinger, Dirk Hoper, Rainer G. Ulrich, Martin Beer
Summary: The discovery of rustrela virus (RusV)-associated encephalitis in two different species expands our knowledge of susceptible species. By using an advanced enrichment method prior to sequencing, we have greatly improved the ratio of virus-to-background sequence and updated the genome structure of RusV. The newly determined complete RusV genomes provide valuable insights into this novel rubivirus.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Mandy Schaefer, Florian Pfaff, Dirk Hoeper, Cornelia Silaghi
Summary: Studies on tick-pathogen-host interactions are important for identifying vaccine candidates and bioactive molecules against ticks and tick-borne diseases.
Article
Microbiology
Ann Kathrin Ahrens, Hans-Christoph Selinka, Claudia Wylezich, Hubert Wonnemann, Ole Sindt, Hartmut H. H. Hellmer, Florian Pfaff, Dirk Hoeper, Thomas C. C. Mettenleiter, Martin Beer, Timm C. C. Harder
Summary: Avian influenza viruses (AIV) have a wide host range and can occasionally be transmitted to humans. Surface water plays a crucial role in AIV epidemiology as it serves as a reservoir in aquatic wild birds. However, environmental samples often have low virus loads, making further subtype and pathotype testing difficult. Passive surveillance based on oral and cloacal swabs of diseased and dead wild birds remains the most sensitive method.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Kyriakos Tsangaras, Jens Mayer, Omar Mirza, Anisha Dayaram, Damien P. Higgins, Benn Bryant, Michelle Campbell-Ward, Cheryl Sangster, Andrea Casteriano, Dirk Hoper, Martin Beer, Alex D. Greenwood
Summary: Through high-throughput sequencing of DNA and cDNA from Southern white rhinoceros, gammaretroviruses were detected in the genomes of the white and black rhinoceroses. These viruses were not found in other perissodactyls. The newly identified proviruses were designated as SimumERV and DicerosERV. Phylogenetic analysis suggests a close evolutionary relationship between these rhinoceros gammaretroviruses and those found in rodents, potentially indicating an African origin for these viruses.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Arnt Ebinger, Susanne Fischer, Dirk Hoeper
Summary: Metagenomics is a powerful tool for identifying novel pathogens, with the limit of detection being a critical parameter. A probability-based model was developed and validated to assess the sample-specific limit of detection in metagenomics experiments.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)