Article
Biotechnology & Applied Microbiology
Carolin Gabbert, Susen Schaake, Theresa Lueth, Christoph Much, Christine Klein, Jan O. Aasly, Matthew J. Farrer, Joanne Trinh
Summary: This study utilized Oxford Nanopore sequencing to determine the frequency and pathogenicity of GBA1 variants in Norwegian Parkinson's disease patients and controls. The findings showed that the NGMLR/Minimap2-BCFtools pipeline had the highest accuracy for variant calls. Thirteen rare GBA1 variants were identified, with two predicted to be (likely) pathogenic. Parkinson's disease patients were found to have a 4.11 times higher odds of carrying the common GBA1 variants compared to controls.
Article
Biotechnology & Applied Microbiology
Thomas Sauvage, Alexandre Cormier, Passerini Delphine
Summary: This study compared the performance of three library preparation strategies provided by Oxford nanopore Technologies (ONT). The results showed that ligation (LIG) had the best performance, followed by tagmentation (TAG), and amplification (PCR) had the worst performance. PCR produced the most sequencing noise, while LIG had the largest and most homogeneous output.
Article
Food Science & Technology
Maria del Socorro Toxqui Rodriguez, Joran Vanhollebeke, Sofie Derycke
Summary: Seafood is a highly traded food commodity, but its supply and labeling accuracy are often uncertain. This study evaluated the feasibility of using the MinION sequencer and DNA barcoding to authenticate seafood products. The results showed that MinION sequencing could accurately identify some species, but its ability to detect mixed samples still needs improvement.
Article
Microbiology
Annika Brinkmann, Sophie-Luisa Ulm, Steven Uddin, Sophie Foerster, Dominique Seifert, Rainer Oehme, Merle Corty, Lars Schaade, Janine Michel, Andreas Nitsche
Summary: Since December 2019, the scientific community has been sharing real-time data on the SARS-CoV-2 virus, facilitating analyses like virus evolution, transmission chain tracking, protein modeling, and therapeutic target identification. They have developed and evaluated an amplification-based approach for whole-genome sequencing of SARS-CoV-2, which can prepare sequencing libraries in 10 minutes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lucas G. Huggins, Vito Colella, Neil D. Young, Rebecca J. Traub
Summary: Apicomplexan haemoparasites cause significant morbidity and mortality, and traditional diagnostic methods have limitations. The nanopore sequencing method can accurately detect multiple pathogens, improving taxonomic resolution.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Ilaria Massaiu, Paola Songia, Mattia Chiesa, Vincenza Valerio, Donato Moschetta, Valentina Alfieri, Veronika A. Myasoedova, Michael Schmid, Luca Cassetta, Gualtiero Colombo, Yuri D'Alessandra, Paolo Poggio
Summary: Transcript sequencing is essential in understanding biological processes in diagnostic and clinical medicine. Long-read sequencing technologies, like those offered by Oxford Nanopore Technologies, can overcome limitations of short-read RNA-Seq approaches and provide improved sensitivity for identifying genes and their expression levels, particularly for non-coding genes. The study demonstrated the ability to achieve desired accuracy levels by sequencing a certain number of reads through the ONT MinION platform for human cell RNA studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Tiira Johansson, Satu Koskela, Dawit A. Yohannes, Jukka Partanen, Paivi Saavalainen
Summary: Identification of HLA alleles from NGS data is challenging due to gene polymorphism and mosaic nature. ONT's single-molecule sequencing technology shows promise in HLA typing, with advantages in read length and real-time sequencing. Despite some limitations like noisy reads, the study demonstrates accurate HLA typing using ONT MinION technology.
FRONTIERS IN GENETICS
(2021)
Review
Microbiology
Lee J. Kerkhof
Summary: This minireview discusses the improvements in Oxford Nanopore sequencing technology that make the MinION a viable platform for microbial ecology studies. By increasing sequence accuracy, obtaining quantifiable signals, providing a user-friendly data analysis pathway, and requiring modest additional equipment for field sequencing, MinION sequencing has become an attractive option for laboratories with low capital costs and reasonable per sample costs.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Forestry
Dwi Wahyuni, Fifi Gus Dwiyanti, Rahadian Pratama, Muhammad Majiidu, Henti Hendalastuti Rachmat, Iskandar Zulkarnaen Siregar
Summary: This study utilized ONT technology to generate a large amount of DNA sequence data for Kapur, successfully constructing a partial chloroplast genome and identifying the close genetic relationships between species of the genus Dryobalanops.
Article
Biochemical Research Methods
Scott D. Brown, Lisa Dreolini, Jessica F. Wilson, Miruna Balasundaram, Robert A. Holt
Summary: This study presents a cost-effective and accurate plasmid sequencing method using the MinION device from Oxford Nanopore Technologies as an alternative to capillary-based sequencing. The procedure allows for the identification of plasmid identity and mutations, achieving high accuracy in consensus sequence generation. This pipeline offers significant cost savings compared to outsourcing clinical-grade sequencing, providing accessible high-quality plasmid sequence verification.
BMC BIOINFORMATICS
(2023)
Article
Biology
Jin Sun, Runsheng Li, Chong Chen, Julia D. Sigwart, Kevin M. Kocot
Summary: Choosing the best assembly approach is crucial for high-quality genome assembly in molluscs. Recent advances in long-read sequencing technologies have led to a variety of assemblers, but benchmarking on molluscan genomes is lacking. This study evaluated 10 assemblers on two published molluscan genomes, providing recommendations for different genome properties.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Clinical Neurology
Letizia Straniero, Valeria Rimoldi, Edoardo Monfrini, Salvatore Bonvegna, Giada Melistaccio, Julie Lake, Giulia Solda, Massimo Aureli, Shankaracharya, Pamela Keagle, Tatiana Foroud, John E. Landers, Cornelis Blauwendraat, Anna Zecchinelli, Roberto Cilia, Alessio Di Fonzo, Gianni Pezzoli, Stefano Duga, Rosanna Asselta
Summary: The study evaluated the contribution of rare variants in genes responsible for lysosomal storage disorders (LSDs) to the risk of Parkinson's disease (PD) associated with the GBA gene. It found a significantly increased burden of deleterious variants in LSD genes in PD patients and identified the second variation in GBA and variants in genes causing mucopolysaccharidoses as the strongest modifiers of GBA penetrance.
MOVEMENT DISORDERS
(2022)
Article
Genetics & Heredity
Courtney L. Hall, Rupesh K. Kesharwani, Nicole R. Phillips, John Planz, Fritz J. Sedlazeck, Roxanne R. Zascavage
Summary: Short tandem repeat (STR) markers are important in forensic genetic analysis, and next generation sequencing can provide more detailed information. This study demonstrates a new method (STRspy) that can accurately obtain STR loci and their surrounding sequence information from third generation sequencing data with high error rates.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Biology
Mikhail A. Pyatnitskiy, Viktoriia A. Arzumanian, Sergey P. Radko, Konstantin G. Ptitsyn, Igor V. Vakhrushev, Ekaterina Poverennaya, Elena A. Ponomarenko
Summary: Researchers have evaluated the use of new technology developed by Oxford Nanopore Technologies to study the structure and abundance of ribonucleic acids and their application in activated biological processes. The study found that at least two replicates are required to obtain reproducible results.
Article
Food Science & Technology
Yan Ryan, Abbie Harrison, Hannah Trivett, Catherine Hartley, Jonathan David, Graeme C. Clark, Julian A. Hiscox
Summary: This study used Oxford Nanopore Technologies (ONT) direct RNA sequencing to detect and quantify RNA depurination events caused by the toxin ricin. A novel software tool called RIPpore was developed to accurately measure the adenine modification of ribosomal RNA in respiratory epithelial cells induced by ricin. The results demonstrate that this base change is specific to RIP activity and can be detected using neutralizing antibodies against ricin. The study highlights the potential of ONT and direct RNA sequencing to detect and quantify depurination events caused by ribosome-inactivating proteins like ricin.
Article
Gastroenterology & Hepatology
Marlene Schwarzfischer, Anna Niechcial, Kristina Handler, Yasser Morsy, Marcin Wawrzyniak, Andrea S. Laimbacher, Kirstin Atrott, Roberto Manzini, Katharina Baebler, Larissa Hering, Egle Katkeviciute, Janine Hafliger, Silvia Lang, Maja E. Keller, Jerome Woodtli, Lisa Eisenbeiss, Thomas Kraemer, Elisabeth M. Schraner, Mahesa Wiesendanger, Sebastian Zeissig, Gerhard Rogler, Andreas E. Moor, Michael Scharl, Marianne R. Spalinger
Summary: This study investigates the interaction between the PTPN22 gene variation and food-grade titanium dioxide nanoparticles in the pathogenesis of inflammatory bowel disease (IBD). The results show that the ingestion of titanium dioxide nanoparticles makes mice carrying the PTPN22 variation susceptible to IBD and triggers severe intestinal inflammation. This demonstrates that environmental factors can interact with genetic risk variants and reverse a protective mechanism into a disease-promoting effect.
Article
Biochemistry & Molecular Biology
Laura J. Smith, Magdalena M. Bolsinger, Kai-Yin Chau, Matthew E. Gegg, Anthony H. Schapira
Summary: Sequence variants or mutations in the GBA gene are the most important risk factor for Parkinson's disease. This study characterizes the effects of the E326K variant in human cells and finds that it behaves differently compared to other common GBA mutations. However, lipid imbalance and alpha-synuclein pathology are still observed.
HUMAN MOLECULAR GENETICS
(2023)
Article
Gastroenterology & Hepatology
Joana Torres, Maria Chaparro, Mette Julsgaard, Konstantinos Katsanos, Zuzana Zelinkova, Manasi Agrawal, Sandro Ardizzone, Marjo Campmans-Kuijpers, Gabriele Dragoni, Marc Ferrante, Gionata Fiorino, Emma Flanagan, Catarina Frias Gomes, Ailsa Hart, Charlotte Rose Hedin, Pascal Juillerat, Annemarie Mulders, Par Myrelid, Aoibhlinn O'Toole, Pauline Riviere, Michael Scharl, Christian Philipp Selinger, Elena Sonnenberg, Murat Toruner, Jantien Wieringa, C. Janneke Van der Woude
JOURNAL OF CROHNS & COLITIS
(2023)
Article
Biochemistry & Molecular Biology
Adam R. R. Smith, David M. M. Richards, Katie Lunnon, Anthony H. V. Schapira, Anna Migdalska-Richards
Summary: Parkinson's disease (PD) is a common movement disorder, and mutations in the GBA1 gene are the most common genetic risk factor for PD. PD-GBA1 is distinct from idiopathic PD in terms of age of onset, neuropsychiatric symptoms, and cognitive impairment. This study found differences in DNA methylation levels of the SNCA gene between PD-GBA1 and idiopathic PD, suggesting the existence of different genetic subtypes within PD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Electra Brunialti, Alessandro Villa, Marco Toffoli, Sara Lucas Del Pozo, Nicoletta Rizzi, Clara Meda, Adriana Maggi, Anthony H. V. Schapira, Paolo Ciana
Summary: Microglia are heterogenous cells in the nervous system that have distinct populations contributing to specific processes, including neuroprotection. Our study found that male microglia tend to have a more pro-inflammatory phenotype, while female microglia are more sensitive to glucocerebrosidase inhibition. Furthermore, glucocerebrosidase inhibition impaired the ability of female microglia to enhance the Nrf2-dependent detoxification pathway in neurons.
Article
Clinical Neurology
Tom Foltynie, Sonia Gandhi, Cristina Gonzalez-Robles, Marie-Louise Zeissler, Georgia Mills, Roger Barker, James Carpenter, Anette Schrag, Anthony Schapira, Oliver Bandmann, Stephen Mullin, Joy Duffen, Kevin McFarthing, Jeremy Chataway, Mahesh Parmar, Camille Carroll
Summary: Multi-arm, multi-stage platform designs have improved the efficiency of clinical trials in the field of oncology. Foltynie et al. discuss the challenges and considerations of using this approach to assess potential disease-modifying treatments in progressive neurological conditions such as Parkinson's disease.
Article
Biotechnology & Applied Microbiology
David Dylus, Adrian Altenhoff, Sina Majidian, Fritz J. Sedlazeck, Christophe Dessimoz
Summary: Current methods for phylogenetic tree inference are computationally expensive and laborious, with limitations in sequencing coverage, assembly and annotation quality. To address this, Read2Tree directly processes raw sequencing reads into gene groups, bypassing traditional steps in phylogeny inference, and achieves high accuracy. It outperforms assembly-based approaches in terms of speed and accuracy across various datasets, including a yeast tree of life and classification of Coronaviridae samples. Read2Tree enables comparative genomics at scale without genome assembly or annotation.
NATURE BIOTECHNOLOGY
(2023)
Review
Genetics & Heredity
Nathan D. Olson, Justin Wagner, Nathan Dwarshuis, Karen H. Miga, Fritz J. Sedlazeck, Marc Salit, Justin M. Zook
Summary: Genetic variant calling from DNA sequencing has enabled understanding of germline variation in hundreds of thousands of humans. Advances in long reads, deep learning, de novo assembly, and pangenomes have expanded access to variant calls in challenging genomic regions. Benchmarking strategies are important to assess the robustness of variant-calling strategies.
NATURE REVIEWS GENETICS
(2023)
Letter
Clinical Neurology
Marco Toffoli, Anthony H. V. Schapira, Christos Proukakis
MOVEMENT DISORDERS
(2023)
Article
Biochemical Research Methods
Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz J. Sedlazeck, Peter H. Sudmant, Justin Wagner, Justin M. Zook
Summary: By using PGR-TK, we can analyze complex genome structures and haplotype variations. We demonstrate the capability of PGR-TK in analyzing the class II major histocompatibility complex, Y-chromosome genes associated with male infertility, and X-chromosome genes linked to eye disorders. Furthermore, we showcase its application in 395 complex repetitive medically important genes, highlighting its ability to resolve complex variations in previously unanalyzable regions of the genome.
Article
Neurosciences
Marco Toffoli, Harneek Chohan, Stephen Mullin, Aaron Jesuthasan, Selen Yalkic, Sofia Koletsi, Elisa Menozzi, Soraya Rahall, Naomi Limbachiya, Nadine Loefflad, Abigail Higgins, Jonathan Bestwick, Sara Lucas-Del-Pozo, Federico Fierli, Audrey Farbos, Roxana Mezabrovschi, Chiao Lee-Yin, Anette Schrag, David Moreno-Martinez, Derralynn Hughes, Alastair Noyce, Kevin Colclough, Aaron R. Jeffries, Christos Proukakis, Anthony H. V. Schapira
Summary: This study compared the motor and non-motor phenotypes of GBA1 carriers and non-carriers. The results showed that GBA1-positive PD patients had worse performance in visual cognitive tasks and olfaction compared to GBA1-negative PD patients. However, the study did not replicate previous findings of more frequent prodromal PD signs in non-affected GBA1 carriers.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Biochemical Research Methods
Nae-Chyun Chen, Luis F. Paulin, Fritz J. Sedlazeck, Sergey Koren, Adam M. Phillippy, Ben Langmead
Summary: In this study, a method called levioSAM2 is described, which performs fast and accurate lift-over between genome assemblies using a whole-genome map. By aligning reads to a high-quality reference and lifting them to an older reference, levioSAM2 improves the accuracy of variant calling on the old reference. This method enables efficient and accurate read mapping and variant calling by combining fast lift-over and selective re-mapping.
Article
Clinical Neurology
Cornelis Blauwendraat, Nahid Tayebi, Elizabeth Geena Woo, Grisel Lopez, Luca Fierro, Marco Toffoli, Naomi Limbachiya, Derralynn Hughes, Vanessa Pitz, Dhairya Patel, Dan Vitale, Mathew J. Koretsky, Dena Hernandez, Raquel Real, Roy N. Alcalay, Mike A. Nalls, Huw R. Morris, Anthony H. V. Schapira, Manisha Balwani, Ellen Sidransky
Summary: This study investigated the contribution of PD risk variants to risk for PD in patients with GD1. The results showed that patients with GD1 who developed PD had a significantly higher PD genetic risk score than those without PD. This suggests that common risk variants may affect underlying biological pathways.
MOVEMENT DISORDERS
(2023)