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
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
Biotechnology & Applied Microbiology
Zhao Chen, David L. Erickson, Jianghong Meng
Summary: Oxford Nanopore sequencing is widely used for bacterial pathogen genome assembly, but high error rates in long reads necessitate polishing with Illumina short reads. NextPolish outperformed Pilon in improving genomic analyses of bacterial pathogens, requiring varying numbers of rounds for different strains. Simulated and real reads showed that the accuracy of genomic analyses depended on the optimization tool and the specific bacterial strain.
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)
Article
Pharmacology & Pharmacy
Koen Deserranno, Laurentijn Tilleman, Kaat Rubben, Dieter Deforce, Filip Van Nieuwerburgh
Summary: Pharmacogenomics (PGx) studies the impact of genomic variation on drug response and allows personalized dosing. Current PGx testing methods cannot identify large structural variants and star-alleles. This study successfully enriched 1,036 PGx-relevant genes using Oxford Nanopore Technologies and demonstrated accurate variant and star-allele calling. It also showed that up to three samples can be multiplexed without significant decrease in variant calling performance.
FRONTIERS IN PHARMACOLOGY
(2023)
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
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
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)
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
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
Genetics & Heredity
Zuyu Yang, Andrea Guarracino, Patrick J. Biggs, Michael A. Black, Nuzla Ismail, Jana Renee Wold, Tony R. Merriman, Pjotr Prins, Erik Garrison, Joep de Ligt
Summary: Whole genome sequencing has revolutionized infectious disease surveillance. However, using a linear reference genome may introduce biases when studying highly variable bacterial genomes. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants, improving mapping rates and variant calling for pathogens such as Neisseria meningitidis.
FRONTIERS IN GENETICS
(2023)
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
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
Parasitology
Luz Helena Patino, Nathalia Ballesteros, Marina Munoz, Jesus Jaimes, Adriana C. Castillo-Castaneda, Roy Madigan, Alberto Paniz-Mondolfi, Juan David Ramirez
Summary: The study introduced a new 771 bp HSP70-Long marker based on the 70-kDa heat shock protein gene for accurate identification of diverse Leishmania species and coinfection events in clinical samples. Both the HSP70-Long and HSP70-Short markers demonstrated strong discriminatory capabilities in distinguishing different Leishmania species and detecting instances of coinfection.
PARASITES & VECTORS
(2023)
Article
Obstetrics & Gynecology
Anna Oberle, Lara Urban, Stefanie Falch-Leis, Chiara Ennemoser, Yoko Nagai, Kyota Ashikawa, Patricia A. Ulm, Markus Hengstschlaeger, Michael Feichtinger
Summary: This study investigated the feasibility of using nanopore technology for full-length 16S rRNA gene sequencing as an alternative approach for endometrial microbiome analysis. Results from experiments on 33 patients seeking infertility treatment showed that nanopore sequencing was reliable and could accurately assess and compare the microbiome composition of different patients.
REPRODUCTIVE BIOMEDICINE ONLINE
(2021)
Article
Genetics & Heredity
Satomi Mitsuhashi, Martin C. Frith, Naomichi Matsumoto
Summary: The study conducted a genome-wide survey of human tandem repeats using long read genome sequencing data, finding that known disease-associated tandem repeats are generally longer and more polymorphic in the population. Additionally, the lengths of disease-causing tandem repeats were found to be correlated with nearby GWAS SNP genotypes.
BMC MEDICAL GENOMICS
(2021)
Article
Genetics & Heredity
Sachiko Ohori, Rie S. Tsuburaya, Masako Kinoshita, Etsuko Miyagi, Takeshi Mizuguchi, Satomi Mitsuhashi, Martin C. Frith, Naomichi Matsumoto
Summary: Whole-exome sequencing (WES) can detect single-nucleotide variants and pathogenic copy-number variations in causal genes, but may overlook pathogenic variations in out-of-target genome regions. To address this limitation, whole-genome sequencing (WGS) was employed to identify a 97-kb heterozygous deletion involving MBD5 in an undiagnosed patient. Additionally, rare structural variations were found in the patient, demonstrating the utility of long-read WGS in investigating potentially pathogenic SVs.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Lara Juergens, Felix Manske, Elvira Hubert, Tabea Kischka, Lea Floetotto, Oliver Klaas, Victoria Shabardina, Christoph Schliemann, Wojciech Makalowski, Klaus Wethmar
Summary: This study analyzed genetic variations in patient samples from various cancers and found that 66.5% of samples were affected by somatic single nucleotide variants in uORFs. These variants altered uAUG, uStop, and aTIS codons, with functional evaluation showing significant translational deregulation caused by 19 uORF variants.
Article
Biochemistry & Molecular Biology
Nicolas Rosa, Victoria Shabardina, Hristina Ivanova, Arnau Sebe-Pedros, David Yule, Geert Bultynck
Summary: Recent research has found that human Bcl-2 can form a complex with CO.IP3R-A channels and modulate their Ca2+ flux properties through its BH4 domain. This suggests that Bcl-2 may have interacted with the IP3R of early organisms and suppressed Ca2+ flux.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Martin C. Frith
Summary: Protein fossils in genomes provide valuable insights into the ancient evolution of TEs and genomes. A recent study discovered ancient fossils in the human genome, which exhibit extreme sequence conservation and may have gene-regulatory functions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Matias Rodriguez, Wojciech Makalowski
Summary: This study investigated the presence of TEs in 64 Apicomplexa genomes and found that TEs comprise a small portion of these genomes compared to other organisms, with many genomes showing no apparent traces of TEs. LTR Gypsy-like TEs and LINE-like TEs were identified, but Class II transposons were absent.
Article
Biology
Reza Halabian, Wojciech Makalowski
Summary: This article studies the prevalence of 3' DNA transduction phenomenon driven by non-LTR retroelements in the human genome and its impact on genome structure. The authors analyzed a new dataset from the 1000 Genomes Project and found that transduction events are dynamic within the genome and vary among individuals, contributing to structural variations in the human genome.
Article
Biochemistry & Molecular Biology
Felix Manske, Lynn Ogoniak, Lara Juergens, Norbert Grundmann, Wojciech Makalowski, Klaus Wethmar
Summary: Upstream open reading frames (uORFs) are short sequences found in the leader sequences of most eukaryotic transcripts, which play important roles in translational regulation and peptide generation. The updated uORFdb database provides comprehensive sequence information, graphical displays, and genetic variation data for over 2.4 million human uORFs and over 4.2 million uORFs in other species. It also contains somatic variation data from whole-genome sequencing analyses of cancer samples.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Martin C. Frith, Jim Shaw, John L. Spouge
Summary: We propose a sequence-sampling approach that optimizes sensitivity for a wide range of sequence comparison methods, particularly for randomly evolving sequences. It increases specificity for real biological DNA by avoiding simple repeats. Our approach extends the concepts of universal hitting sets and polar sets, providing insights into accurate and rapid sequence analysis.
Article
Biochemistry & Molecular Biology
Victoria Shabardina, Pedro Romero Charria, Gonzalo Bercedo Saborido, Ester Diaz-Mora, Ana Cuenda, Inaki Ruiz-Trillo, Juan Jose Sanz-Ezquerro
Summary: p38 kinases play a key role in the cellular stress response in animals, mediating the cell response to various stress stimuli. It is unknown how the diversity of stress function in this kinase subfamily evolved.
Article
Biochemical Research Methods
Yin Yao, Martin C. C. Frith
Summary: Protein fossils, derived from transposable elements, decayed genes, and viral integrations, can provide insights into evolutionary history and relationships, but current methods for detecting them are not optimized. We present a powerful DNA-protein homology search method that is more sensitive and faster than blastx in detecting transposable element protein fossils.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Editorial Material
Oncology
Giovanni Pascarella, Martin Frith, Piero Carninci
CLINICAL AND TRANSLATIONAL MEDICINE
(2023)
Article
Genetics & Heredity
Jonas Bohn, Reza Halabian, Lukas Schrader, Victoria Shabardina, Raphael Steffen, Yutaka Suzuki, Ulrich R. Ernst, Juergen Gadau, Wojciech Makalowski
Summary: The study focuses on the genome assembly and annotation of the California harvester ant Pogonomyrmex californicus. The genome size was estimated to be 241Mb, with 17,889 genes annotated, including 15,688 protein-coding genes with a 95% completeness level. This genome assembly will enable further research on the genomic mechanisms underlying social polymorphism, aggression regulation, and adaptation to dry habitats in P. californicus.
G3-GENES GENOMES GENETICS
(2021)