A5087580656- Cytomegalovirus and herpesvirus research
- Herpesvirus Infections and Treatments
- Cancer Genomics and Diagnostics
- Viral-associated cancers and disorders
- Plant Virus Research Studies
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Animal Virus Infections Studies
- RNA modifications and cancer
- Virus-based gene therapy research
- Plant and Fungal Interactions Research
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Poxvirus research and outbreaks
- Animal Disease Management and Epidemiology
- Viral Infectious Diseases and Gene Expression in Insects
- Pancreatic and Hepatic Oncology Research
- Insect Resistance and Genetics
- RNA Research and Splicing
- Genetic factors in colorectal cancer
- Viral Infections and Immunology Research
- Esophageal Cancer Research and Treatment
- Hepatitis B Virus Studies
- Mycobacterium research and diagnosis
Cancer Center Amsterdam
2022-2025
Amsterdam University Medical Centers
2021-2025
Dutch Cancer Society
2022-2024
Vrije Universiteit Amsterdam
2021-2024
University of Szeged
2017-2022
Mississippi State University
2021
Stanford University
2019
Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability speed biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) achieve delivery genomic fragmentomic data liquid biopsies. Copy number aberrations fragmentation patterns determined in less than 24 h sample collection. The tumor-derived fraction calculated plasma lung patients bladder was highly...
Shallow genome-wide cell-free DNA (cfDNA) sequencing holds great promise for non-invasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single nucleotide variations (SNVs) are, however, much harder to identify with low depth due errors. Here we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA consensus calling based on long-read nanopore enable simultaneous multimodal tumor...
In this study, we used the amplified isoform sequencing technique from Pacific Biosciences to characterize poly(A)+ fraction of lytic transcriptome herpes simplex virus type 1 (HSV-1). Our analysis detected 34 formerly unidentified protein-coding genes, ten non-coding RNAs, as well 17 polycistronic and complex transcripts. This work also led us identify many transcript isoforms, including 13 splice 68 end variants, several overlaps. Additionally, determined previously unascertained...
Third-generation sequencing is an emerging technology that capable of solving several problems earlier approaches were not able to, including the identification transcripts isoforms and overlapping transcripts. In this study, we used long-read for analysis pseudorabies virus (PRV) transcriptome, Oxford Nanopore Technologies MinION, PacBio RS-II, Illumina HiScanSQ platforms. We also data from our previous short-read studies comparison results in order to confirm obtained data. Our...
Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, including splice...
The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for analysis of polyadenylated fraction viral transcriptome using both cDNA and direct RNA sequencing methods. We identified annotated altogether 132 novel transcripts transcript isoforms, including 4 coding non-coding molecules, 47 length variants, 5 splice as well 23 polycistronic 49 complex transcripts. All protein-coding...
Assays that account for the biological properties and fragmentation of cell-free DNA (cfDNA) can improve performance liquid biopsy. However, preanalytic physiological differences between individuals on fragmentomic analysis are poorly defined.We analyzed impact collection tube, plasma processing time, physiology size distribution cfDNA, their genome-wide representation, sequence diversity at cfDNA fragment ends using shallow whole-genome sequencing.Neither different stabilizing tubes nor...
The structure of cell-free DNA (cfDNA) is altered in the blood patients with cancer. From whole-genome sequencing, we retrieve cfDNA fragment-end composition using a new software (FrEIA [fragment end integrated analysis]), as well size and tumor fraction three independent cohorts (n = 925 cancer from >10 types 321 control samples). At 95% specificity, detect 72% samples at least one measure, including 64% early-stage 220). detection correlates shorter overall (p 0.0086) recurrence-free...
Abstract Background Existing methods to detect tumor signal in liquid biopsy have focused on the analysis of nuclear cell-free DNA (cfDNA). However, non-nuclear cfDNA and particular mitochondrial (mtDNA) has been understudied. We hypothesize that an increase mtDNA plasma could reflect presence cancer, leveraging enhance cancer detection. Results survey 203 healthy 664 samples from three collection centers covering 12 types with whole genome sequencing catalogue fraction. The fraction is...
Abstract Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, late classes. In this study, a massively parallel sequencing technique that based on PacBio Single Molecule Real-time platform, was used for quantifying the poly(A) fraction of lytic transcriptome pseudorabies virus (PRV) throughout 12-hour interval infection PK-15 cells. Other...
Abstract Background Alternative polyadenylation is commonly examined using cDNA sequencing, which known to be affected by template-switching artifacts. However, the effects of such artifacts on alternative are generally disregarded, while attributed internal priming. Results Here, we analyzed both long-read sequencing and direct RNA data two organisms, generated different platforms. We developed a filtering algorithm takes into consideration that can source artifactual when out spurious...
Long-read sequencing (LRS) has become increasingly important in RNA research due to its strength resolving complex transcriptomic architectures. In this regard, currently two LRS platforms have demonstrated adequate performance: the Single Molecule Real-Time Sequencing by Pacific Biosciences (PacBio) and nanopore Oxford Nanopore Technologies (ONT). Even though these techniques produce lower coverage are more error prone than short-read sequencing, they continue be successful identifying...
African swine fever virus (ASFV) is a large DNA belonging to the Asfarviridae family. Despite its agricultural importance, little known about fundamental molecular mechanisms of this pathogen. Short-read sequencing (SRS) can produce huge amount high-precision reads for transcriptomic profiling, but it inefficient comprehensively annotating transcriptomes. Long-read (LRS) overcome some SRS’s limitations, also has drawbacks, such as low-coverage and high error rate. The limitations two...
Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various methods have distinct strengths limitations, use of multiplatform approaches proven to be valuable. aim this study provide a more complete picture on transcriptomic architecture EBV.In work, we apply...
Abstract Pseudorabies virus (PRV) is an alphaherpesvirus of swine. PRV has a large double-stranded DNA genome and, as the latest investigations have revealed, very complex transcriptome. Here, we present RNA-Seq dataset, derived from both short- and long-read sequencing. The dataset contains 1.3 million 100 bp paired-end reads that were obtained Illumina random-primed libraries, well 10 50 single-end generated by polyA-seq. Pacific Biosciences RSII non-amplified method yielded 57,021 inserts...
DATA REPORT article Front. Genet., 28 July 2020Sec. Genomic Assay Technology Volume 11 - 2020 | https://doi.org/10.3389/fgene.2020.00758
Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity these platforms transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read (LRS) can overcome limitations by reading full-length transcripts. Employment technologies has led redefinition complexities in reported organisms. In this study, we applied LRS from Pacific Biosciences Oxford Nanopore Technologies profile vaccinia virus (VACV)...
Abstract Long-read sequencing (LRS) has become a standard approach for transcriptome analysis in recent years. Bovine alphaherpesvirus 1 (BoHV-1) is an important pathogen of cattle worldwide. This study reports the profiling dynamic lytic BoHV-1 using two long-read techniques, Oxford Nanopore Technologies MinION, and LoopSeq synthetic LRS methods, multiple library preparation protocols. In this work, we annotated viral mRNAs non-coding transcripts, large number transcript isoforms, including...
In this study, we applied short- and long-read RNA sequencing techniques, as well PCR analysis to investigate the transcriptome of porcine endogenous retrovirus (PERV) expressed from cultured kidney cell line PK-15. This has revealed six novel transcripts eight transcript isoforms, including five length three splice variants. We were able establish whether a deletion in is result splicing mRNAs or genomic one PERV clones. Additionally, re-annotated formerly identified molecules. Our higher...
Abstract Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is a prototypic baculovirus infecting specific insects. AcMNPV contains large double-stranded DNA genome encoding complex transcriptome. This virus has widespread application as vector for the expression of heterologous proteins. Here, we present dataset, derived from Oxford Nanopore Technologies (ONT) long-read sequencing platform. We used both cDNA and direct RNA techniques. The dataset 520,310 1,309,481 host cell reads...
Abstract Background High ovarian cancer mortality rates motivate the development of effective and patient-friendly diagnostics. Here, we explored potential molecular testing in samples for detection. Methods Home-collected urine, cervicovaginal self-samples, clinician-taken cervical scrapes were prospectively collected from 54 patients diagnosed with a highly suspicious mass (benign n = 25, malignant 29). All tested nine methylation markers, using quantitative methylation-specific PCRs that...