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Jauhiainen MK, Mohanraj U, Perdomo MF, Hagström J, Haglund C, Mäkitie AA, Söderlund-Venermo M, Sinkkonen ST. Presence of herpesviruses, parvoviruses, and polyomaviruses in sinonasal lymphoma. Eur Arch Otorhinolaryngol 2024; 281:4201-4211. [PMID: 38758242 PMCID: PMC11266225 DOI: 10.1007/s00405-024-08702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
PURPOSE Sinonasal lymphoma (SL) is a rare lymphatic neoplasm of the nasal cavities, paranasal sinuses and nasopharynx. Whereas some risk factors for SL subtypes have been identified, their aetiology is unknown. Along with other predisposing factors, the viral association of lymphomas, such as Epstein-Barr virus (EBV) and Burkitt and Hodgkin lymphomas, is well-established. Modern molecular biology techniques have enabled the discovery of novel human viruses, exemplified by the protoparvovirus cutavirus (CuV), associated with cutaneous T-cell lymphoma. These findings, and the anatomical location of the sinonasal tract with its rich microbiome and infectious agents, justify in-depth studies among SL. METHODS We analysed the presence of 20 viruses of Orthoherpesviridae, Parvoviridae, and Polyomaviridae by qPCR in 24 SL tumours. We performed RNAscope in situ hybridisation (RISH) to localize the viruses. Parvovirus-specific IgG was analysed by enzyme immunoassay and targeted next-generation sequencing (NGS) was applied to detect CuV in plasma. RESULTS We detected viral DNA in 15/24 (63%) tumours; nine of EBV, six of human herpesvirus (HHV) -7, four each of HHV-6B and parvovirus B19, two of cytomegalovirus, and one each of CuV and Merkel-cell polyomavirus. We found tumours with up to four viruses per tumour, and localized CuV and EBV DNAs by RISH. Two of the ten plasma samples exhibited CuV IgG, and one plasma sample demonstrated CuV viremia by NGS. CONCLUSION Viruses were frequent findings in SL. The EBV detection rate was high in diffuse large B-cell lymphoma, and co-detections with other viruses were prevalent.
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Affiliation(s)
- Maria K Jauhiainen
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland.
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- The Doctoral Programme in Clinical Research, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Ushanandini Mohanraj
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maria F Perdomo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology, University Hospital of Helsinki, Helsinki, Finland
- Department of Oral Pathology and Radiology, University of Turku, Turku, Finland
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caj Haglund
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Surgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Antti A Mäkitie
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saku T Sinkkonen
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland
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Carneiro J, Pascoal F, Semedo M, Pratas D, Tomasino MP, Rego A, Carvalho MDF, Mucha AP, Magalhães C. Mapping human pathogens in wastewater using a metatranscriptomic approach. ENVIRONMENTAL RESEARCH 2023; 231:116040. [PMID: 37150387 PMCID: PMC10172761 DOI: 10.1016/j.envres.2023.116040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
The monitoring of cities' wastewaters for the detection of potentially pathogenic viruses and bacteria has been considered a priority during the COVID-19 pandemic to monitor public health in urban environments. The methodological approaches frequently used for this purpose include deoxyribonucleic acid (DNA)/Ribonucleic acid (RNA) isolation followed by quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)‒qPCR targeting pathogenic genes. More recently, the application of metatranscriptomic has opened opportunities to develop broad pathogenic monitoring workflows covering the entire pathogenic community within the sample. Nevertheless, the high amount of data generated in the process requires an appropriate analysis to detect the pathogenic community from the entire dataset. Here, an implementation of a bioinformatic workflow was developed to produce a map of the detected pathogenic bacteria and viruses in wastewater samples by analysing metatranscriptomic data. The main objectives of this work was the development of a computational methodology that can accurately detect both human pathogenic virus and bacteria in wastewater samples. This workflow can be easily reproducible with open-source software and uses efficient computational resources. The results showed that the used algorithms can predict potential human pathogens presence in the tested samples and that active forms of both bacteria and virus can be identified. By comparing the computational method implemented in this study to other state-of-the-art workflows, the implementation analysis was faster, while providing higher accuracy and sensitivity. Considering these results, the processes and methods to monitor wastewater for potential human pathogens can become faster and more accurate. The proposed workflow is available at https://github.com/waterpt/watermonitor and can be implemented in currently wastewater monitoring programs to ascertain the presence of potential human pathogenic species.
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Affiliation(s)
- João Carneiro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal.
| | - Francisco Pascoal
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/n, 4169- 007, Porto, Portugal
| | - Miguel Semedo
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal
| | - Diogo Pratas
- IEETA - Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Portugal; Department of Virology, University of Helsinki, Finland; Department of Electronics Telecommunications and Informatics, University of Aveiro, Portugal
| | - Maria Paola Tomasino
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal
| | - Adriana Rego
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal
| | - Maria de Fátima Carvalho
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal; School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Portugal
| | - Ana Paula Mucha
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/n, 4169- 007, Porto, Portugal
| | - Catarina Magalhães
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros Do Porto de Leixões, Av. General Norton de Matos, S/n, 4450-208, Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/n, 4169- 007, Porto, Portugal
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3
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Herpesviruses, polyomaviruses, parvoviruses, papillomaviruses, and anelloviruses in vestibular schwannoma. J Neurovirol 2023; 29:226-231. [PMID: 36857017 DOI: 10.1007/s13365-023-01112-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 03/02/2023]
Abstract
Etiology of vestibular schwannoma (VS) is unknown. Viruses can infect and reside in neural tissues for decades, and new viruses with unknown tumorigenic potential have been discovered. The presence of herpesvirus, polyomavirus, parvovirus, and anellovirus DNA was analyzed by quantitative PCR in 46 formalin-fixed paraffin-embedded VS samples. Five samples were analyzed by targeted next-generation sequencing. Viral DNA was detected altogether in 24/46 (52%) tumor samples, mostly representing anelloviruses (46%). Our findings show frequent persistence of anelloviruses, considered normal virome, in VS. None of the other viruses showed an extensive presence, thereby suggesting insignificant role in VS.
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Silva JM, Qi W, Pinho AJ, Pratas D. AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. Gigascience 2022; 12:giad101. [PMID: 38091509 PMCID: PMC10716826 DOI: 10.1093/gigascience/giad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC-biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the model's ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances-namely, local, medium, or distant associations. FINDINGS This article addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference and alignment free, providing additional methodologies for testing, including a highly flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar. CONCLUSIONS The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multithreading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.
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Affiliation(s)
- Jorge M Silva
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse, 190, 8057, Zurich, Switzerland
- SIB, Swiss Institute of Bioinformatics, 1202, Geneva, Switzerland
| | - Armando J Pinho
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Diogo Pratas
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
- Department of Virology, University of Helsinki, Haartmaninkatu, 3, 00014 Helsinki, Finland
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Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
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Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
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6
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Mielonen OI, Pratas D, Hedman K, Sajantila A, Perdomo MF. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses 2022; 14:v14010133. [PMID: 35062338 PMCID: PMC8779449 DOI: 10.3390/v14010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023] Open
Abstract
Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.
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Affiliation(s)
- Outi I. Mielonen
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
| | - Diogo Pratas
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Klaus Hedman
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Maria F. Perdomo
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Correspondence:
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7
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Monteiro J, Pratas D, Videira A, Pereira F. Revisiting the Neurospora crassa mitochondrial genome. Lett Appl Microbiol 2021; 73:495-505. [PMID: 34265094 DOI: 10.1111/lam.13538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/30/2022]
Abstract
The mitochondrial genome of Neurospora crassa has been less studied than its nuclear counterpart, yet it holds great potential for understanding the diversity and evolution of this important fungus. Here we describe a new mitochondrial DNA (mtDNA) complete sequence of a N. crassa wild type strain. The genome with 64 839 bp revealed 21 protein-coding genes and several hypothetical open reading frames with no significant homology to any described gene. Five large repetitive regions were identified across the genome, including partial or complete genes. The largest repeated region holds a partial nd2 section that was also detected in Neurospora intermedia, suggesting a rearrangement that occurred before the N. crassa speciation. Interestingly, N. crassa has a palindrome adjacent to the partial nd2 repeated region possibly related to the genomic rearrangement, which is absent in N. intermedia. Finally, we compared the sequences of the three available N. crassa complete mtDNAs and found low levels of intraspecific variability. Most differences among strains were due to small indels in noncoding regions. The revisiting of the N. crassa mtDNA forms the basis for future studies on mitochondrial genome organization and variability.
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Affiliation(s)
- J Monteiro
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.,Department of Molecular Biology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - D Pratas
- Department of Virology, University of Helsinki, Helsinki, Finland.,Department of Electronics, Telecommunications and Informatics, University of Aveiro, Aveiro, Portugal.,Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Aveiro, Portugal
| | - A Videira
- Department of Molecular Biology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,Institute for Cellular and Molecular Biology (IBMC), University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - F Pereira
- IDENTIFICA Genetic Testing, Maia, Portugal.,Department of Life Sciences, Centre for Functional Ecology, University of Coimbra, Coimbra, Portugal
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Almeida JR, Pratas D, Oliveira JL. A semi-automatic methodology for analysing distributed and private biobanks. Comput Biol Med 2020; 130:104180. [PMID: 33360272 DOI: 10.1016/j.compbiomed.2020.104180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
Abstract
Privacy issues limit the analysis and cross-exploration of most distributed and private biobanks, often raised by the multiple dimensionality and sensitivity of the data associated with access restrictions and policies. These characteristics prevent collaboration between entities, constituting a barrier to emergent personalized and public health challenges, namely the discovery of new druggable targets, identification of disease-causing genetic variants, or the study of rare diseases. In this paper, we propose a semi-automatic methodology for the analysis of distributed and private biobanks. The strategies involved in the proposed methodology efficiently enable the creation and execution of unified genomic studies using distributed repositories, without compromising the information present in the datasets. We apply the methodology to a case study in the current Covid-19, ensuring the combination of the diagnostics from multiple entities while maintaining privacy through a completely identical procedure. Moreover, we show that the methodology follows a simple, intuitive, and practical scheme.
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Affiliation(s)
- João Rafael Almeida
- DETI/IEETA, University of Aveiro, Aveiro, Portugal; Department of Computation, University of A Coruña, A Coruña, Spain.
| | - Diogo Pratas
- DETI/IEETA, University of Aveiro, Aveiro, Portugal; Department of Virology, University of Helsinki, Helsinki, Finland.
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Pratas D, Toppinen M, Pyöriä L, Hedman K, Sajantila A, Perdomo MF. A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level. Gigascience 2020; 9:giaa086. [PMID: 32815536 PMCID: PMC7439602 DOI: 10.1093/gigascience/giaa086] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/25/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. FINDINGS TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. CONCLUSIONS TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.
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Affiliation(s)
- Diogo Pratas
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
| | - Mari Toppinen
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
| | - Lari Pyöriä
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
| | - Klaus Hedman
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
- HUSLAB, Helsinki University Hospital, Topeliuksenkatu 32, 00290 Helsinki, Finland
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Kytösuontie 11, 00300, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute of Health and Welfare, PO Box 30 FI-00271 Helsinki, Finland
| | - Maria F Perdomo
- Department of Virology, University of Helsinki, Haartmaninkatu 3, Helsinki, 00290, Finland
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