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Szakállas N, Barták BK, Valcz G, Nagy ZB, Takács I, Molnár B. Can long-read sequencing tackle the barriers, which the next-generation could not? A review. Pathol Oncol Res 2024; 30:1611676. [PMID: 38818014 PMCID: PMC11137202 DOI: 10.3389/pore.2024.1611676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
The large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable genomic data. In contrast to the previous short-reads, longer lengths can provide a better insight into the potential health threatening genetic abnormalities. Long-reads offer more accurate variant identification and genome assembly methods, indicating advances in nucleotide deflect-related studies. In this review, we introduce the historical background of sequencing technologies and show their benefits and limits, as well. Furthermore, we highlight the differences between short- and long-read approaches, including their unique advances and difficulties in methodologies and evaluation. Additionally, we provide a detailed description of the corresponding bioinformatics and the current applications.
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Affiliation(s)
- Nikolett Szakállas
- Department of Biological Physics, Faculty of Science, Eötvös Loránd University, Budapest, Hungary
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
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2
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Yan Q, Zhang G, Zhang X, Huang L. A Review of Transcriptomics and Metabolomics in Plant Quality and Environmental Response: From Bibliometric Analysis to Science Mapping and Future Trends. Metabolites 2024; 14:272. [PMID: 38786749 PMCID: PMC11123105 DOI: 10.3390/metabo14050272] [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: 03/13/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Transcriptomics and metabolomics offer distinct advantages in investigating the differentially expressed genes and cellular entities that have the greatest influence on end-phenotype, making them crucial techniques for studying plant quality and environmental responses. While numerous relevant articles have been published, a comprehensive summary is currently lacking. This review aimed to understand the global and longitudinal research trends of transcriptomics and metabolomics in plant quality and environmental response (TMPQE). Utilizing bibliometric methods, we presented a comprehensive science mapping of the social structure, conceptual framework, and intellectual foundation of TMPQE. We uncovered that TMPQE research has been categorized into three distinct stages since 2020. A citation analysis of the 29 most cited articles, coupled with a content analysis of recent works (2020-2023), highlight five potential research streams in plant quality and environmental responses: (1) biosynthetic pathways, (2) abiotic stress, (3) biotic stress, (4) development and ripening, and (5) methodologies and tools. Current trends and future directions are shaped by technological advancements, species diversity, evolving research themes, and an environmental ecology focus. Overall, this review provides a novel and comprehensive perspective to understand the longitudinal trend on TMPQE.
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Affiliation(s)
| | | | | | - Linfang Huang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, HaiDian District, Beijing 100193, China; (Q.Y.); (G.Z.); (X.Z.)
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3
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Delandre O, Lamer O, Loreau JM, Papa Mze N, Fonta I, Mosnier J, Gomez N, Javelle E, Pradines B. Long-Read Sequencing and De Novo Genome Assembly Pipeline of Two Plasmodium falciparum Clones ( Pf3D7, PfW2) Using Only the PromethION Sequencer from Oxford Nanopore Technologies without Whole-Genome Amplification. BIOLOGY 2024; 13:89. [PMID: 38392307 PMCID: PMC10886359 DOI: 10.3390/biology13020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024]
Abstract
Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of P. falciparum (Pf3D7 and PfW2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human Plasmodium with ONT Fastq only. De novo assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the Pf3D7 and PfW2, respectively. The genome size was estimated at 23,235,407 base pairs for the Pf3D7 clone and 21,712,038 base pairs for the PfW2 clone. The average genome coverage depth was estimated at 787X and 653X for the Pf3D7 and PfW2 clones, respectively. This study proposes an assembly processing pipeline for the human Plasmodium genome using software adapted to large ONT data and the high AT percentage of Plasmodium. This search provides all the parameters which were optimized for use with the software selected in the pipeline.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Ombeline Lamer
- Unité Bactériologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Aix-Marseille Univ, INSERM, SSA, IRBA, MCT, 13005 Marseille, France
| | - Jean-Marie Loreau
- French Armed Forces Center for Epidemiology and Public Health (CESPA), 13014 Marseille, France
| | - Nasserdine Papa Mze
- Service de Biologie, Unité de Microbiologie, Hôpital Mignot, Centre Hospitalier de Versailles, 78150 Versailles, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Emilie Javelle
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Centre National de Référence du Paludisme, 13005 Marseille, France
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Nafea AM, Wang Y, Wang D, Salama AM, Aziz MA, Xu S, Tong Y. Application of next-generation sequencing to identify different pathogens. Front Microbiol 2024; 14:1329330. [PMID: 38348304 PMCID: PMC10859930 DOI: 10.3389/fmicb.2023.1329330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/18/2023] [Indexed: 02/15/2024] Open
Abstract
Early and precise detection and identification of various pathogens are essential for epidemiological monitoring, disease management, and reducing the prevalence of clinical infectious diseases. Traditional pathogen detection techniques, which include mass spectrometry, biochemical tests, molecular testing, and culture-based methods, are limited in application and are time-consuming. Next generation sequencing (NGS) has emerged as an essential technology for identifying pathogens. NGS is a cutting-edge sequencing method with high throughput that can create massive volumes of sequences with a broad application prospects in the field of pathogen identification and diagnosis. In this review, we introduce NGS technology in detail, summarizes the application of NGS in that identification of different pathogens, including bacteria, fungi, and viruses, and analyze the challenges and outlook for using NGS to identify clinical pathogens. Thus, this work provides a theoretical basis for NGS studies and provides evidence to support the application of NGS in distinguishing various clinical pathogens.
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Affiliation(s)
- Aljuboori M. Nafea
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Duanyang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ahmed M. Salama
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, China
- Medical Laboratory at Sharkia Health Directorate, Ministry of Health, Sharkia, Egypt
| | - Manal A. Aziz
- College of Medicine, Department of Microbiology, Ibn Sina University of Medical and Pharmaceutical Science, Baghdad, Iraq
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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5
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Soikkeli M, Murros A, Rantala A, Txoperena O, Kilpi OP, Kainlauri M, Sovanto K, Maestre A, Centeno A, Tukkiniemi K, Gomes Martins D, Zurutuza A, Arpiainen S, Prunnila M. Wafer-Scale Graphene Field-Effect Transistor Biosensor Arrays with Monolithic CMOS Readout. ACS APPLIED ELECTRONIC MATERIALS 2023; 5:4925-4932. [PMID: 37779890 PMCID: PMC10536967 DOI: 10.1021/acsaelm.3c00706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/14/2023] [Indexed: 10/03/2023]
Abstract
The reliability of analysis is becoming increasingly important as point-of-care diagnostics are transitioning from single-analyte detection toward multiplexed multianalyte detection. Multianalyte detection benefits greatly from complementary metal-oxide semiconductor (CMOS) integrated sensing solutions, offering miniaturized multiplexed sensing arrays with integrated readout electronics and extremely large sensor counts. The development of CMOS back end of line integration compatible graphene field-effect transistor (GFET)-based biosensing has been rapid during the past few years, in terms of both the fabrication scale-up and functionalization toward biorecognition from real sample matrices. The next steps in industrialization relate to improving reliability and require increased statistics. Regarding functionalization toward truly quantitative sensors, on-chip bioassays with improved statistics require sensor arrays with reduced variability in functionalization. Such multiplexed bioassays, whether based on graphene or on other sensitive nanomaterials, are among the most promising technologies for label-free electrical biosensing. As an important step toward that, we report wafer-scale fabrication of CMOS-integrated GFET arrays with high yield and uniformity, designed especially for biosensing applications. We demonstrate the operation of the sensing platform array with 512 GFETs in simultaneous detection for the sodium chloride concentration series. This platform offers a truly statistical approach on GFET-based biosensing and further to quantitative and multianalyte sensing. The reported techniques can also be applied to other fields relying on functionalized GFETs, such as gas or chemical sensing or infrared imaging.
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Affiliation(s)
- Miika Soikkeli
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Anton Murros
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Arto Rantala
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Oihana Txoperena
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Olli-Pekka Kilpi
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Markku Kainlauri
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Kuura Sovanto
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Arantxa Maestre
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Alba Centeno
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Kari Tukkiniemi
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - David Gomes Martins
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Amaia Zurutuza
- Graphenea
Semiconductor SLU, Paseo Mikeletegi 83, 20009-San Sebastian, Spain
| | - Sanna Arpiainen
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
| | - Mika Prunnila
- VTT
Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT, Espoo, Finland
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6
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Paulose AK, Hou YJ, Huang YS, Chakkalaparambil Dileep N, Chiu CL, Pal A, Kalaimani VM, Lin ZH, Chang CR, Chen CP, Lin YC, Cheng CY, Cheng SH, Cheng CM, Wang YL. Rapid Escherichia coli Cloned DNA Detection in Serum Using an Electrical Double Layer-Gated Field-Effect Transistor-Based DNA Sensor. Anal Chem 2023; 95:6871-6878. [PMID: 37080900 DOI: 10.1021/acs.analchem.2c05719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
In this study, a rapid diagnosis platform was developed for the detection of Escherichia coli O157:H7. An electrical double layer (EDL)-gated field-effect transistor-based biosensor (BioFET) as a point-of-care testing device is demonstrated with its high sensitivity, portability, high selectivity, quick response, and ease of use. The specially designed ssDNA probe was immobilized on the extended gate electrode to bind the target complementary DNA segment of E. coli, resulting in a sharp drain current change within minutes. The limit of detection for target DNA is validated to a concentration of 1 fM in buffer solution and serum. Meanwhile, the results of a Kelvin probe force microscope were shown to have reduced surface potential of the DNA immobilized sensors before and after the cDNA detection, which is consistent with the decreased drain current of the BioFET. A 1.2 kb E. coli duplex DNA synthesized in plasmid was sonicated and detected in serum samples with the sensor array. Gel electrophoresis was used to confirm the efficiency of sonication by elucidating the length of DNA. Those results show that the EDL-gated BioFET system is a promising platform for rapid identification of pathogens for future clinical needs.
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Affiliation(s)
- Akhil K Paulose
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yueh-Ju Hou
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811726, Taiwan, ROC
| | - Yu-Shan Huang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | | | - Chia-Lin Chiu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Arnab Pal
- International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Vishal Mani Kalaimani
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Zong-Hong Lin
- Department of Biomedical Engineering, National Taiwan University, Taipei 10617, Taiwan, ROC
| | - Chuang-Rung Chang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Cheng-Pin Chen
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Yi-Chun Lin
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chien-Yu Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Shu-Hsing Cheng
- Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan 32748, Taiwan
| | - Chao-Min Cheng
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
| | - Yu-Lin Wang
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
- College of Semiconductor Research, National Tsing Hua University, Hsinchu 30013, Taiwan, ROC
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7
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Liu R, Zhang Y, Liu M, Ni Y, Yue Y, Wu S, Li S. Electrochemical sensor based on Fe3O4/α-Fe2O3@Au magnetic nanocomposites for sensitive determination of the TP53 gene. Bioelectrochemistry 2023; 152:108429. [PMID: 37023617 DOI: 10.1016/j.bioelechem.2023.108429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/09/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023]
Abstract
Considering the high cost and tedious process of gene sequencing, there is an urgent need to develop portable and efficient sensors for the TP53 gene. Here, we developed a novel electrochemical sensor that detected the TP53 gene using magnetic peptide nucleic acid (PNA)-modified Fe3O4/α-Fe2O3@Au nanocomposites. Cyclic voltammetry and electrochemical impedance spectroscopy confirmed the successful stepwise construction of the sensor, especially the high-affinity binding of PNA to DNA strands, which induced different electron transfer rates and resulted in current changes. Variations in the differential pulse voltammetry current observed during hybridization at different surface PNA probe densities, hybridization times, and hybridization temperatures were explored. The biosensing strategy obtained a limit of detection of 0.26 pM, a limit of quantification of 0.85 pM, and a wide linear range (1 pM-1 μM), confirming that the Fe3O4/α-Fe2O3@Au nanocomposites and the strategy based on magnetic separation and magnetically induced self-assembly improved the binding efficiency of nucleic acid molecules. The biosensor was a label-free and enzyme-free device with excellent reproducibility and stability that could identify single-base mismatched DNA without additional DNA amplification procedures, and the serum spiked experiments revealed the feasibility of the detection approach.
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8
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Eren K, Taktakoğlu N, Pirim I. DNA Sequencing Methods: From Past to Present. Eurasian J Med 2022; 54:47-56. [PMID: 36655445 PMCID: PMC11163357 DOI: 10.5152/eurasianjmed.2022.22280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/18/2022] [Indexed: 01/19/2023] Open
Abstract
Next-generation sequencing (NGS) is a highly effective genetic diagnostic test used in disease diagnosis. Although the Sanger method is used as the traditional method in genome studies, the use of NGS methods has been increasing with the development of technology. The foundation of next-generation sequencing was laid with the methods developed by Allan Maxam-Walter Gilbert and 2 Nobel laureates, Frederick Sanger. Initially, first-generation sequencing methods completed a certain part of the DNA with great efforts in a few days, while in today's technology, the entire DNA of even the most complex organisms is sequenced in 1 day. Second- and third-generation sequencing methods have been developed with improvements in cost, time, and accuracy of sequencing. The data obtained from these methods are interpreted with bioinformatics and contributed to the development of next-generation sequencing technology. These developments have increased the interest in studies on the relationship between next-generation sequencing and DNA or RNA depending on diseases. In this review, past and present methods of next-generation sequencing technologies are mentioned in detail and the difficulties and conveniences of these methods are reviewed.
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Affiliation(s)
- Kübra Eren
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
| | - Nursema Taktakoğlu
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
| | - Ibrahim Pirim
- Faculty of Medicine, Department of Medical Biology and Genetic, Izmir Katip Celebi University, Izmir, Turkey
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9
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van der Laan L, Rooney K, Trooster TM, Mannens MM, Sadikovic B, Henneman P. DNA methylation episignatures: insight into copy number variation. Epigenomics 2022; 14:1373-1388. [PMID: 36537268 DOI: 10.2217/epi-2022-0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Kathleen Rooney
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Tessa Ma Trooster
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Marcel Mam Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, N5A 3K7, Canada.,Verspeeten Clinical Genome Centre, London Health Science Centre, London, Ontario, N6A 5W9, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Amsterdam, 1105 AZ, The Netherlands
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10
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Abdelhalim H, Berber A, Lodi M, Jain R, Nair A, Pappu A, Patel K, Venkat V, Venkatesan C, Wable R, Dinatale M, Fu A, Iyer V, Kalove I, Kleyman M, Koutsoutis J, Menna D, Paliwal M, Patel N, Patel T, Rafique Z, Samadi R, Varadhan R, Bolla S, Vadapalli S, Ahmed Z. Artificial Intelligence, Healthcare, Clinical Genomics, and Pharmacogenomics Approaches in Precision Medicine. Front Genet 2022; 13:929736. [PMID: 35873469 PMCID: PMC9299079 DOI: 10.3389/fgene.2022.929736] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Precision medicine has greatly aided in improving health outcomes using earlier diagnosis and better prognosis for chronic diseases. It makes use of clinical data associated with the patient as well as their multi-omics/genomic data to reach a conclusion regarding how a physician should proceed with a specific treatment. Compared to the symptom-driven approach in medicine, precision medicine considers the critical fact that all patients do not react to the same treatment or medication in the same way. When considering the intersection of traditionally distinct arenas of medicine, that is, artificial intelligence, healthcare, clinical genomics, and pharmacogenomics—what ties them together is their impact on the development of precision medicine as a field and how they each contribute to patient-specific, rather than symptom-specific patient outcomes. This study discusses the impact and integration of these different fields in the scope of precision medicine and how they can be used in preventing and predicting acute or chronic diseases. Additionally, this study also discusses the advantages as well as the current challenges associated with artificial intelligence, healthcare, clinical genomics, and pharmacogenomics.
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Affiliation(s)
- Habiba Abdelhalim
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Asude Berber
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mudassir Lodi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rihi Jain
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Achuth Nair
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Anirudh Pappu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Kush Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vignesh Venkat
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Cynthia Venkatesan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Raghu Wable
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Matthew Dinatale
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Allyson Fu
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Vikram Iyer
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Ishan Kalove
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Marc Kleyman
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Joseph Koutsoutis
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - David Menna
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Mayank Paliwal
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Nishi Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Thirth Patel
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zara Rafique
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Rothela Samadi
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Roshan Varadhan
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Shreyas Bolla
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Sreya Vadapalli
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States
| | - Zeeshan Ahmed
- Rutgers Institute for Health, Health Care Policy and Aging Research, Rutgers University, New Brunswick, NJ, United States.,Department of Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers Biomedical and Health Sciences, New Brunswick, NJ, United States
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11
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Lee SD, Wu M, Lo KW, Yip KY. Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement. BMC Genomics 2022; 23:422. [PMID: 35668367 PMCID: PMC9169298 DOI: 10.1186/s12864-022-08649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/24/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND After an infection, human cells may contain viral genomes in the form of episomes or integrated DNA. Comparing the genomic sequences of different strains of a virus in human cells can often provide useful insights into its behaviour, activity and pathology, and may help develop methods for disease prevention and treatment. To support such comparative analyses, the viral genomes need to be accurately reconstructed from a large number of samples. Previous efforts either rely on customized experimental protocols or require high similarity between the sequenced genomes and a reference, both of which limit the general applicability of these approaches. In this study, we propose a pipeline, named ASPIRE, for reconstructing viral genomes accurately from short reads data of human samples, which are increasingly available from genome projects and personal genomics. ASPIRE contains a basic part that involves de novo assembly, tiling and gap filling, and additional components for iterative refinement, sequence corrections and wrapping. RESULTS Evaluated by the alignment quality of sequencing reads to the reconstructed genomes, these additional components improve the assembly quality in general, and in some particular samples quite substantially, especially when the sequenced genome is significantly different from the reference. We use ASPIRE to reconstruct the genomes of Epstein Barr Virus (EBV) from the whole-genome sequencing data of 61 nasopharyngeal carcinoma (NPC) samples and provide these sequences as a resource for EBV research. CONCLUSIONS ASPIRE improves the quality of the reconstructed EBV genomes in published studies and outperforms TRACESPipe in some samples considered.
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Affiliation(s)
- Sau-Dan Lee
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Man Wu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong. .,Current address: Sanford Burnham Prebys Medical Discovery Institute, La Jolla, 92037, CA, USA.
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12
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Kuhl LP, Marostica PJC, Macedo AJ, Kuhl G, Siebert M, Manica D, Sekine L, Schweiger C. High microbiome variability in pediatric tracheostomy cannulas in patients with similar clinical characteristics. Braz J Otorhinolaryngol 2022; 89:254-263. [PMID: 35680554 PMCID: PMC10071543 DOI: 10.1016/j.bjorl.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/03/2022] [Accepted: 05/01/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES To evaluate the bacterial microbiome found in tracheostomy cannulas of a group of children diagnosed with glossoptosis secondary to Robin Sequence (RS), and its clinical implications. METHODS Pediatric patients were enrolled in the study at the time of the cannula change in the hospital. During this procedure, the removed cannula was collected and stored for amplicon sequencing of 16s rRNA. DNA extraction was performed using DNeasy PowerBiofilm Kit (QIAGEN® ‒ Cat nº 24000-50) while sequencing was performed with the S5 (Ion S5™ System, Thermo Fisher Scientific), following Brazilian Microbiome Project (BMP) protocol. RESULTS All 12 patients included in the study were using tracheostomy uncuffed cannulas of the same brand, had tracheostomy performed for over 1-year and had used the removed cannula for approximately 3-months. Most abundant genera found were Aggregatibacter, Pseudomonas, Haemophilus, Neisseria, Staphylococcus, Fusobacterium, Moraxella, Streptococcus, Alloiococcus, and Capnocytophaga. Individual microbiome of each individual was highly variable, not correlating to any particular clinical characteristic. CONCLUSION The microbiome of tracheostomy cannulas is highly variable, even among patients with similar clinical characteristics, making it challenging to determine a standard for normality.
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Affiliation(s)
- Leonardo Palma Kuhl
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Otorrinolaringologia e Cirurgia Cérvico-Facial, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Porto Alegre, RS, Brazil.
| | - Paulo José Cauduro Marostica
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre, Serviço de Pneumologia Pediátrica, Porto Alegre, RS, Brazil
| | - Alexandre José Macedo
- Universidade Federal do Rio Grande do Sul (UFRGS), Faculdade de Farmácia e Centro de Biotecnologia, Porto Alegre, RS, Brazil
| | - Gabriel Kuhl
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Otorrinolaringologia e Cirurgia Cérvico-Facial, Porto Alegre, RS, Brazil
| | - Marina Siebert
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Gastroenterologia e Hepatologia, Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre (HCPA), Laboratório de Pesquisa Básica e Avançada em Neurociência (BRAIN), Porto Alegre, RS, Brazil; Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Porto Alegre, RS, Brazil
| | - Denise Manica
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Otorrinolaringologia e Cirurgia Cérvico-Facial, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Porto Alegre, RS, Brazil
| | - Leo Sekine
- Universidade Federal do Rio Grande do Sul (UFRGS), Faculdade de Medicina, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Cláudia Schweiger
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Otorrinolaringologia e Cirurgia Cérvico-Facial, Porto Alegre, RS, Brazil; Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Saúde da Criança e do Adolescente, Porto Alegre, RS, Brazil
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Napieralski A, Nowak R. Basecalling Using Joint Raw and Event Nanopore Data Sequence-to-Sequence Processing. SENSORS (BASEL, SWITZERLAND) 2022; 22:2275. [PMID: 35336445 PMCID: PMC8954548 DOI: 10.3390/s22062275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Third-generation DNA sequencers provided by Oxford Nanopore Technologies (ONT) produce a series of samples of an electrical current in the nanopore. Such a time series is used to detect the sequence of nucleotides. The task of translation of current values into nucleotide symbols is called basecalling. Various solutions for basecalling have already been proposed. The earlier ones were based on Hidden Markov Models, but the best ones use neural networks or other machine learning models. Unfortunately, achieved accuracy scores are still lower than competitive sequencing techniques, like Illumina's. Basecallers differ in the input data type-currently, most of them work on a raw data straight from the sequencer (time series of current). Still, the approach of using event data is also explored. Event data is obtained by preprocessing of raw data and dividing it into segments described by several features computed from raw data values within each segment. We propose a novel basecaller that uses joint processing of raw and event data. We define basecalling as a sequence-to-sequence translation, and we use a machine learning model based on an encoder-decoder architecture of recurrent neural networks. Our model incorporates twin encoders and an attention mechanism. We tested our solution on simulated and real datasets. We compare the full model accuracy results with its components: processing only raw or event data. We compare our solution with the existing ONT basecaller-Guppy. Results of numerical experiments show that joint raw and event data processing provides better basecalling accuracy than processing each data type separately. We implement an application called Ravvent, freely available under MIT licence.
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15
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Athanasopoulou K, Boti MA, Adamopoulos PG, Skourou PC, Scorilas A. Third-Generation Sequencing: The Spearhead towards the Radical Transformation of Modern Genomics. Life (Basel) 2021; 12:life12010030. [PMID: 35054423 PMCID: PMC8780579 DOI: 10.3390/life12010030] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/14/2022] Open
Abstract
Although next-generation sequencing (NGS) technology revolutionized sequencing, offering a tremendous sequencing capacity with groundbreaking depth and accuracy, it continues to demonstrate serious limitations. In the early 2010s, the introduction of a novel set of sequencing methodologies, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Sequencing (ONT), gave birth to third-generation sequencing (TGS). The innovative long-read technologies turn genome sequencing into an ease-of-handle procedure by greatly reducing the average time of library construction workflows and simplifying the process of de novo genome assembly due to the generation of long reads. Long sequencing reads produced by both TGS methodologies have already facilitated the decipherment of transcriptional profiling since they enable the identification of full-length transcripts without the need for assembly or the use of sophisticated bioinformatics tools. Long-read technologies have also provided new insights into the field of epitranscriptomics, by allowing the direct detection of RNA modifications on native RNA molecules. This review highlights the advantageous features of the newly introduced TGS technologies, discusses their limitations and provides an in-depth comparison regarding their scientific background and available protocols as well as their potential utility in research and clinical applications.
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16
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Tirado TC, Moura LL, Shigunov P, Figueiredo FB. Methodological Appraisal of Literature Concerning the Analysis of Genetic Variants or Protein Levels of Complement Components on Susceptibility to Infection by Trypanosomatids: A Systematic Review. Front Immunol 2021; 12:780810. [PMID: 34899745 PMCID: PMC8656155 DOI: 10.3389/fimmu.2021.780810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/25/2022] Open
Abstract
Background Trypanosomatids are protozoa responsible for a wide range of diseases, with emphasis on Chagas Disease (CD) and Leishmaniasis, which are in the list of most relevant Neglected Tropical Diseases (NTD) according to World Health Organization (WHO). During the infectious process, immune system is immediately activated, and parasites can invade nucleated cells through a broad diversity of receptors. The complement system − through classical, alternative and lectin pathways − plays a role in the first line of defense against these pathogens, acting in opsonization, phagocytosis and lysis of parasites. Genetic modifications in complement genes, such as Single Nucleotide Polymorphisms (SNPs), can influence host susceptibility to these parasites and modulate protein expression. Methods In March and April 2021, a literature search was conducted at the PubMed and Google Scholar databases and the reference lists obtained were verified. After applying the inclusion and exclusion criteria, the selected studies were evaluated and scored according to eleven established criteria regarding their thematic approach and design, aiming at the good quality of publications. Results Twelve papers were included in this systematic review: seven investigating CD and five focusing on Leishmaniasis. Most articles presented gene and protein approaches, careful determination of experimental groups, and adequate choice of experimental techniques, although several of them were not up-to-date. Ten studies explored the association of polymorphisms and haplotypes with disease progression, with emphasis on lectin complement pathway genes. Decreased and increased patient serum protein levels were associated with susceptibility to CD and Visceral Leishmaniasis, respectively. Conclusion This systematic review shows the influence of genetic alterations in complement genes on the progression of several infectious diseases, with a focus on conditions caused by trypanosomatids, and contributes suggestions and evidence to improve experimental design in future research proposals.
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Affiliation(s)
- Thais Cristina Tirado
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Larine Lowry Moura
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Patrícia Shigunov
- Laboratório de Biologia Básica de Células-Tronco, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
| | - Fabiano Borges Figueiredo
- Laboratório de Biologia Celular, Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba, Brazil
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Huebner T, Steffens M, Scholl C. Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe. Mol Diagn Ther 2021; 26:89-103. [PMID: 34905151 PMCID: PMC8766366 DOI: 10.1007/s40291-021-00567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 11/26/2022]
Abstract
On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.
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Affiliation(s)
- Tatjana Huebner
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany.
| | - Michael Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, North Rhine-Westphalia, Germany
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18
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Scatena C, Murtas D, Tomei S. Cutaneous Melanoma Classification: The Importance of High-Throughput Genomic Technologies. Front Oncol 2021; 11:635488. [PMID: 34123788 PMCID: PMC8193952 DOI: 10.3389/fonc.2021.635488] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Cutaneous melanoma is an aggressive tumor responsible for 90% of mortality related to skin cancer. In the recent years, the discovery of driving mutations in melanoma has led to better treatment approaches. The last decade has seen a genomic revolution in the field of cancer. Such genomic revolution has led to the production of an unprecedented mole of data. High-throughput genomic technologies have facilitated the genomic, transcriptomic and epigenomic profiling of several cancers, including melanoma. Nevertheless, there are a number of newer genomic technologies that have not yet been employed in large studies. In this article we describe the current classification of cutaneous melanoma, we review the current knowledge of the main genetic alterations of cutaneous melanoma and their related impact on targeted therapies, and we describe the most recent high-throughput genomic technologies, highlighting their advantages and disadvantages. We hope that the current review will also help scientists to identify the most suitable technology to address melanoma-related relevant questions. The translation of this knowledge and all actual advancements into the clinical practice will be helpful in better defining the different molecular subsets of melanoma patients and provide new tools to address relevant questions on disease management. Genomic technologies might indeed allow to better predict the biological - and, subsequently, clinical - behavior for each subset of melanoma patients as well as to even identify all molecular changes in tumor cell populations during disease evolution toward a real achievement of a personalized medicine.
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Affiliation(s)
- Cristian Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Daniela Murtas
- Department of Biomedical Sciences, Section of Cytomorphology, University of Cagliari, Cagliari, Italy
| | - Sara Tomei
- Omics Core, Integrated Genomics Services, Research Department, Sidra Medicine, Doha, Qatar
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Garcia-Garcia S, Cortese MF, Rodríguez-Algarra F, Tabernero D, Rando-Segura A, Quer J, Buti M, Rodríguez-Frías F. Next-generation sequencing for the diagnosis of hepatitis B: current status and future prospects. Expert Rev Mol Diagn 2021; 21:381-396. [PMID: 33880971 DOI: 10.1080/14737159.2021.1913055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Hepatitis B virus (HBV) causes a complex and persistent infection with a major impact on patients health. Viral-genome sequencing can provide valuable information for characterizing virus genotype, infection dynamics and drug and vaccine resistance. AREAS COVERED This article reviews the current literature to describe the next-generation sequencing progress that facilitated a more comprehensive study of HBV quasispecies in diagnosis and clinical monitoring. EXPERT OPINION HBV variability plays a key role in liver disease progression and treatment efficacy. Second-generation sequencing improved the sensitivity for detecting and quantifying mutations, mixed genotypes and viral recombination. Third-generation sequencing enables the analysis of the entire HBV genome, although the high error rate limits its use in clinical practice.
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Affiliation(s)
- Selene Garcia-Garcia
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francisco Rodríguez-Algarra
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David Tabernero
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
| | - Ariadna Rando-Segura
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Josep Quer
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Maria Buti
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
| | - Francisco Rodríguez-Frías
- Liver Pathology Unit, Departments of Biochemistry and Microbiology, Hospital Universitari Vall d'Hebron, Universitat Autònoma De Barcelona, Barcelona Spain
- Clinical Biochemistry Research Group, Vall d'Hebron Institut Recerca (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Centro De Investigación Biomédica En Red De Enfermedades Hepáticas Y Digestivas, Instituto De Salud Carlos III, Madrid Spain
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Nagarajan V, Sarvaka S, Chandiramouli R. Adsorption studies of nucleobases on ε-arsenene nanosheet based on first-principles research. J Mol Graph Model 2020; 103:107827. [PMID: 33370614 DOI: 10.1016/j.jmgm.2020.107827] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/18/2022]
Abstract
The electronic attributes and energetics of ε-arsenene nanosheet (ε-As) are explored with regard to the density functional theory basis. Initially, based on formation energy (-3.715 eV/atom), we ensured the structural firmness of ε-As. The ε-As is used as a base substrate to adsorb nucleobases viz., adenine (A), guanine (G), thymine (T), cytosine (C) & uracil (U). The surface adsorption of nucleobases on ε-As is analysed based on band structure, the density of states, adsorption energy, energy gap variation & charge transfer. Besides, we observed the exothermic nature of binding energy (ranging from -0.453 eV to -0.819 eV) upon nucleobase adsorption on ε-As. Also, the energy gap variation & charge transfer takes place owing to adsorption of nucleobases on the ε-As sheet. The present report reveals the adsorption of nucleobases on ε-arsenene nanosheet.
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Affiliation(s)
- V Nagarajan
- School of Electrical & Electronics Engineering, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613 401, India
| | - S Sarvaka
- School of Chemical & Biotechnology, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613 401, India
| | - R Chandiramouli
- School of Electrical & Electronics Engineering, SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613 401, India.
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Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher's Precision ID mtDNA Whole Genome Assay. Genes (Basel) 2020; 11:genes11111303. [PMID: 33158032 PMCID: PMC7692767 DOI: 10.3390/genes11111303] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
The advent of massively parallel sequencing (MPS) in the past decade has opened the doors to mitochondrial whole-genome sequencing. Mitochondrial (mt) DNA is used in forensics due to its high copy number per cell and maternal mode of inheritance. Consequently, we have implemented the Thermo Fisher Precision ID mtDNA Whole Genome panel coupled with the Ion Chef™ and Ion S5™ for MPS analysis in the California Department of Justice, Missing Persons DNA Program. Thirty-one mostly challenging samples (degraded, inhibited, low template, or mixed) were evaluated for this study. The majority of these samples generated single source full or partial genome sequences with MPS, providing information in cases where previously there was none. The quantitative and sensitive nature of MPS analysis was beneficial, but also led to detection of low-level contaminants. In addition, we found Precision ID to be more susceptible to inhibition than our legacy Sanger assay. Overall, the success rate (full single source hypervariable regions I and II (HVI/HVII) for Sanger and control region for MPS result) for these challenging samples increased from 32.3% with Sanger sequencing to 74.2% with the Precision ID assay. Considering the increase in success rate, the simple workflow and the higher discriminating potential of whole genome data, the Precision ID platform is a significant improvement for the CA Department of Justice Missing Persons DNA Program.
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Božanić Urbančič N, Battelino S, Tesovnik T, Trebušak Podkrajšek K. The Importance of Early Genetic Diagnostics of Hearing Loss in Children. MEDICINA (KAUNAS, LITHUANIA) 2020; 56:E471. [PMID: 32937936 PMCID: PMC7558651 DOI: 10.3390/medicina56090471] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/30/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022]
Abstract
Hearing loss is one of the most common sensory deficits. It carries severe medical and social consequences, and therefore, universal newborn hearing screening was introduced at the beginning of this century. Affected patients can have hearing loss as a solitary deficit (non-syndromic hearing loss) or have other organs affected as well (syndromic hearing loss). In around 60% of cases, congenital hearing loss has a genetic etiology, where disease-causing variants can change any component of the hearing pathway. Genetic testing is usually performed by sequencing. Sanger sequencing enables analysis of the limited number of genes strictly preselected according to the clinical presentation and the prevalence among the hearing loss patients. In contrast, next-generation sequencing allows broad analysis of the numerous genes related to hearing loss, exome, or the whole genome. Identification of the genetic etiology is possible, and it makes the foundation for the genetic counselling in the family. Furthermore, it enables the identification of the comorbidities that may need a referral for specialty care, allows early treatment, helps with identification of candidates for cochlear implant, appropriate aversive/protective management, and is the foundation for the development of novel therapeutic options.
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Affiliation(s)
- Nina Božanić Urbančič
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, 1000 Ljubljana, Slovenia;
- Department of Otorhinolaryngology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Saba Battelino
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, 1000 Ljubljana, Slovenia;
- Department of Otorhinolaryngology, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Tine Tesovnik
- University Children’s Hospital, University Medical Centre Ljubljana, Bohoriceva 20, 1000 Ljubljana, Slovenia; (T.T.); (K.T.P.)
| | - Katarina Trebušak Podkrajšek
- University Children’s Hospital, University Medical Centre Ljubljana, Bohoriceva 20, 1000 Ljubljana, Slovenia; (T.T.); (K.T.P.)
- Faculty of Medicine, Institute of Biochemistry, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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Perez-Fernandez C, Morales-Navas M, Aguilera-Sáez LM, Abreu AC, Guardia-Escote L, Fernández I, Garrido-Cárdenas JA, Colomina MT, Giménez E, Sánchez-Santed F. Medium and long-term effects of low doses of Chlorpyrifos during the postnatal, preweaning developmental stage on sociability, dominance, gut microbiota and plasma metabolites. ENVIRONMENTAL RESEARCH 2020; 184:109341. [PMID: 32179266 DOI: 10.1016/j.envres.2020.109341] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental pathology characterized by altered verbalizations, reduced social interaction behavior, and stereotypies. Environmental factors have been associated with its development. Some researchers have focused on pesticide exposure. Chlorpyrifos (CPF) is the most used Organophosphate. Previous developmental studies with CPF showed decreased, enhanced or no effect on social outcomes eminently in mice. The study of CPF exposure during preweaning stages on social behavior is sparse in mice and non-existent in rats. d stressors could be at the basis of ASD development, and around postnatal day 10 in the rat is equivalent to the human birthday in neurodevelopmental terms. We explored the effects of exposure to low doses (1mg/kg/mL/day) of CPF during this stage regarding: sociability, dominance gut microbiome and plasma metabolomic profile, since alterations in these systems have also been linked to ASD. There was a modest influence of CPF on social behavior in adulthood, with null effects during adolescence. Dominance and hierarchical status were not affected by exposure. Dominance status explained the significant reduction in reaction to social novelty observed on the sociability test. CPF induced a significant gut microbiome dysbiosis and triggered a hyperlipidemic, hypoglycemic/hypogluconeogenesis and a general altered cell energy production in females. These behavioral results in rats extend and complement previous studies with mice and show novel influences on gut metagenomics and plasma lipid profile and metabolomics, but do not stablish a relation between the exposure to CPF and the ASD phenotype. The effects of dominance status on reaction to social novelty have an important methodological meaning for future research on sociability.
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Affiliation(s)
- Cristian Perez-Fernandez
- Department of Psychology and Health Research Center, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | - Miguel Morales-Navas
- Department of Psychology and Health Research Center, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | - Luis Manuel Aguilera-Sáez
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | - Ana Cristina Abreu
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | - Laia Guardia-Escote
- Department of Biochemistry and Biotechnology and Research in Neurobehavior and Health (NEUROLAB), Universitat Rovira i Virgili, 43007, C/ Macel.lí Domingo 1, Tarragona, Spain.
| | - Ignacio Fernández
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | | | - María Teresa Colomina
- Department of Psychology and Research Center for Behavior Assessment (CRAMC), Universitat Rovira i Virgili, 43007, C/ Carretera de Valls, s/n, Tarragona, Spain.
| | - Estela Giménez
- Department of Biology and Geology, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
| | - Fernando Sánchez-Santed
- Department of Psychology and Health Research Center, University of Almería, Ctra. Sacramento, s/n, 04120, Almería, Spain.
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Abstract
It is essential to address research into low-cost technologies, as those employed on a wide scale demand a great amount of resources. The main goal of this work was to analyze the research on low cost technologies worldwide by studying the scientific output recorded in the Scopus database. This analysis makes it possible to determine the evolution of research into low cost technologies. In particular, we analyzed the distribution of this research by the different scientific categories, the categories’ evolution over time, the types of publications, the geographical distribution throughout different countries, the main institutions in each scientific category, and the areas of research identified through the main keywords indexed in the publications. A remarkable finding of this work has been that the universities that are most active in low-cost technologies are those in the most technologically advanced countries. There is only one exception to the above statement and it is in the field of medicine, where the most technologically developed countries are not always the most interested in this field. Given the trends observed in recent years, there is a need for a major change and for low-cost technologies to become an area of interest in countries with emerging economies.
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Dewetted Gold Nanostructures onto Exfoliated Graphene Paper as High Efficient Glucose Sensor. NANOMATERIALS 2019; 9:nano9121794. [PMID: 31888252 PMCID: PMC6955950 DOI: 10.3390/nano9121794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 11/17/2022]
Abstract
Non-enzymatic electrochemical glucose sensing was obtained by gold nanostructures on graphene paper, produced by laser or thermal dewetting of 1.6 and 8 nm-thick Au layers, respectively. Nanosecond laser annealing produces spherical nanoparticles (AuNPs) through the molten-phase dewetting of the gold layer and simultaneous exfoliation of the graphene paper. The resulting composite electrodes were characterized by X-ray photoelectron spectroscopy, cyclic voltammetry, scanning electron microscopy, micro Raman spectroscopy and Rutherford back-scattering spectrometry. Laser dewetted electrode presents graphene nanoplatelets covered by spherical AuNPs. The sizes of AuNPs are in the range of 10-150 nm. A chemical shift in the XPS Au4f core-level of 0.25-0.3 eV suggests the occurrence of AuNPs oxidation, which are characterized by high stability under the electrochemical test. Thermal dewetting leads to electrodes characterized by faceted not oxidized gold structures. Glucose was detected in alkali media at potential of 0.15-0.17 V vs. saturated calomel electrode (SCE), in the concentration range of 2.5μM-30 mM, exploiting the peak corresponding to the oxidation of two electrons. Sensitivity of 1240 µA mM-1 cm-2, detection limit of 2.5 μM and quantifications limit of 20 μM were obtained with 8 nm gold equivalent thickness. The analytical performances are very promising and comparable to the actual state of art concerning gold based electrodes.
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Shi Z, Rothrock MJ, Ricke SC. Applications of Microbiome Analyses in Alternative Poultry Broiler Production Systems. Front Vet Sci 2019; 6:157. [PMID: 31179291 PMCID: PMC6543280 DOI: 10.3389/fvets.2019.00157] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 05/07/2019] [Indexed: 01/01/2023] Open
Abstract
While most of the focus on poultry microbiome research has been directed toward conventional poultry production, there is increasing interest in characterizing microbial populations originating from alternative or non-conventional poultry production. This is in part due to the growing general popularity in locally produced foods and more specifically the attractiveness of free-range or pasture raised poultry. Most of the focus of microbiome characterization in pasture flock birds has been on live bird production, primarily on the gastrointestinal tract. Interest in environmental impacts on production responses and management strategies have been key factors for comparative microbiome studies. This has important ramifications since these birds are not only raised under different conditions, but the grower cycle can be longer and in some cases slower growing breeds used. The impact of different feed additives is also of interest with some microbiome-based studies having examined the effect of feeding these additives to birds grown under pasture flock conditions. In the future, microbiome research approaches offer unique opportunities to develop better live bird management strategies and design optimal feed additive approaches for pasture flock poultry production systems.
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Affiliation(s)
- Zhaohao Shi
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
| | - Michael J Rothrock
- Egg Safety and Quality Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States
| | - Steven C Ricke
- Center for Food Safety, Food Science Department, University of Arkansas, Fayetteville, AR, United States
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Hsieh HY, Peng YH, Lin SF, Chen LC, Yu TC, Chiou CF, Lee J. Triple-Junction Optoelectronic Sensor with Nanophotonic Layer Integration for Single-Molecule Level Decoding. ACS NANO 2019; 13:4486-4495. [PMID: 30856319 DOI: 10.1021/acsnano.9b00019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Interest in developing a rapid and robust DNA sequencing platform has surged over the past decade. Various next-/third-generation sequencing mechanisms have been employed to replace the traditional Sanger sequencing method. In sequencing by synthesis, a signal is monitored by a scanning charge-coupled device (CCD) to identify thousands to millions of incorporated dNTPs with distinctive fluorophores on a chip. Because one reaction site usually occupies dozens of pixels on a CCD detector, a bottleneck related to the bandwidth of CCD imaging limits the throughputs of the sequencing performance and causes trade-offs among speed, accuracy, read length, and the numbers of reaction sites in parallel. Thus, current research aims to align one reaction site to a few pixels by directly stacking nanophotonic layers onto a CMOS detector to minimize the size of the sequencing platforms and accelerate the processing procedures. This article reports a custom integrated optoelectronic device based on a triple-junction photodiode (TPD) CMOS sensor in conjunction with NPL integration for real-time illumination and detection of fluorescent molecules.
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Affiliation(s)
- Hsin-Yi Hsieh
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Yu-Hsuan Peng
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Sheng-Fu Lin
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Li-Ching Chen
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Teng-Chien Yu
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Chung-Fan Chiou
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
| | - Johnsee Lee
- Personal Genomics, Inc. , Hsinchu Biomedical Science Park , Zhubei , Hsinchu 30261 , Taiwan
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Chen C, Zhou M, Yan XG, Chen YX, Cui M, Chen HC, Fu ZF, Zhao L. A recombinant canine distemper virus expressing interleukin-7 enhances humoral immunity. J Gen Virol 2019; 100:602-615. [DOI: 10.1099/jgv.0.001247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Chen Chen
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Ming Zhou
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Xiao-geng Yan
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Yi-xi Chen
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Min Cui
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Huan-chun Chen
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
| | - Zhen-fang Fu
- 4Department of Pathology, University of Georgia, Athens, GA, USA
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
| | - Ling Zhao
- 3College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
- 1State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, PR China
- 2Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agriculture University, Wuhan, PR China
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Plasmodium genomics: an approach for learning about and ending human malaria. Parasitol Res 2018; 118:1-27. [PMID: 30402656 DOI: 10.1007/s00436-018-6127-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/19/2018] [Indexed: 12/31/2022]
Abstract
Malaria causes high levels of morbidity and mortality in human beings worldwide. According to the World Health Organization (WHO), about half a million people die of this disease each year. Malaria is caused by six species of parasites belonging to the Plasmodium genus: P. falciparum, P. knowlesi, P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. Currently, malaria is being kept under control with varying levels of elimination success in different countries. The development of new molecular tools as well as the use of next-generation sequencing (NGS) technologies and novel bioinformatic approaches has improved our knowledge of malarial epidemiology, diagnosis, treatment, vaccine development, and surveillance strategies. In this work, the genetics and genomics of human malarias have been analyzed. Since the first P. falciparum genome was sequenced in 2002, various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.
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Highly selective, reusable electrochemical impedimetric DNA sensors based on carbon nanotube/polymer composite electrode without surface modification. Biosens Bioelectron 2018; 118:16-22. [DOI: 10.1016/j.bios.2018.07.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/02/2018] [Accepted: 07/16/2018] [Indexed: 12/30/2022]
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Paleček E, Heyrovský M, Dorčák V. J. Heyrovský's Oscillographic Polarography. Roots of Present Chronopotentiometric Analysis of Biomacromolecules. ELECTROANAL 2018. [DOI: 10.1002/elan.201800109] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Emil Paleček
- Institute of Biophysics of the CAS; Královopolská 135 612 65 Brno Czech Republic
| | - Michael Heyrovský
- J. Heyrovský Institute of Physical Chemistry of the CAS; Dolejškova 2155/3 182 23 Prague 8 Czech Republic
| | - Vlastimil Dorčák
- Institute of Biophysics of the CAS; Královopolská 135 612 65 Brno Czech Republic
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Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F. Trends in plant research using molecular markers. PLANTA 2018; 247:543-557. [PMID: 29243155 DOI: 10.1007/s00425-017-2829-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 05/21/2023]
Abstract
A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.
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Affiliation(s)
- Emil Paleček
- Biophysical Chemistry and Molecular Oncology; Institute of Biophysics AS CR, v.v.i.; Kralovopolska 135 612 65 Brno Czech Republic
| | - Martin Bartošík
- Regional Centre for Applied Molecular Oncology; Masaryk Memorial Cancer Institute; Zluty kopec 7 656 53 Brno Czech Republic
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Abstract
In this article, the trends in human parasitology have been studied through the analysis of the number of publications in this area. The parameters studied were: number of articles, language, countries and institutions with the highest number of publications, and keywords with greater presence in the articles of human parasitology. The results of the analysis confirm the growing interest in this area, observing an exponential growth in the number of publications in the last decades. We also verified that the main country in terms of scientific production is the USA, although among the most important institutions, we find non-US centres such as the Oswaldo Cruz Foundation and the London School of Hygiene and Tropical Medicine. For observing the relative importance of the journals that publish articles in this specific topic, an index has been created based on the h-index of the journal with publications related to human parasitology and divided by every 100 items. This rank is led fist by 'Journal of Medical Entomology' closely followed by 'Parasitology'. The analysis of the keywords allows to draw conclusions about the great importance of malaria in the current world research. A change in analytical methodology is also observed, and molecular techniques are now being imposed. These techniques, in the near future, have to influence in an improvement in the treatments and prevention of the diseases caused by parasites. Finally, it can be seen that diseases traditionally studied as helminthiasis and amebiasis are currently as well studied as others such as toxoplasmosis or leishmaniasis.
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Yin B, Xie W, Liang L, Deng Y, He S, He F, Zhou D, Tlili C, Wang D. Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection. ACS OMEGA 2017; 2:7127-7135. [PMID: 31457292 PMCID: PMC6645049 DOI: 10.1021/acsomega.7b01245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/06/2017] [Indexed: 05/11/2023]
Abstract
In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.
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Drewes S, Straková P, Drexler JF, Jacob J, Ulrich RG. Assessing the Diversity of Rodent-Borne Viruses: Exploring of High-Throughput Sequencing and Classical Amplification/Sequencing Approaches. Adv Virus Res 2017; 99:61-108. [PMID: 29029730 DOI: 10.1016/bs.aivir.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rodents are distributed throughout the world and interact with humans in many ways. They provide vital ecosystem services, some species are useful models in biomedical research and some are held as pet animals. However, many rodent species can have adverse effects such as damage to crops and stored produce, and they are of health concern because of the transmission of pathogens to humans and livestock. The first rodent viruses were discovered by isolation approaches and resulted in break-through knowledge in immunology, molecular and cell biology, and cancer research. In addition to rodent-specific viruses, rodent-borne viruses are causing a large number of zoonotic diseases. Most prominent examples are reemerging outbreaks of human hemorrhagic fever disease cases caused by arena- and hantaviruses. In addition, rodents are reservoirs for vector-borne pathogens, such as tick-borne encephalitis virus and Borrelia spp., and may carry human pathogenic agents, but likely are not involved in their transmission to human. In our days, next-generation sequencing or high-throughput sequencing (HTS) is revolutionizing the speed of the discovery of novel viruses, but other molecular approaches, such as generic RT-PCR/PCR and rolling circle amplification techniques, contribute significantly to the rapidly ongoing process. However, the current knowledge still represents only the tip of the iceberg, when comparing the known human viruses to those known for rodents, the mammalian taxon with the largest species number. The diagnostic potential of HTS-based metagenomic approaches is illustrated by their use in the discovery and complete genome determination of novel borna- and adenoviruses as causative disease agents in squirrels. In conclusion, HTS, in combination with conventional RT-PCR/PCR-based approaches, resulted in a drastically increased knowledge of the diversity of rodent viruses. Future improvements of the used workflows, including bioinformatics analysis, will further enhance our knowledge and preparedness in case of the emergence of novel viruses. Classical virological and additional molecular approaches are needed for genome annotation and functional characterization of novel viruses, discovered by these technologies, and evaluation of their zoonotic potential.
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Affiliation(s)
- Stephan Drewes
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Petra Straková
- Institute of Vertebrate Biology v.v.i., Academy of Sciences, Brno, Czech Republic
| | - Jan F Drexler
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Germany
| | - Jens Jacob
- Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Horticulture and Forests, Vertebrate Research, Münster, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany; German Center for Infection Research (DZIF), Partner site Hamburg-Luebeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany.
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37
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Advanced microbial analysis for wastewater quality monitoring: metagenomics trend. Appl Microbiol Biotechnol 2017; 101:7445-7458. [DOI: 10.1007/s00253-017-8490-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/19/2017] [Indexed: 12/20/2022]
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Kaisers W, Schwender H, Schaal H. Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data. Int J Mol Sci 2017; 18:ijms18091900. [PMID: 28872584 PMCID: PMC5618549 DOI: 10.3390/ijms18091900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 01/13/2023] Open
Abstract
Merging data from multiple samples is required to detect low expressed transcripts or splicing events that might be present only in a subset of samples. However, the exact number of required replicates enabling the detection of such rare events often remains a mystery but can be approached through probability theory. Here, we describe a probabilistic model, relating the number of observed events in a batch of samples with observation probabilities. Therein, samples appear as a heterogeneous collection of events, which are observed with some probability. The model is evaluated in a batch of 54 transcriptomes of human dermal fibroblast samples. The majority of putative splice-sites (alignment gap-sites) are detected in (almost) all samples or only sporadically, resulting in an U-shaped pattern for observation probabilities. The probabilistic model systematically underestimates event numbers due to a bias resulting from finite sampling. However, using an additional assumption, the probabilistic model can predict observed event numbers within a <10% deviation from the median. Single samples contain a considerable amount of uniquely observed putative splicing events (mean 7122 in alignments from TopHat alignments and 86,215 in alignments from STAR). We conclude that the probabilistic model provides an adequate description for observation of gap-sites in transcriptome data. Thus, the calculation of required sample sizes can be done by application of a simple binomial model to sporadically observed random events. Due to the large number of uniquely observed putative splice-sites and the known stochastic noise in the splicing machinery, it appears advisable to include observation of rare splicing events into analysis objectives. Therefore, it is beneficial to take scores for the validation of gap-sites into account.
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Affiliation(s)
- Wolfgang Kaisers
- Department for Anaesthesiology, Heinrich Heine University, 40225 Düsseldorf, Germany.
- BMFZ, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Holger Schwender
- BMFZ, Heinrich Heine University, 40225 Düsseldorf, Germany.
- Mathematical Institute, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Heiner Schaal
- BMFZ, Heinrich Heine University, 40225 Düsseldorf, Germany.
- Institute for Virology, Heinrich Heine University, 40225 Düsseldorf, Germany.
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39
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Garrido-Cardenas JA, Manzano-Agugliaro F. The metagenomics worldwide research. Curr Genet 2017; 63:819-829. [PMID: 28401295 DOI: 10.1007/s00294-017-0693-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022]
Abstract
Metagenomics is the technique, or set of techniques, whose main objective is to determine the microbial population that can be found in a determined environment, studied in the context of its community. For this, it uses the techniques of massive sequencing, or next generation sequencing, due to the difficulties presented by traditional techniques when trying to transfer all the microorganisms present in a given environment to the laboratory. Metagenomics is a newly created technique, which was born at the beginning of the twenty-first century, and since then the interest of the world scientific community in fields as diverse as medicine, biotechnology, agriculture or genetics has not left to grow. In this article, the authors make a historical review of the metagenomics, analyze and evaluate the different massive sequencing platforms used for metagenomic assays, review the current literature on this subject and advance future problems with which researchers who decide to go deeper in this field could find. In this way, the prior knowledge of the researcher will facilitate the approach of his research.
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