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Basirpour B, Tabaripour R, Jafarian F, Fakhar M, Ziaei Hezarjaribi H, Gholami S. Applications of the powerful next-generation sequencing tool for detecting parasitic infections: towards a smart laboratory platform. Microb Pathog 2025:107746. [PMID: 40419199 DOI: 10.1016/j.micpath.2025.107746] [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: 11/03/2024] [Revised: 04/15/2025] [Accepted: 05/24/2025] [Indexed: 05/28/2025]
Abstract
Parasitic infections are a group of infectious diseases that are mainly caused by helminths and protozoa. Recently, emerging diagnostic techniques have been developed to not only elevate the chance of parasite detection but also increase the accurate diagnosis. Next-generation sequencing (NGS) technologies are highlighted among different genomic-based methods due to their wide-spectrum application. NGS presents an opportunity for clinical use in detecting parasitic infections. Also, it allows for the characterization of parasites, as well as the identification of drug resistance. Incorporating NGS into the diagnostic process has the potential to create innovative laboratory platforms that transform the field of parasitology and enhance patient care. The NGS technique has been used in understanding genetic interrelationships among parasites and the detection of parasites in various samples. It is anticipated that these approaches will be changed to the point of care diagnostic testing due to their accuracy and rapid action. Moreover, their efficiency in diagnosing multiple organisms with one sampling, changes these methods into pioneers in diagnostic tests. Here, the applications of NGS as a powerful tool in diagnosing clinically important parasites and how this tool is developing parasitic disease diagnostics are discussed.
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Affiliation(s)
- Bahareh Basirpour
- Department of Parasitology, Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Rabeeh Tabaripour
- Department of Parasitology, Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farzane Jafarian
- Department of Parasitology, Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Fakhar
- Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran; Department of Medical Microbiology and Immunology, School of Medicine, Qom University of Medical Sciences, Qom, Iran.
| | - Hajar Ziaei Hezarjaribi
- Department of Parasitology, Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shirzad Gholami
- Department of Parasitology, Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran; Toxoplasmosis Research Center, Mazandaran Registry Center for Hydatid Cyst, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Kringel D, Lötsch J. Knowledge of the genetics of human pain gained over the last decade from next-generation sequencing. Pharmacol Res 2025; 214:107667. [PMID: 39988004 DOI: 10.1016/j.phrs.2025.107667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 02/11/2025] [Accepted: 02/18/2025] [Indexed: 02/25/2025]
Abstract
Next-generation sequencing (NGS) technologies have revolutionized pain research by providing comprehensive insights into genetic variation across the genome. Recent studies have expanded the known spectrum of mutations in genes such as SCN9A and NTRK1, which are commonly mutated in hereditary sensory neuropathies. NGS has uncovered critical alternative splicing events and facilitated single-cell transcriptomics, revealing cellular heterogeneity within tissues. An NGS-based classifier predicted extremely high opioid requirements with 80 % accuracy, highlighting the importance of tailoring opioid therapy based on genetic profiles. Key genes such as GDF5, COL11A1, and TRPV1 have been linked to osteoarthritis risk and pain sensitivity, while HLA-DRB1, TNF, and P2X7 play critical roles in inflammation and pain modulation in rheumatoid arthritis. Innovative tools, such as an atlas of the somatosensory system in neuropathic pain, have been developed based on NGS data, focusing on the dorsal root and trigeminal ganglia. This approach allows the analysis of cellular changes during the development of chronic pain. In the study of rare variants, NGS outperforms single nucleotide variant candidate studies and classical genome-wide association approaches. The complex data generated by NGS enables integrated multi-omics approaches, allowing deeper exploration of the molecular and cellular basis of pain perception. In addition, the characterization of non-coding RNAs has opened new therapeutic avenues. NGS-based pain research faces challenges related to complex data analysis and interpretation of rare genetic variants with unknown biological functions. Nevertheless, NGS offers significant potential for improving personalized pain management and highlights the need for interdisciplinary collaboration to translate findings into clinical practice.
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Affiliation(s)
- Dario Kringel
- Goethe - University, Institute of Clinical Pharmacology, Theodor Stern Kai 7, Frankfurt am Main 60590, Germany
| | - Jörn Lötsch
- Goethe - University, Institute of Clinical Pharmacology, Theodor Stern Kai 7, Frankfurt am Main 60590, Germany; University of Helsinki, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, P.O. Box 63, 00014, Finland; Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Theodor-Stern-Kai 7, Frankfurt am Main 60596, Germany.
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3
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Liberty JT, Lin H, Kucha C, Sun S, Alsalman FB. Innovative approaches to food traceability with DNA barcoding: Beyond traditional labels and certifications. ECOLOGICAL GENETICS AND GENOMICS 2025; 34:100317. [DOI: 10.1016/j.egg.2024.100317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Klein A, Zhong J, Landi MT, Zhang T. Sherlock-Genome: an R Shiny application for genomic analysis and visualization. BMC Genomics 2025; 26:44. [PMID: 39819269 PMCID: PMC11740398 DOI: 10.1186/s12864-024-11147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 12/09/2024] [Indexed: 01/19/2025] Open
Abstract
MOTIVATION Next-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery. RESULTS We developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies. Following FAIR principles, Sherlock-Genome provides a platform and guidelines for managing and sharing finalized sample-level WGS analysis results, enabling users to upload results, inspect analyses locally, and perform integrative analyses. It includes modules for major cancer genomic analyses, allowing interactive data visualizations and integrative analyses with other data types. Sherlock-Genome supports both local and cloud deployment, facilitating the sharing of results for related publications. This tool has the potential to be widely adopted in cancer genomics, significantly enhancing the accessibility and usability of sample-level WGS analysis results for comprehensive biological discovery and research advancements. AVAILABILITY AND IMPLEMENTATION The source code and installation instructions for Sherlock-Genome can be accessed via Github https://github.com/xtmgah/Sherlock-Genome . Documentation and data requirements for user project data can also be found on the same GitHub page.
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Affiliation(s)
- Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jun Zhong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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5
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Chhabra R. Molecular and modular intricacies of precision oncology. Front Immunol 2024; 15:1476494. [PMID: 39507541 PMCID: PMC11537923 DOI: 10.3389/fimmu.2024.1476494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 09/30/2024] [Indexed: 11/08/2024] Open
Abstract
Precision medicine is revolutionizing the world in combating different disease modalities, including cancer. The concept of personalized treatments is not new, but modeling it into a reality has faced various limitations. The last decade has seen significant improvements in incorporating several novel tools, scientific innovations and governmental support in precision oncology. However, the socio-economic factors and risk-benefit analyses are important considerations. This mini review includes a summary of some commendable milestones, which are not just a series of successes, but also a cautious outlook to the challenges and practical implications of the advancing techno-medical era.
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Affiliation(s)
- Ravneet Chhabra
- Business Department, Biocytogen Boston Corporation, Waltham, MA, United States
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Khan S, Bano N, Ahamad S, John U, Dar NJ, Bhat SA. Excitotoxicity, Oxytosis/Ferroptosis, and Neurodegeneration: Emerging Insights into Mitochondrial Mechanisms. Aging Dis 2024:AD.2024.0125-1. [PMID: 39122453 DOI: 10.14336/ad.2024.0125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Mitochondrial dysfunction plays a pivotal role in the development of age-related diseases, particularly neurodegenerative disorders. The etiology of mitochondrial dysfunction involves a multitude of factors that remain elusive. This review centers on elucidating the role(s) of excitotoxicity, oxytosis/ferroptosis and neurodegeneration within the context of mitochondrial bioenergetics, biogenesis, mitophagy and oxidative stress and explores their intricate interplay in the pathogenesis of neurodegenerative diseases. The effective coordination of mitochondrial turnover processes, notably mitophagy and biogenesis, is assumed to be critically important for cellular resilience and longevity. However, the age-associated decrease in mitophagy impedes the elimination of dysfunctional mitochondria, consequently impairing mitochondrial biogenesis. This deleterious cascade results in the accumulation of damaged mitochondria and deterioration of cellular functions. Both excitotoxicity and oxytosis/ferroptosis have been demonstrated to contribute significantly to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's Disease (HD), Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS). Excitotoxicity, characterized by excessive glutamate signaling, initiates a cascade of events involving calcium dysregulation, energy depletion, and oxidative stress and is intricately linked to mitochondrial dysfunction. Furthermore, emerging concepts surrounding oxytosis/ferroptosis underscore the importance of iron-dependent lipid peroxidation and mitochondrial engagement in the pathogenesis of neurodegeneration. This review not only discusses the individual contributions of excitotoxicity and ferroptosis but also emphasizes their convergence with mitochondrial dysfunction, a key driver of neurodegenerative diseases. Understanding the intricate crosstalk between excitotoxicity, oxytosis/ferroptosis, and mitochondrial dysfunction holds potential to pave the way for mitochondrion-targeted therapeutic strategies. Such strategies, with a focus on bioenergetics, biogenesis, mitophagy, and oxidative stress, emerge as promising avenues for therapeutic intervention.
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Affiliation(s)
- Sameera Khan
- Department of Zoology, Aligarh Muslim University, Aligarh-202002, India
| | - Nargis Bano
- Department of Zoology, Aligarh Muslim University, Aligarh-202002, India
| | - Shakir Ahamad
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, India
| | - Urmilla John
- School of Studies in Neuroscience, Jiwaji University, Gwalior, India; School of Studies in Zoology, Jiwaji University, Gwalior, India
| | - Nawab John Dar
- CNB, SALK Institute of Biological Sciences, La Jolla, CA 92037, USA
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7
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Vaga CF, Seiblitz IGL, Stolarski J, Capel KCC, Quattrini AM, Cairns SD, Huang D, Quek RZB, Kitahara MV. 300 million years apart: the extreme case of macromorphological skeletal convergence between deltocyathids and a turbinoliid coral (Anthozoa, Scleractinia). INVERTEBR SYST 2024; 38:IS23053. [PMID: 38744500 DOI: 10.1071/is23053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/16/2024]
Abstract
The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus , molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. ZooBank: urn:lsid:zoobank.org:pub:5F1C0E25-3CC6-4D1F-B1F0-CD9D0014678E.
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Affiliation(s)
- C F Vaga
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - I G L Seiblitz
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
| | - J Stolarski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, PL-00-818 Warsaw, Poland
| | - K C C Capel
- Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Invertebrate Department, National Museum of Rio de Janeiro, Federal University of Rio de Janeiro, 20940-040, Rio de Janeiro, Brazil
| | - A M Quattrini
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - S D Cairns
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA
| | - D Huang
- Lee Kong Chian Natural History Museum, National University of Singapore, Conservatory Drive, Singapore 117377, Singapore; and Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - R Z B Quek
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; and Yale-NUS College, National University of Singapore, Singapore 138527, Singapore
| | - M V Kitahara
- Department of Invertebrate Zoology, Smithsonian Institution, Washington, DC, 20560-0163, USA; and Center for Marine Biology, University of São Paulo, 11602-109, São Sebastião, SP, Brazil; and Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090 São Paulo, Brazil
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8
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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9
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Akash A, Bencurova E, Dandekar T. How to make DNA data storage more applicable. Trends Biotechnol 2024; 42:17-30. [PMID: 37591721 DOI: 10.1016/j.tibtech.2023.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
The storage of digital data is becoming a worldwide problem. DNA has been recognized as a biological solution due to its ability to store genetic information without alteration over long periods. The first demonstrations of high-capacity long-lasting DNA digital data storage have been shown. However, high storage costs and slow retrieval of the data must be overcome to make DNA data storage more applicable and marketable. Herein, we discuss the issues and recent advances in DNA data storage methods and highlight pathways to make this technology more applicable to real-world digital data storage. We envision that a combination of molecular biology, nanotechnology, novel polymers, electronics, and automation with systematic development will allow DNA data storage sufficient for everyday use.
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Affiliation(s)
- Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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10
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Leatham B, McNall K, Subramanian HKK, Jacky L, Alvarado J, Yurk D, Wang M, Green DC, Tsongalis GJ, Rajagopal A, Schwartz JJ. A rapid, multiplex digital PCR assay to detect gene variants and fusions in non-small cell lung cancer. Mol Oncol 2023; 17:2221-2234. [PMID: 37714814 PMCID: PMC10620117 DOI: 10.1002/1878-0261.13523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/22/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023] Open
Abstract
Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation-based multiplex dPCR assay capable of detecting 12 single-nucleotide and insertion/deletion (indel) variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1, and NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target-signal encoding to improve the specificity of variant detection by reducing background noise by up to an order of magnitude. The assay reported an overall 100% positive percent agreement (PPA) and 98.5% negative percent agreement (NPA) compared with a sequencing-based assay in a cohort of 62 human formalin-fixed paraffin-embedded (FFPE) samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed dPCR assay as a potential reflex solution for challenging NSCLC samples.
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Affiliation(s)
| | | | | | | | | | - Dominic Yurk
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Mimi Wang
- ChromaCode IncCarlsbadCAUSA
- Slack TechnologiesSan FranciscoCAUSA
| | - Donald C. Green
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Gregory J. Tsongalis
- Department of Pathology and Laboratory MedicineDartmouth Hitchcock Medical CenterLebanonNHUSA
| | - Aditya Rajagopal
- ChromaCode IncCarlsbadCAUSA
- Department of Electrical EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Biomedical EngineeringUniversity of Southern CaliforniaLos AngelesCAUSA
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11
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Magdy Mohamed Abdelaziz Barakat S, Sallehuddin R, Yuhaniz SS, R. Khairuddin RF, Mahmood Y. Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges. PeerJ Comput Sci 2023; 9:e1180. [PMID: 37547391 PMCID: PMC10403225 DOI: 10.7717/peerj-cs.1180] [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: 04/07/2022] [Accepted: 04/27/2023] [Indexed: 08/08/2023]
Abstract
Background The development of sequencing technology increases the number of genomes being sequenced. However, obtaining a quality genome sequence remains a challenge in genome assembly by assembling a massive number of short strings (reads) with the presence of repetitive sequences (repeats). Computer algorithms for genome assembly construct the entire genome from reads in two approaches. The de novo approach concatenates the reads based on the exact match between their suffix-prefix (overlapping). Reference-guided approach orders the reads based on their offsets in a well-known reference genome (reads alignment). The presence of repeats extends the technical ambiguity, making the algorithm unable to distinguish the reads resulting in misassembly and affecting the assembly approach accuracy. On the other hand, the massive number of reads causes a big assembly performance challenge. Method The repeat identification method was introduced for misassembly by prior identification of repetitive sequences, creating a repeat knowledge base to reduce ambiguity during the assembly process, thus enhancing the accuracy of the assembled genome. Also, hybridization between assembly approaches resulted in a lower misassembly degree with the aid of the reference genome. The assembly performance is optimized through data structure indexing and parallelization. This article's primary aim and contribution are to support the researchers through an extensive review to ease other researchers' search for genome assembly studies. The study also, highlighted the most recent developments and limitations in genome assembly accuracy and performance optimization. Results Our findings show the limitations of the repeat identification methods available, which only allow to detect of specific lengths of the repeat, and may not perform well when various types of repeats are present in a genome. We also found that most of the hybrid assembly approaches, either starting with de novo or reference-guided, have some limitations in handling repetitive sequences as it is more computationally costly and time intensive. Although the hybrid approach was found to outperform individual assembly approaches, optimizing its performance remains a challenge. Also, the usage of parallelization in overlapping and reads alignment for genome assembly is yet to be fully implemented in the hybrid assembly approach. Conclusion We suggest combining multiple repeat identification methods to enhance the accuracy of identifying the repeats as an initial step to the hybrid assembly approach and combining genome indexing with parallelization for better optimization of its performance.
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Affiliation(s)
| | - Roselina Sallehuddin
- Computer Science, School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Siti Sophiayati Yuhaniz
- Advanced Informatics Department, Razak Faculty of Technology and Informatics, Universiti Teknologi Malaysia, Kuala Lumpur, Kuala Lumpur, Malaysia
| | | | - Yasir Mahmood
- Faculty of Information Technology, The University of Lahore, Lahore, Lahore, Pakistan
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12
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Hadar N, Weintraub G, Gudes E, Dolev S, Birk OS. GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture. Database (Oxford) 2023; 2023:baad043. [PMID: 37311148 DOI: 10.1093/database/baad043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
In recent years, there are a huge influx of genomic data and a growing need for its phenotypic correlations, yet existing genomic databases do not allow easy storage and accessibility to the combined phenotypic-genotypic information. Freely accessible allele frequency (AF) databases, such as gnomAD, are crucial for evaluating variants but lack correlated phenotype data. The Sequence Read Archive (SRA) accumulates hundreds of thousands of next-generation sequencing (NGS) samples tagged by their submitters and various attributes. However, samples are stored in large raw format files, inaccessible for a common user. To make thousands of NGS samples and their corresponding additional attributes easily available to clinicians and researchers, we generated a pipeline that continuously downloads raw human NGS data uploaded to SRA using SRAtoolkit and preprocesses them using GATK pipeline. Data are then stored efficiently in a cloud data lake and can be accessed via a representational state transfer application programming interface (REST API) and a user-friendly website. We thus generated GeniePool, a simple and intuitive web service and API for querying NGS data from SRA with direct access to information related to each sample and related studies, providing significant advantages over existing databases for both clinical and research usages. Utilizing data lake infrastructure, we were able to generate a multi-purpose tool that can serve many clinical and research use cases. We expect users to explore the meta-data served via GeniePool both in daily clinical practice and in versatile research endeavours. Database URL https://geniepool.link.
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Affiliation(s)
- Noam Hadar
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Genetics Institute, Soroka Medical Center, Beer Sheva 84101, Israel
| | - Grisha Weintraub
- Department of Computer Science, Faculty of Natural Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ehud Gudes
- Department of Computer Science, Faculty of Natural Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Shlomi Dolev
- Department of Computer Science, Faculty of Natural Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
- Genetics Institute, Soroka Medical Center, Beer Sheva 84101, Israel
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13
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Xi J, Li Y, Zhang H, Bai Z. Dynamic variations of the gastric microbiota: Key therapeutic points in the reversal of Correa's cascade. Int J Cancer 2023; 152:1069-1084. [PMID: 36029278 DOI: 10.1002/ijc.34264] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 01/21/2023]
Abstract
Correa's cascade is a dynamic process in the development of intestinal-type gastric cancer (GC), and its pathological features, gastric microbiota and interactions between microorganisms and their hosts vary at different developmental stages. The characteristics of cells, tissues and gastric microbiota before or after key therapeutic points are critical for monitoring malignant transformation and early tumour reversal. This review summarises the pathological features of gastric mucosa, characteristics of gastric microbiota, specific microbial markers, microbe-microbe interactions and microbe-host interactions at different stages in Correa's cascade. The markers related to each Correa's cascade point were analysed in detail. We attempted to identify key therapeutic points for early cancer reversal and provide a novel approach to reduce the incidence of GC and improve precise treatment.
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Affiliation(s)
- Jiahui Xi
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine, Gansu Province, Lanzhou, China
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumour, Gansu Provincial Hospital, Lanzhou, China
| | - Hui Zhang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,General Surgery Department, The First Hospital of Lanzhou University, Lanzhou, China
| | - Zhongtian Bai
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China.,Key Laboratory of Biotherapy and Regenerative Medicine, Gansu Province, Lanzhou, China.,General Surgery Department, The First Hospital of Lanzhou University, Lanzhou, China
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14
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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15
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Alamil M, Thébaud G, Berthier K, Soubeyrand S. Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics. Front Microbiol 2022; 13:983938. [PMID: 36274731 PMCID: PMC9581327 DOI: 10.3389/fmicb.2022.983938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial communities and to infer transmission links in infectious disease outbreaks. The performance of such characterizations and inferences cannot be analytically assessed in general and are often grounded on computer-intensive evaluations. Then, being able to simulate within-host genetic diversity across time under various demo-genetic assumptions is paramount to assess the performance of the approaches of interest. In this context, we built an original model that can be simulated to investigate the temporal evolution of genotypes and their frequencies under various demo-genetic assumptions. The model describes the growth and the mutation of genotypes at the nucleotide resolution conditional on an overall within-host viral kinetics, and can be tuned to generate fast non-equilibrium demo-genetic dynamics. We ran simulations of this model and computed classic diversity indices to characterize the temporal variation of within-host genetic diversity (from high-throughput amplicon sequences) of virus populations under three demographic kinetic models of viral infection. Our results highlight how demographic (viral load) and genetic (mutation, selection, or drift) factors drive variations in within-host diversity during the course of an infection. In particular, we observed a non-monotonic relationship between pathogen population size and genetic diversity, and a reduction of the impact of mutation on diversity when a non-specific host immune response is activated. The large variation in the diversity patterns generated in our simulations suggests that the underlying model provides a flexible basis to produce very diverse demo-genetic scenarios and test, for instance, methods for the inference of transmission links during outbreaks.
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Affiliation(s)
- Maryam Alamil
- INRAE, BioSP, Avignon, France
- Department of Mathematics and Computer Science, Alfaisal University, Riyadh, Saudi Arabia
- *Correspondence: Maryam Alamil ;
| | - Gaël Thébaud
- PHIM Plant Health Institute, INRAE, Univ Montpellier, CIRAD, Institut Agro, IRD, Montpellier, France
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16
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Aardema ML, Campana MG, Wagner NE, Ferreira FC, Fonseca DM. A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes. PLoS Negl Trop Dis 2022; 16:e0010689. [PMID: 35939523 PMCID: PMC9387926 DOI: 10.1371/journal.pntd.0010689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 08/18/2022] [Accepted: 07/20/2022] [Indexed: 12/30/2022] Open
Abstract
Understanding patterns of diversification, genetic exchange, and pesticide resistance in arthropod disease vectors is necessary for effective population management. With the availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for a large number of genetic markers. To this end, the targeting of gene sequences of known function can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens such as avian malaria parasites that are detrimental to birds. Here we describe the development of a targeted, gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we sequenced samples from several members of the complex, as well as from distinct populations of the relatively under-studied Culex quinquefasciatus. The data generated was then used to examine taxonomic divergence and population clustering between and within these mosquitoes. We also used this data to investigate genetic variants present in our samples that had previously been shown to correlate with insecticide-resistance. Broadly, our gene capture approach successfully enriched the genomic regions of interest, and proved effective for facilitating examinations of taxonomic divergence and geographic clustering within the Cx. pipiens complex. It also allowed us to successfully survey genetic variation associated with insecticide resistance in Culex mosquitoes. This enrichment protocol will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of these ubiquitous and increasingly damaging disease vectors. The mosquito taxa that make up the Culex pipiens complex are important vectors of the agents of several human diseases such as West Nile and St. Louis encephalitides, and lymphatic filariasis. They are also important vectors of avian malaria, which impacts livestock and wildlife. The development of effective strategies for the control of these mosquitoes requires knowledge of their origins, distribution, dispersal patterns, and the extent to which discreet taxonomic entities within the complex interbreed. To achieve these objectives, it is necessary to compare patterns of genetic diversity across many mosquito samples, which can be cost-prohibitive. To address this limitation, we developed a targeted, gene-based assay that allowed us to cost-effectively genotype a large number of genetic variants from a representative global sampling of individual Cx. pipiens complex mosquitoes. We show that this assay is a powerful tool for examining genetic structure and hybridization among populations. We also explore its utility for surveying alleles previously shown to be associated with insecticide resistance. Future use of this enrichment assay and the bioinformatics methods described here will allow researchers to study evolutionary patterns across the Cx. pipiens complex as well as monitor the presence of genetic variation that could affect control efforts.
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Affiliation(s)
- Matthew L. Aardema
- Department of Biology, Montclair State University, Montclair, New Jersey, United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- * E-mail: (MLA); (DMF)
| | - Michael G. Campana
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States of America
| | - Nicole E. Wagner
- Center for Vector Biology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Francisco C. Ferreira
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States of America
- Center for Vector Biology, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Dina M. Fonseca
- Center for Vector Biology, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail: (MLA); (DMF)
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17
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Alves G, Ogurtsov A, Karlsson R, Jaén-Luchoro D, Piñeiro-Iglesias B, Salvà-Serra F, Andersson B, Moore ERB, Yu YK. Identification of Antibiotic Resistance Proteins via MiCId's Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:917-931. [PMID: 35500907 PMCID: PMC9164240 DOI: 10.1021/jasms.1c00347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 06/01/2023]
Abstract
Fast and accurate identifications of pathogenic bacteria along with their associated antibiotic resistance proteins are of paramount importance for patient treatments and public health. To meet this goal from the mass spectrometry aspect, we have augmented the previously published Microorganism Classification and Identification (MiCId) workflow for this capability. To evaluate the performance of this augmented workflow, we have used MS/MS datafiles from samples of 10 antibiotic resistance bacterial strains belonging to three different species: Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The evaluation shows that MiCId's workflow has a sensitivity value around 85% (with a lower bound at about 72%) and a precision greater than 95% in identifying antibiotic resistance proteins. In addition to having high sensitivity and precision, MiCId's workflow is fast and portable, making it a valuable tool for rapid identifications of bacteria as well as detection of their antibiotic resistance proteins. It performs microorganismal identifications, protein identifications, sample biomass estimates, and antibiotic resistance protein identifications in 6-17 min per MS/MS sample using computing resources that are available in most desktop and laptop computers. We have also demonstrated other use of MiCId's workflow. Using MS/MS data sets from samples of two bacterial clonal isolates, one being antibiotic-sensitive while the other being multidrug-resistant, we applied MiCId's workflow to investigate possible mechanisms of antibiotic resistance in these pathogenic bacteria; the results showed that MiCId's conclusions agree with the published study. The new version of MiCId (v.07.01.2021) is freely available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.
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Affiliation(s)
- Gelio Alves
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Aleksey Ogurtsov
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Roger Karlsson
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Nanoxis
Consulting AB, 40234 Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
| | - Beatriz Piñeiro-Iglesias
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
| | - Francisco Salvà-Serra
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
- Microbiology,
Department of Biology, University of the
Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Björn Andersson
- Bioinformatics
Core Facility at Sahlgrenska Academy, University
of Gothenburg, Box 413, 40530 Gothenburg, Sweden
| | - Edward R. B. Moore
- Department
of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
- Department
of Clinical Microbiology, Sahlgrenska University
Hospital, 40234 Gothenburg, Sweden
- Center
for Antibiotic Resistance Research (CARe), University of Gothenburg, 40016 Gothenburg, Sweden
- Culture Collection
University of Gothenburg (CCUG), Sahlgrenska
Academy of the University of Gothenburg, 40234 Gothenburg, Sweden
| | - Yi-Kuo Yu
- National
Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, United States
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18
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Mahmud S, Biswas S, Afrose S, Mita MA, Hasan MR, Shimu MSS, Paul GK, Chung S, Saleh MA, Alshehri S, Ghoneim MM, Alruwaily M, Kim B. Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs's cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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Affiliation(s)
- Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Mst. Sharmin Sultana Shimu
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Gobindo Kumar Paul
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sanghyun Chung
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
| | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.B.); (S.A.); (M.A.M.); (M.R.H.); (M.S.S.S.); (G.K.P.); (M.A.S.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Momammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Maha Alruwaily
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
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19
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Jiang M, Zhou H, Jiang S, Yu H. A Review of Circulating Tumor DNA in the Diagnosis and Monitoring of Esophageal Cancer. Med Sci Monit 2022; 28:e934106. [PMID: 35210388 PMCID: PMC8886734 DOI: 10.12659/msm.934106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is a type of cell-free DNA released by tumor cells after necrosis and apoptosis, and it can be actively secreted by tumor cells. Since ctDNA is derived from various tumor sites, it can provide far more comprehensive genomic and epigenomic information than a single-site biopsy. Therefore, ctDNA can overcome tumor heterogeneity, which is the major limitation of a traditional tissue biopsy approach. Noninvasive ctDNA assays allow continuous real-time monitoring of the molecular status of cancers. Recently, ctDNA assays have been widely used in clinical practice, including cancer diagnosis, evaluation of therapeutic efficacy and prognosis, and monitoring of relapse and metastasis. Although ctDNA shows a high diagnostic performance in advanced esophageal cancer, it is far from satisfactory for early diagnosis of esophageal cancer. Monitoring the dynamic changes of ctDNA is beneficial for the evaluation of therapeutic efficacy and prediction of early recurrence in esophageal cancer. It is necessary to establish standards for individualized ctDNA detection in the evaluation of treatment response and surveillance of esophageal cancer and to develop clinical practice guideline for the systemic treatment of patients with "ctDNA recurrence." This review aims to provide an update on the role of ctDNA in the diagnosis and monitoring of esophageal cancer.
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Affiliation(s)
- Min Jiang
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Huilin Zhou
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Su Jiang
- Department of Rehabilitation, Taizhou People’s Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Hong Yu
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
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20
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Next generation sequencing of human platelet antigens for routine clinical investigations and donor screening. Transfus Med Rev 2022; 36:87-96. [DOI: 10.1016/j.tmrv.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/21/2022]
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21
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Fabiańska I, Borutzki S, Richter B, Tran HQ, Neubert A, Mayer D. LABRADOR-A Computational Workflow for Virus Detection in High-Throughput Sequencing Data. Viruses 2021; 13:v13122541. [PMID: 34960810 PMCID: PMC8704571 DOI: 10.3390/v13122541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing (HTS) allows detection of known and unknown viruses in samples of broad origin. This makes HTS a perfect technology to determine whether or not the biological products, such as vaccines are free from the adventitious agents, which could support or replace extensive testing using various in vitro and in vivo assays. Due to bioinformatics complexities, there is a need for standardized and reliable methods to manage HTS generated data in this field. Thus, we developed LABRADOR—an analysis pipeline for adventitious virus detection. The pipeline consists of several third-party programs and is divided into two major parts: (i) direct reads classification based on the comparison of characteristic profiles between reads and sequences deposited in the database supported with alignment of to the best matching reference sequence and (ii) de novo assembly of contigs and their classification on nucleotide and amino acid levels. To meet the requirements published in guidelines for biologicals’ safety we generated a custom nucleotide database with viral sequences. We tested our pipeline on publicly available HTS datasets and showed that LABRADOR can reliably detect viruses in mixtures of model viruses, vaccines and clinical samples.
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22
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Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells. Exp Mol Med 2021; 53:1344-1355. [PMID: 34521988 PMCID: PMC8492700 DOI: 10.1038/s12276-021-00668-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/04/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
DHFR gene amplification is commonly present in methotrexate (MTX)-resistant colon cancer cells and acute lymphoblastic leukemia. In this study, we proposed an integrative framework to characterize the amplified region by using a combination of single-molecule real-time sequencing, next-generation optical mapping, and chromosome conformation capture (Hi-C). We identified an amplification unit spanning 11 genes, from the DHFR gene to the ATP6AP1L gene position, with high adjusted interaction frequencies on chromosome 5 (~2.2 Mbp) and a twenty-fold tandemly amplified region, and novel inversions at the start and end positions of the amplified region as well as frameshift insertions in most of the MSH and MLH genes were detected. These mutations might stimulate chromosomal breakage and cause the dysregulation of mismatch repair. Characterizing the tandem gene-amplified unit may be critical for identifying the mechanisms that trigger genomic rearrangements. These findings may provide new insight into the mechanisms underlying the amplification process and the evolution of drug resistance. Sequencing a large region of DNA containing many surplus copies of genes linked to drug resistance in colon cancer cells may illuminate how these genomic rearrangements arise. Such regions of gene amplification are highly repetitive, making them impossible to sequence using ordinary methods, and little is known about how they are generated. Using advanced methods, Jeong-Sun Seo at Seoul National University Bundang Hospital in South Korea and co-workers sequenced a region of gene amplification in colon cancer cells. The amplified region was approximately 20 times the length of that in healthy cells and contained many copies of an eleven-gene segment, including a gene implicated in drug resistance. The region also contained mutations in chromosomal repair genes which would disrupt repair pathways. These results illuminate the genetic changes that lead to gene amplification and drug resistance in cancer cells.
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23
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Dragoš VŠ, Stegel V, Blatnik A, Klančar G, Krajc M, Novaković S. New Approach for Detection of Normal Alternative Splicing Events and Aberrant Spliceogenic Transcripts with Long-Range PCR and Deep RNA Sequencing. BIOLOGY 2021; 10:706. [PMID: 34439939 PMCID: PMC8389194 DOI: 10.3390/biology10080706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/21/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
RNA sequencing is a promising technique for detecting normal and aberrant RNA isoforms. Here, we present a new single-gene, straightforward 1-day hands-on protocol for detection of splicing alterations with deep RNA sequencing from blood. We have validated our method's accuracy by detecting previously published normal splicing isoforms of STK11 gene. Additionally, the same technique was used to provide the first comprehensive catalogue of naturally occurring alternative splicing events of the NBN gene in blood. Furthermore, we demonstrate that our approach can be used for detection of splicing impairment caused by genetic variants. Therefore, we were able to reclassify three variants of uncertain significance: NBN:c.584G>A, STK11:c.863-5_863-3delCTC and STK11:c.615G>A. Due to the simplicity of our approach, it can be incorporated into any molecular diagnostics laboratory for determination of variant's impact on splicing.
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Affiliation(s)
- Vita Šetrajčič Dragoš
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (V.Š.D.); (V.S.); (G.K.)
- Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Vida Stegel
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (V.Š.D.); (V.S.); (G.K.)
| | - Ana Blatnik
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (A.B.); (M.K.)
| | - Gašper Klančar
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (V.Š.D.); (V.S.); (G.K.)
| | - Mateja Krajc
- Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (A.B.); (M.K.)
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia; (V.Š.D.); (V.S.); (G.K.)
- Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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24
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John A, Muenzen K, Ausmees K. Evaluation of serverless computing for scalable execution of a joint variant calling workflow. PLoS One 2021; 16:e0254363. [PMID: 34242357 PMCID: PMC8270184 DOI: 10.1371/journal.pone.0254363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Advances in whole-genome sequencing have greatly reduced the cost and time of obtaining raw genetic information, but the computational requirements of analysis remain a challenge. Serverless computing has emerged as an alternative to using dedicated compute resources, but its utility has not been widely evaluated for standardized genomic workflows. In this study, we define and execute a best-practice joint variant calling workflow using the SWEEP workflow management system. We present an analysis of performance and scalability, and discuss the utility of the serverless paradigm for executing workflows in the field of genomics research. The GATK best-practice short germline joint variant calling pipeline was implemented as a SWEEP workflow comprising 18 tasks. The workflow was executed on Illumina paired-end read samples from the European and African super populations of the 1000 Genomes project phase III. Cost and runtime increased linearly with increasing sample size, although runtime was driven primarily by a single task for larger problem sizes. Execution took a minimum of around 3 hours for 2 samples, up to nearly 13 hours for 62 samples, with costs ranging from $2 to $70.
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Affiliation(s)
- Aji John
- Department of Biology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Kathleen Muenzen
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States of America
| | - Kristiina Ausmees
- Department of Information Technology, Uppsala University, Uppsala, Sweden
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25
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Theis KR, Florova V, Romero R, Borisov AB, Winters AD, Galaz J, Gomez-Lopez N. Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes. Crit Rev Microbiol 2021; 47:517-542. [PMID: 33823747 DOI: 10.1080/1040841x.2021.1905606] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sneathia is an emerging pathogen implicated in adverse reproductive and perinatal outcomes. Although scarce, recent data suggest that vaginally residing Sneathia becomes pathogenic following its ascension into the upper urogenital tract, amniotic fluid, placenta, and foetal membranes. The role of Sneathia in women's health and disease is generally underappreciated because the cultivation of these bacteria is limited by their complex nutritional requirements, slow growth patterns, and anaerobic nature. For this reason, molecular methods are typically required for the detection and differential diagnosis of Sneathia infections. Here, we review the laboratory methods used for the diagnosis of Sneathia infections, the molecular mechanisms underlying its virulence, and its sensitivity to antibiotics. We further review the evidence of Sneathia's contributions to the pathogenesis of bacterial vaginosis, chorioamnionitis, preterm prelabour rupture of membranes, spontaneous preterm labour, stillbirth, maternal and neonatal sepsis, HIV infection, and cervical cancer. Collectively, growing evidence indicates that Sneathia represents an important yet underappreciated pathogen affecting the development and progression of several adverse clinical conditions diagnosed in pregnant women and their neonates, as well as in non-pregnant women.
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Affiliation(s)
- Kevin R Theis
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Violetta Florova
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA.,Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.,Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.,Detroit Medical Center, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Andrei B Borisov
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Andrew D Winters
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Detroit, MI, USA.,Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
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26
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Ha CWY, Devkota S. The new microbiology: cultivating the future of microbiome-directed medicine. Am J Physiol Gastrointest Liver Physiol 2020; 319:G639-G645. [PMID: 32996782 PMCID: PMC7792672 DOI: 10.1152/ajpgi.00093.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The discovery of human-associated microscopic life forms has captivated the scientific community since their first documentation in the 17th century. Subsequent isolation and cultivation of microorganisms have spurred great leaps in medicine, including the discovery of antibiotics, identifying pathogens that cause infectious diseases, and vaccine development. The realization that there is a vast discrepancy between the number of microscopic cell counts and how many could thrive in the laboratory motivated the advent of sequencing-based approaches to characterize the uncultured fraction of the microbiota, leading to an unprecedented view into their composition and putative function on all bodily surfaces. It soon became apparent that specific members of the microbiota can be our commensal partners with new implications on various aspects of health, as well as a rich source of therapeutic compounds and tools for biotechnology. Harnessing the immense repertoire of microbial properties, however, inadvertently requires pure cultures for validation and manipulation of candidate genes, proteins, or metabolic pathways, just as mammalian cell culture has become an indispensable tool for mechanistic understanding of host biology. Yet, this renewed interest in growing microorganisms, individually or as a consortium, is stalled by the laborious nature of conventional cultivation methods. Addressing this unmet need through implementation of improved media design and new cultivation techniques is arguably instrumental to future milestones in translational microbiome research.
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Affiliation(s)
- Connie W. Y. Ha
- Division of Gastroenterology, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Suzanne Devkota
- Division of Gastroenterology, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
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27
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Medina-Martínez JS, Arango-Ossa JE, Levine MF, Zhou Y, Gundem G, Kung AL, Papaemmanuil E. Isabl Platform, a digital biobank for processing multimodal patient data. BMC Bioinformatics 2020; 21:549. [PMID: 33256603 PMCID: PMC7708092 DOI: 10.1186/s12859-020-03879-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The widespread adoption of high throughput technologies has democratized data generation. However, data processing in accordance with best practices remains challenging and the data capital often becomes siloed. This presents an opportunity to consolidate data assets into digital biobanks-ecosystems of readily accessible, structured, and annotated datasets that can be dynamically queried and analysed. RESULTS We present Isabl, a customizable plug-and-play platform for the processing of multimodal patient-centric data. Isabl's architecture consists of a relational database (Isabl DB), a command line client (Isabl CLI), a RESTful API (Isabl API) and a frontend web application (Isabl Web). Isabl supports automated deployment of user-validated pipelines across the entire data capital. A full audit trail is maintained to secure data provenance, governance and ensuring reproducibility of findings. CONCLUSIONS As a digital biobank, Isabl supports continuous data utilization and automated meta analyses at scale, and serves as a catalyst for research innovation, new discoveries, and clinical translation.
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Affiliation(s)
| | | | - Max F Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yangyu Zhou
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gunes Gundem
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew L Kung
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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28
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Abstract
Artificial intelligence (AI) is having an increasing impact on the field of pathology, as computation techniques allow computers to perform tasks previously performed by people. Here, we offer a simple and practical guide to AI methods used in pathology, such as digital image analysis, next-generation sequencing, and natural language processing. We not only provide a comprehensive review, but also discuss relevant history and future directions of AI in pathology. We additionally provide a short tabular dictionary of AI terminology which will help practicing pathologists and researchers to understand this field.
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29
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Berg G, Rybakova D, Fischer D, Cernava T, Vergès MCC, Charles T, Chen X, Cocolin L, Eversole K, Corral GH, Kazou M, Kinkel L, Lange L, Lima N, Loy A, Macklin JA, Maguin E, Mauchline T, McClure R, Mitter B, Ryan M, Sarand I, Smidt H, Schelkle B, Roume H, Kiran GS, Selvin J, Souza RSCD, van Overbeek L, Singh BK, Wagner M, Walsh A, Sessitsch A, Schloter M. Microbiome definition re-visited: old concepts and new challenges. MICROBIOME 2020; 8:103. [PMID: 32605663 PMCID: PMC7329523 DOI: 10.1186/s40168-020-00875-0] [Citation(s) in RCA: 921] [Impact Index Per Article: 184.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/22/2020] [Indexed: 05/03/2023]
Abstract
The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.
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Affiliation(s)
- Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Daria Rybakova
- Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Tomislav Cernava
- Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Trevor Charles
- Waterloo Centre for Microbial Research, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
- Metagenom Bio, 550 Parkside Drive, Unit A9, Waterloo, ON, N2L 5 V4, Canada
| | - Xiaoyulong Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Luca Cocolin
- European Food Information Council, Brussels, Belgium
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Summit, Lee, MO, 's, USA
| | | | - Maria Kazou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Lene Lange
- BioEconomy, Research, & Advisory, Valby, Denmark
| | - Nelson Lima
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Alexander Loy
- Department of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, Austria
| | | | - Emmanuelle Maguin
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Tim Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, UK
| | - Ryan McClure
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Birgit Mitter
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Inga Sarand
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | | | - G Seghal Kiran
- Dept of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - Rafael Soares Correa de Souza
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Leo van Overbeek
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Michael Wagner
- Department of Microbial Ecology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Aaron Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Angela Sessitsch
- Bioresources Unit, AIT Austrian Institute of Technology, Tulln, Austria
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30
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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31
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Quek RZB, Jain SS, Neo ML, Rouse GW, Huang D. Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Ecol Resour 2020; 20:807-818. [PMID: 32077619 PMCID: PMC7468246 DOI: 10.1111/1755-0998.13150] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/01/2020] [Accepted: 02/10/2020] [Indexed: 01/09/2023]
Abstract
Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.
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Affiliation(s)
- Randolph Z. B. Quek
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Sudhanshi S. Jain
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Mei Lin Neo
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Greg W. Rouse
- Scripps Institution of OceanographyUniversity of California San DiegoSan DiegoCAUSA
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
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32
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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33
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Mabvakure BM, Rott R, Dobrowsky L, Van Heusden P, Morris L, Scheepers C, Moore PL. Advancing HIV Vaccine Research With Low-Cost High-Performance Computing Infrastructure: An Alternative Approach for Resource-Limited Settings. Bioinform Biol Insights 2019; 13:1177932219882347. [PMID: 35173421 PMCID: PMC8842485 DOI: 10.1177/1177932219882347] [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: 09/04/2019] [Accepted: 09/21/2019] [Indexed: 11/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized biological research by generating genomic data that were once unaffordable by traditional first-generation sequencing technologies. These sequencing methodologies provide an opportunity for in-depth analyses of host and pathogen genomes as they are able to sequence millions of templates at a time. However, these large datasets can only be efficiently explored using bioinformatics analyses requiring huge data storage and computational resources adapted for high-performance processing. High-performance computing allows for efficient handling of large data and tasks that may require multi-threading and prolonged computational times, which is not feasible with ordinary computers. However, high-performance computing resources are costly and therefore not always readily available in low-income settings. We describe the establishment of an affordable high-performance computing bioinformatics cluster consisting of 3 nodes, constructed using ordinary desktop computers and open-source software including Linux Fedora, SLURM Workload Manager, and the Conda package manager. For the analysis of large antibody sequence datasets and for complex viral phylodynamic analyses, the cluster out-performed desktop computers. This has demonstrated that it is possible to construct high-performance computing capacity capable of analyzing large NGS data from relatively low-cost hardware and entirely free (open-source) software, even in resource-limited settings. Such a cluster design has broad utility beyond bioinformatics to other studies that require high-performance computing.
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Affiliation(s)
- Batsirai M Mabvakure
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Peter Van Heusden
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Cathrine Scheepers
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- Center for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Service (NHLS), Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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Zare F, Nabavi S. Copy Number Variation Detection Using Total Variation. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:423-428. [PMID: 32515750 PMCID: PMC7278034 DOI: 10.1145/3307339.3342181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Next-generation sequencing (NGS) technologies offer new opportunities for precise and accurate identification of genomic aberrations, including copy number variations (CNVs). For high-throughput NGS data, using depth of coverage has become a major approach to identify CNVs, especially for whole exome sequencing (WES) data. Due to the high level of noise and biases of read-count data and complexity of the WES data, existing CNV detection tools identify many false CNV segments. Besides, NGS generates a huge amount of data, requiring to use effective and efficient methods. In this work, we propose a novel segmentation algorithm based on the total variation approach to detect CNVs more precisely and efficiently using WES data. The proposed method also filters out outlier read-counts and identifies significant change points to reduce false positives. We used real and simulated data to evaluate the performance of the proposed method and compare its performance with those of other commonly used CNV detection methods. Using simulated and real data, we show that the proposed method outperforms the existing CNV detection methods in terms of accuracy and false discovery rate and has a faster runtime compared to the circular binary segmentation method.
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Affiliation(s)
| | - Sheida Nabavi
- Corresponding author. This study was supported by a grant from the National Institutes of Health (NIH, R00LM011595, PI: Nabavi).
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Lee CL, Lee CH, Chuang CK, Chiu HC, Chen YJ, Chou CL, Wu PS, Chen CP, Lin HY, Lin SP. Array-CGH increased the diagnostic rate of developmental delay or intellectual disability in Taiwan. Pediatr Neonatol 2019; 60:453-460. [PMID: 30581099 DOI: 10.1016/j.pedneo.2018.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 10/03/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Unexplained developmental delay or intellectual disability (DD/ID) has an estimated prevalence of about 3%-5% in the general population of Taiwan. Array comparative genomic hybridization (array-CGH) is a high-resolution tool that can detect about 50 Kb chromosome aberrations. A previous study has reported a detection rate of 10%-20% for this array.1 This study aimed to investigate and compare the diagnosis rate for DD/ID using array-CGH and conventional chromosome study in DD/ID patients in Taiwan. METHODS We enrolled 177 patients with DD/ID who underwent array-CGH examination at the MacKay Memory Hospital between June 2010 and September 2017. The copy number variants (CNV) were classified into the following three groups: pathogenic (potential pathologic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance, VOUS), according to the ACMG guideline.2 RESULTS: Of the 177 enrolled patients, 100 (56.5%) were men and 77 (43.5%) were women. Ages ranged from 3 months to 50 years, with a median age of 5.2 years. Total 32.0% (32/100) male patients had pathogenic CNV, and 32.5% (25/77) female patients had pathogenic CNV. The ratio of pathogenic CNV in male and female patients was not significantly different (p = 0.379). The proportions of pathogenic CNV at <3 years, 3-6 years, 6-12 years, 12-18 years, and >18 years of age were 32.3% (31/96), 19.4% (6/31), 34.8% (8/23), 16.7% (2/12), and 66.7% (10/15), respectively. The overall diagnosed rate of DD/ID with pathogenic CNV was 27.7% (49/177) using array-CGH in this study. There were 105 patients with conventional karyotyping and array-CGH data at the same time. Nineteen (18.1%) patients had visible chromosomal abnormality. Total 32/105 (30.5%) patients could find at least one pathogenic CNVs. The array-CGH had a higher diagnosed rate than the conventional karyotyping in clinical application. CONCLUSIONS Although array-CGH could not detect point mutation, balanced translocations, inversions, or low-level mosaicism, the diagnosis rate in clinical application was up to 46.3% and 2.5 times that of conventional karyotyping analysis (18.1%). This study demonstrated that array-CGH is a powerful diagnostic tool and should be the first genetic test instead of conventional karyotyping analysis for patients with unexplained DD/ID.
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Affiliation(s)
- Chung-Lin Lee
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, E-DA Hospital, I-Shou University, Kaohsiung City, Taiwan
| | | | - Huei-Ching Chiu
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yen-Jiun Chen
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chao-Ling Chou
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan
| | | | - Chih-Ping Chen
- Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Departments of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsiang-Yu Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan; Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan.
| | - Shuan-Pei Lin
- Department of Pediatrics, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medicine, Mackay Medical College, New Taipei City 25245, Taiwan; Division of Genetics and Metabolism, Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Infant and Child Care, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan.
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Jung H, Winefield C, Bombarely A, Prentis P, Waterhouse P. Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes. TRENDS IN PLANT SCIENCE 2019; 24:700-724. [PMID: 31208890 DOI: 10.1016/j.tplants.2019.05.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 05/16/2023]
Abstract
The commercial release of third-generation sequencing technologies (TGSTs), giving long and ultra-long sequencing reads, has stimulated the development of new tools for assembling highly contiguous genome sequences with unprecedented accuracy across complex repeat regions. We survey here a wide range of emerging sequencing platforms and analytical tools for de novo assembly, provide background information for each of their steps, and discuss the spectrum of available options. Our decision tree recommends workflows for the generation of a high-quality genome assembly when used in combination with the specific needs and resources of a project.
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Affiliation(s)
- Hyungtaek Jung
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia.
| | - Christopher Winefield
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, 7647 Christchurch, New Zealand
| | - Aureliano Bombarely
- Department of Bioscience, University of Milan, Milan 20133, Italy; School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Peter Prentis
- School of Earth, Environmental, and Biological Sciences, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Peter Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biological Sciences, University of Sydney, Sydney, NSW 2006, Australia.
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Pereira De Martinis EC, Almeida OGGD. Relating next-generation sequencing and bioinformatics concepts to routine microbiological testing. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2019. [DOI: 10.29333/ejgm/108690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Lippi G, Favaloro EJ. Laboratory hemostasis: from biology to the bench. Clin Chem Lab Med 2019; 56:1035-1045. [PMID: 29455188 DOI: 10.1515/cclm-2017-1205] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 01/19/2018] [Indexed: 12/29/2022]
Abstract
Physiological hemostasis is an intricate biological system, where procoagulant and anticoagulant forces interplay and preserves blood fluidity when blood vessels are intact, or trigger clot formation to prevent excessive bleeding when blood vessels are injured. The modern model of hemostasis is divided into two principal phases. The first, defined as primary hemostasis, involves the platelet-vessel interplay, whilst the second, defined as secondary hemostasis, mainly involves coagulation factors, damaged cells and platelet surfaces, where the so-called coagulation cascade rapidly develops. The activation and amplification of the coagulation cascade is finely modulated by the activity of several physiological inhibitors. Once bleeding has been efficiently stopped by blood clot formation, dissolution of the thrombus is essential to restore vessel permeability. This process, known as fibrinolysis, also develops through coordinate action of a vast array of proteins and enzymes. An accurate diagnosis of hemostasis disturbance entails a multifaceted approach, encompassing family and personal history of hemostatic disorders, accurate collection of clinical signs and symptoms, integrated with laboratory hemostasis testing. Regarding laboratory testing, a reasonable approach entails classifying hemostasis testing according to cost, complexity and available clinical information. Laboratory workout may hence initiate with some rapid and inexpensive "screening" tests, characterized by high negative predictive value, then followed by second- or third-line analyses, specifically aimed to clarify the nature and severity of bleeding or thrombotic phenotype. This article aims to provide a general overview of the hemostatic process, and to provide some general suggestions to optimally facilitate laboratory hemostasis testing.
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Affiliation(s)
- Giuseppe Lippi
- Section of Clinical Biochemistry, University Hospital of Verona, Piazzale LA Scuro, 37100 - Verona, Italy
| | - Emmanuel J Favaloro
- Department of Clinical and Laboratory Haematology, Sydney Centres for Thrombosis and Haemostasis, Institute of Clinical Pathology and Medical Research and Westmead Hospital, Westmead, NSW, Australia
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D'Argenio V. The High-Throughput Analyses Era: Are We Ready for the Data Struggle? High Throughput 2018; 7:E8. [PMID: 29498666 PMCID: PMC5876534 DOI: 10.3390/ht7010008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/16/2018] [Accepted: 02/27/2018] [Indexed: 12/23/2022] Open
Abstract
Recent and rapid technological advances in molecular sciences have dramatically increased the ability to carry out high-throughput studies characterized by big data production. This, in turn, led to the consequent negative effect of highlighting the presence of a gap between data yield and their analysis. Indeed, big data management is becoming an increasingly important aspect of many fields of molecular research including the study of human diseases. Now, the challenge is to identify, within the huge amount of data obtained, that which is of clinical relevance. In this context, issues related to data interpretation, sharing and storage need to be assessed and standardized. Once this is achieved, the integration of data from different -omic approaches will improve the diagnosis, monitoring and therapy of diseases by allowing the identification of novel, potentially actionably biomarkers in view of personalized medicine.
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Affiliation(s)
- Valeria D'Argenio
- CEINGE-Biotecnologie Avanzate, via G. Salvatore 486, 80145 Naples, Italy.
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, via Pansini 5, 80131 Naples, Italy.
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