Influence of Next-Generation Sequencing and Storage Conditions on miRNA Patterns Generated from PAXgene Blood

Genomic data nowadays is playing a vital role in number of fields such as personalized medicine, forensic, drug discovery, sequence alignment and agriculture, etc. With the advancements and reduction in the cost of next-generation sequencing (NGS) technology, these data are growing exponentially. NGS data are being generated more rapidly than they could be significantly analyzed. Thus, there is much scope for developing novel data compression algorithms to facilitate data analysis along with data transfer and storage directly. An innovative compression technique is proposed here to address the problem of transmission and storage of large NGS data. This paper presents a lossless non-reference-based FastQ file compression approach, segregating the data into three different streams and then applying appropriate and efficient compression algorithms on each. Experiments show that the proposed approach (WBFQC) outperforms other state-of-the-art approaches for compressing NGS data in terms of compression ratio (CR), and compression and decompression time. It also has random access capability over compressed genomic data. An open source FastQ compression tool is also provided here ( http://www.algorithm-skg.com/wbfqc/home.html ).

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Descemet Membrane Endothelial Keratoplasty: NGS Metagenomics-Optimized Tissue Preparation and Surgical Technique. Doctoral Thesis

10.25143/prom-rsu_2021-21_dt ◽

2021 ◽

Author(s):

◽

Davide Borroni ◽

Keyword(s):

Next Generation Sequencing ◽

Turnaround Time ◽

Storage Conditions ◽

Tissue Preparation ◽

Next Generation ◽

Human Donor ◽

Taxonomic Profiling ◽

Storage Media ◽

Hypothermic Storage ◽

Generation Sequencing

Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.

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Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium

BMJ Open Ophthalmology ◽

10.1136/bmjophth-2018-000246 ◽

2019 ◽

Vol 4 (1) ◽

pp. e000246 ◽

Cited By ~ 2

Author(s):

Mohit Parekh ◽

Davide Borroni ◽

Vito Romano ◽

Stephen B Kaye ◽

Davide Camposampiero ◽

...

Keyword(s):

Next Generation Sequencing ◽

Storage Conditions ◽

Next Generation ◽

Human Donor ◽

Taxonomic Profiling ◽

Storage Media ◽

Hypothermic Storage ◽

Corneal Preservation ◽

And Control ◽

Generation Sequencing

ObjectiveTo detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method.MethodsSeven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16 S and 18 S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments.ResultsIn both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples.ConclusionMetagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turn-around time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.

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Cracking the Code of Human Diseases Using Next-Generation Sequencing: Applications, Challenges, and Perspectives

BioMed Research International ◽

10.1155/2015/161648 ◽

2015 ◽

Vol 2015 ◽

pp. 1-15 ◽

Cited By ~ 21

Author(s):

Vincenza Precone ◽

Valentina Del Monaco ◽

Maria Valeria Esposito ◽

Fatima Domenica Elisa De Palma ◽

Anna Ruocco ◽

...

Keyword(s):

Next Generation Sequencing ◽

Molecular Basis ◽

Human Diseases ◽

Next Generation ◽

Ethical Aspects ◽

Human Genomics ◽

Next Generation Sequencing Ngs ◽

Analytical Approaches ◽

And Storage ◽

Generation Sequencing

Next-generation sequencing (NGS) technologies have greatly impacted on every field of molecular research mainly because they reduce costs and increase throughput of DNA sequencing. These features, together with the technology’s flexibility, have opened the way to a variety of applications including the study of the molecular basis of human diseases. Several analytical approaches have been developed to selectively enrich regions of interest from the whole genome in order to identify germinal and/or somatic sequence variants and to study DNA methylation. These approaches are now widely used in research, and they are already being used in routine molecular diagnostics. However, some issues are still controversial, namely, standardization of methods, data analysis and storage, and ethical aspects. Besides providing an overview of the NGS-based approaches most frequently used to study the molecular basis of human diseases at DNA level, we discuss the principal challenges and applications of NGS in the field of human genomics.

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Descemet Membrane Endothelial Keratoplasty: NGS Metagenomics-Optimized Tissue Preparation and Surgical Technique. Summary of the Doctoral Thesis

10.25143/prom-rsu_2021-21_dts ◽

2021 ◽

Author(s):

◽

Davide Borroni ◽

Keyword(s):

Next Generation Sequencing ◽

Turnaround Time ◽

Storage Conditions ◽

Tissue Preparation ◽

Next Generation ◽

Human Donor ◽

Taxonomic Profiling ◽

Storage Media ◽

Hypothermic Storage ◽

Generation Sequencing

Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.

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Collection and Storage of HLA NGS Genotyping Data for the 17th International HLA and Immunogenetics Workshop

10.1101/116871 ◽

2017 ◽

Author(s):

Chia-Jung Chang ◽

Kazutoyo Osoegawa ◽

Robert P. Milius ◽

Martin Maiers ◽

Wenzhong Xiao ◽

...

Keyword(s):

Next Generation Sequencing ◽

Killer Cell ◽

Human Leukocyte ◽

Markup Language ◽

Next Generation ◽

File Transfer ◽

Specific Priming ◽

Ngs Data ◽

And Storage ◽

Generation Sequencing

AbstractFor over 50 years, the International HLA and Immunogenetics Workshops (IHIW) have advanced the fields of histocompatibility and immunogenetics (H&I) via community sharing of technology, experience and reagents, and the establishment of ongoing collaborative projects. In the fall of 2017, the 17th IHIW will focus on the application of next generation sequencing (NGS) technologies for clinical and research goals in the H&I fields. NGS technologies have the potential to allow dramatic insights and advances in these fields, but the scope and sheer quantity of data associated with NGS raise challenges for their analysis, collection, exchange and storage. The 17 th IHIW has adopted a centralized approach to these issues, and we have been developing the tools, services and systems to create an effective system for capturing and managing these NGS data. We have worked with NGS platform and software developers to define a set of distinct but equivalent NGS typing reports that record NGS data in a uniform fashion. The 17th IHIW database applies our standards, tools and services to collect, validate and store those structured, multi-platform data in an automated fashion. We are creating community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database, with the goal of creating a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications.AbbreviationsAbbreviationsCSVComma-Separated ValuesGFEGene Feature EnumerationGLGenotype ListHLAHuman Leukocyte AntigenHMLHistoimmunogenetics Markup LanguageH&IHistocompatibility and ImmunogeneticsIHIWInternational HLA and Immunogenetics WorkshopIMGTImMunoGeneTicsIPDImmunoPolymorphism DatabaseIUPACInternational Union of Pure and Applied ChemistryKIRKiller-cell Immunoglobulin-like ReceptorMIRINGMinimum Information for Reporting Immunogenomic NGS GenotypingNGSNext Generation SequencingPIPrincipal InvestigatorRSCAReference Strand Conformation AnalysisrSSOReverse Sequence-Specific OligoSBTSequence-Based TypingsFTPsecure File Transfer ProtocolSSSequence-SpecificSSOSequence-Specific OligoSSPSequence-Specific PrimingWMDAWorld Marrow Donor AssociationWSWorkshopXMLeXtensible Markup Language

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