scholarly journals Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping

2015 ◽  
Author(s):  
Robert P Milius ◽  
Michael Heuer ◽  
Daniel Valiga ◽  
Kathryn J Doroschak ◽  
Caleb J. Kennedy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Data Exchange ◽  
Consensus Sequence ◽  
Markup Language ◽  
Next Generation ◽  
Multiple Group ◽  
Specific Priming ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and sequence based typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS.

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

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

scholarly journals Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing

2015 ◽  
Author(s):  
Steven J. Mack ◽  
Robert P Milius ◽  
Benjamin D Gifford ◽  
Jürgen Sauter ◽  
Jan Hofmann ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Consensus Sequence ◽  
Primary Data ◽  
Genotype Data ◽  
Next Generation ◽  
Minimum Information ◽  
Structured Information ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information – message annotation, reference context, full genotype, consensus sequence and novel polymorphism – and references to three categories of accessory information – NGS platform documentation, read processing documentation and primary data. These eight categories of information ensure the long-term portability and broad application of this NGS data for all current histocompatibility and immunogenetics use cases. In addition, MIRING can be extended to allow the reporting of genotype data generated using pre-NGS technologies. Because genotyping results reported using MIRING are easily updated in accordance with reference and nomenclature databases, MIRING represents a bold departure from previous methods of reporting HLA and KIR genotyping results, which have provided static and less-portable data. More information about MIRING can be found online at miring.immunogenomics.org.

scholarly journals Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Molecules ◽  
2018 ◽  
Vol 23 (2) ◽  
pp. 399 ◽  
Author(s):  
Sima Taheri ◽  
Thohirah Lee Abdullah ◽  
Mohd Yusop ◽  
Mohamed Hanafi ◽  
Mahbod Sahebi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

scholarly journals ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 50 ◽  
Author(s):  
Michael T. Wolfinger ◽  
Jörg Fallmann ◽  
Florian Eggenhofer ◽  
Fabian Amman
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Motif ◽  
Software Components ◽  
Sequencing Analysis ◽  
Next Generation ◽  
File Formats ◽  
Next Generation Sequencing Analysis ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.

scholarly journals Whole genome sequencing suggests transmission of Corynebacterium diphtheriae-caused cutaneous diphtheria in two siblings, Germany, 2018

2019 ◽  
Vol 24 (2) ◽  
Author(s):  
Anja Berger ◽  
Alexandra Dangel ◽  
Tilmann Schober ◽  
Birgit Schmidbauer ◽  
Regina Konrad ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Corynebacterium Diphtheriae ◽  
Whole Genome ◽  
Next Generation ◽  
Insect Bites ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

In September 2018, a child who had returned from Somalia to Germany presented with cutaneous diphtheria by toxigenic Corynebacterium diphtheriae biovar mitis. The child’s sibling had superinfected insect bites harbouring also toxigenic C. diphtheriae. Next generation sequencing (NGS) revealed the same strain in both patients suggesting very recent human-to-human transmission. Epidemiological and NGS data suggest that the two cutaneous diphtheria cases constitute the first outbreak by toxigenic C. diphtheriae in Germany since the 1980s.

scholarly journals ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 50 ◽  
Author(s):  
Michael T. Wolfinger ◽  
Jörg Fallmann ◽  
Florian Eggenhofer ◽  
Fabian Amman
Keyword(s):  
Next Generation Sequencing ◽  
Sequence Motif ◽  
Software Components ◽  
Sequencing Analysis ◽  
Next Generation ◽  
File Formats ◽  
Next Generation Sequencing Analysis ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.

Current Challenges and Implications of Proteogenomic Approaches in Prostate Cancer

2020 ◽  
Vol 20 (22) ◽  
pp. 1968-1980
Author(s):  
Nidhi Shukla ◽  
Narmadhaa Siva ◽  
Babita Malik ◽  
Prashanth Suravajhala
Keyword(s):  
Prostate Cancer ◽  
Next Generation Sequencing ◽  
Candidate Genes ◽  
Next Generation ◽  
Recent Past ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Omic Data ◽  
Generation Sequencing

In the recent past, next-generation sequencing (NGS) approaches have heralded the omics era. With NGS data burgeoning, there arose a need to disseminate the omic data better. Proteogenomics has been vividly used for characterising the functions of candidate genes and is applied in ascertaining various diseased phenotypes, including cancers. However, not much is known about the role and application of proteogenomics, especially Prostate Cancer (PCa). In this review, we outline the need for proteogenomic approaches, their applications and their role in PCa.

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