16th IHIW: Extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles

  title={16th IHIW: Extending the number of resources and bioinformatics analysis for the investigation of HLA rare alleles},
  author={F. Gonzalez-Galarza and S. Mack and J. Hollenbach and M. Fernandez-Vina and M. Setterholm and J. Kempenich and S. Marsh and Andrew R. Jones and D. Middleton},
  journal={International Journal of Immunogenetics},
Continuing a project presented at the 15th International HLA and Immunogenetics Workshop (IHIWS) on the rarity of HLA alleles, we sought to expand the number of data sources and bioinformatics tools available in the Allele Frequencies Net Database website (AFND, www.allelefrequencies.net). In this 16th IHIWS Rare Alleles project, HLA alleles described in the latest IMGT/HLA Database (release 3.8.0) were queried against different sources including data from registries (stem cell) and from 74… Expand
A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database.
An insight of the high diversity found in the HLA region is provided by examining population data sets stored in AFND, as well as a description of the available data sets for further analyses. Expand
Collection and Storage of HLA NGS Genotyping Data for the 17th International HLA and Immunogenetics Workshop
The 17th IHIW database applies standards, tools and services to collect, validate and store structured, multi-platform data in an automated fashion to create a long-term community resource that integrates these curated data with new NGS sequence and polymorphism data, for advanced analyses and applications. Expand
Collection and storage of HLA NGS genotyping data for the 17th International HLA and Immunogenetics Workshop.
The 17th IHIW database developed the tools, services and systems to create an effective system for capturing and managing next generation sequencing data, and created community resources to enable exploration of the vast store of curated sequence and allele-name data in the IPD-IMGT/HLA Database. Expand
Quality control project of NGS HLA genotyping for the 17th International HLA and Immunogenetics Workshop.
Despite the high HLAgenotype concordance rates of the software, there remains room for improvement in the assembly of more accurate consensus DNA sequences by NGS HLA genotyping software. Expand
Allele Frequency Net Database.
In this chapter, this resource has been widely used in a variety of contexts such as histocompatibility, immunology, epidemiology, pharmacogenetics, and population genetics, among many others. Expand
High-resolution characterization of allelic and haplotypic HLA frequency distribution in a Spanish population using high-throughput next-generation sequencing.
This study provides new 4FL-allele and -haplotype frequencies estimated for the first time in the Spanish population and reveals the high level of heterozygosity and specific haplotypic associations displayed that were not apparent at 2-field level (2FL). Expand
From HLA typing to anti-HLA antibody detection and beyond: The road ahead.
The implementation of next generation sequencing and genome-wide expression analysis together with functional assays may provide useful tools to evaluate the epigenetic modulation in transplantation biology but many efforts are requested for translating in the clinical arena the results obtained in experimental models. Expand
The heterogeneous HLA genetic composition of the Brazilian population and its relevance to the optimization of hematopoietic stem cell donor recruitment.
A heterogeneous genetic composition of the Brazilian population is indicated, such that HLA allele and haplotype frequencies exhibit different distributions among Brazilian regions, which has important implications for donor matching. Expand
A Rare HLA-DRB1*14:22-DQB1*04:01 Haplotype in a Kidney Donor: Implication in the Interpretation of Donor-Specific Antibody in Kidney Transplantation-A Case Report.
The finding of a rare HLA-DRB1*14:22-DQB1*04:01 haplotype in a Thai potential kidney donor and this rare haplotype was also identified in her father and the 2 of her offspring was confirmed by segregation analysis in the kidney donor's family. Expand
A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases.
Predivac-2.0 is a novel approach in epitope-based vaccine design, particularly suited to be applied to virus-related emerging infectious diseases, because the geographic distributions of the viruses are well defined and ethnic populations in need of vaccination can be determined ("ethnicity-oriented approach"). Expand


The IMGT/HLA database
It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences, and regular updates to the website ensure that new and confirmatory sequences are dispersed to the Hla community, and the wider research and clinical communities. Expand
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations
The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations that has been used in a wide variety of contexts, including clinical applications, epidemiology and population genetics. Expand
Common and well-documented HLA alleles: report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics.
A committee to define what human leukocyte antigen (HLA) genotypes do not need to be resolved in external proficiency testing established criteria for proficiency testing, which could be a valuable tool when making clinical histocompatibility decisions. Expand
A bioinformatics approach to ascertaining the rarity of HLA alleles.
A project of the 15th International Histocompatibility Workshop examined the rarity of human leukocyte antigen (HLA) alleles. A section was constructed in the website, www.allelefrequencies.net toExpand
Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics: HLA-NET methodological recommendations
The recommendations of four working groups of the HLA‐NET network at the mid‐term of its activities are reported, which propose to adopt thorough general principles for any HLA population study to ensure that it conforms to (inter)national legislation or recommendations/guidelines. Expand
New reservoirs of HLA alleles: pools of rare variants enhance immune defense.
It is argued that HLA loci carry many new mutant alleles prepared to assume epidemiologically meaningful roles when called on by selection provoked by exposure to new and evolving pathogens. Expand
Next-generation sequencing for HLA typing of class I loci
An automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci is developed and coupled to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus. Expand
Aim A prospective typing project to confirm HLA alleles with an unconfirmed status in the IMGT/HLA database identified sequence errors for 2 HLA-C alleles, C ∗ 03:12 and C ∗ 15:20. C ∗ 03:12 wasExpand
Formation of in vitro crossover products of the DRB loci can occur in late cycles of PCR and clonal sequencing on the 454 GS FLX is a valuable method for revealing both these artifacts and traditional sequencing errors. Expand
HLA-NET methodological recommendations
  • Strategies to work with HLA data in human populations for histocompatibility, clinical transplantation, epidemiology and population genetics
  • 2012