The IPD-IMGT/HLA Database – New developments in reporting HLA variation

Robinson, James T.; Soormally, A.; Hayhurst, James; Marsh, Steven G.E.

doi:10.1016/j.humimm.2016.01.020

Cited by 102 publications

(83 citation statements)

References 37 publications

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“…Human leucocyte antigen (HLA) 1 class I molecules display at the cell surface peptide ligands derived from the degradation of endogenous proteins and present them to cytotoxic T lymphocytes (CTLs). In this way, virally infected or tumor cells can be specifically recognized by the immune system leading to the activation of CTLs that exert their cytotoxic effect on the antigen presenting cell.…”

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confidence: 99%

“…In this way, virally infected or tumor cells can be specifically recognized by the immune system leading to the activation of CTLs that exert their cytotoxic effect on the antigen presenting cell. Classical HLA-I molecules -encoded by genes in the HLA-A, -B and -C loci-encompass over 7000 different proteins derived from more than 10,000 alleles (1). The peptide repertoire associated to a particular class I allotype includes several thousand ligands with defined structural motifs that allow their binding to the class I molecule.…”

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confidence: 99%

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A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Alpízar

Marino

Ramos-Fernández

et al. 2017

Molecular & Cellular Proteomics

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confidence: 99%

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confidence: 99%

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

Alpízar

Marino

Ramos-Fernández

et al. 2017

Molecular & Cellular Proteomics

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“…This is in good agreement with the results from other studies that achieved a high precision for predictions that were based on markers with high information content (Epstein et al , 2000). The most polymorphic site accessible via exome sequencing is the human leukocyte antigen (HLA) cluster on chromosome 6 with more than 15 000 different alleles known up to date (Robinson et al , 2016). Recently, bioinformatics tools became available that allow HLA typing from exome data and can be used additionally to rule out relatedness in questionable dyads (Szolek et al , 2014).…”

Section: Resultsmentioning

confidence: 99%

A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data

Heinrich

Kamphans²,

Mundlos

et al. 2016

Bioinformatics

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MotivationNext generation sequencing technology considerably changed the way we screen for pathogenic mutations in rare Mendelian disorders. However, the identification of the disease-causing mutation amongst thousands of variants of partly unknown relevance is still challenging and efficient techniques that reduce the genomic search space play a decisive role. Often segregation- or linkage analysis are used to prioritize candidates, however, these approaches require correct information about the degree of relationship among the sequenced samples. For quality assurance an automated control of pedigree structures and sample assignment is therefore highly desirable in order to detect label mix-ups that might otherwise corrupt downstream analysis.ResultsWe developed an algorithm based on likelihood ratios that discriminates between different classes of relationship for an arbitrary number of genotyped samples. By identifying the most likely class we are able to reconstruct entire pedigrees iteratively, even for highly consanguineous families. We tested our approach on exome data of different sequencing studies and achieved high precision for all pedigree predictions. By analyzing the precision for varying degrees of relatedness or inbreeding we could show that a prediction is robust down to magnitudes of a few hundred loci.Availability and ImplementationA java standalone application that computes the relationships between multiple samples as well as a Rscript that visualizes the pedigree information is available for download as well as a web service at www.gene-talk.de.Supplementary information Supplementary data are available at Bioinformatics online.

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“…Note that the HLA nomenclature was revised in 2010 [16] . As of Oct. 2015, there were 10,297 class I and 3543 class II known alleles [17,18] . Hence, the pMHC binding profile ("HLA peptidome") varies broadly between individuals.…”

Section: Background On the Immune System And Cancermentioning

confidence: 99%

A primer on recent developments in cancer immunotherapy, with a focus on neoantigen vaccines

Tokuyasu¹,

Huang²

2018

JCMT

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Cancer immunotherapy has now been conclusively shown to be capable of producing durable responses for a substantial number of patients. Adoptive cell transfer and checkpoint blockade therapies in particular both demonstrate that antigen-specific immune responses can be dramatically effective, even in previously refractory late stage disease. Such developments, together with advances in technology, have strongly encouraged revisiting the concept of neoantigen vaccines. Here we introduce basic ideas in the field to allow investigators from diverse backgrounds to understand these developments, grasp current issues, and contribute to further progress.

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The IPD-IMGT/HLA Database – New developments in reporting HLA variation

Cited by 102 publications

References 37 publications

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

A Molecular Basis for the Presentation of Phosphorylated Peptides by HLA-B Antigens

A likelihood ratio-based method to predict exact pedigrees for complex families from next-generation sequencing data

A primer on recent developments in cancer immunotherapy, with a focus on neoantigen vaccines

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